From 0ca3d4a1cc12047dd5c67a3c37b86817407e983f Mon Sep 17 00:00:00 2001 From: mschwoerer <82171591+mschwoer@users.noreply.github.com> Date: Wed, 22 May 2024 16:44:52 +0200 Subject: [PATCH 01/30] auto-fix more linting issues --- alphabase/constants/_const.py | 1 + alphabase/constants/aa.py | 11 +++--- alphabase/constants/atom.py | 6 ++-- alphabase/constants/element.py | 4 +-- alphabase/constants/isotope.py | 9 ++--- alphabase/constants/modification.py | 15 +++----- alphabase/io/hdf.py | 9 ++--- alphabase/io/tempmmap.py | 13 +++---- alphabase/peptide/fragment.py | 15 ++++---- alphabase/peptide/mass_calc.py | 15 ++++---- alphabase/peptide/mobility.py | 2 +- alphabase/peptide/precursor.py | 18 +++++----- alphabase/protein/fasta.py | 31 ++++++++--------- alphabase/protein/protein_level_decoy.py | 2 +- alphabase/psm_reader/__init__.py | 34 +++++++++++++------ alphabase/psm_reader/alphapept_reader.py | 7 ++-- alphabase/psm_reader/dia_psm_reader.py | 5 ++- alphabase/psm_reader/maxquant_reader.py | 10 +++--- alphabase/psm_reader/msfragger_reader.py | 11 +++--- alphabase/psm_reader/pfind_reader.py | 7 ++-- alphabase/psm_reader/psm_reader.py | 12 +++---- alphabase/psm_reader/sage_reader.py | 10 +++--- .../quant_reader/config_dict_loader.py | 9 ++--- .../quant_reader/longformat_reader.py | 17 ++++++---- .../quant_reader/quant_reader_manager.py | 5 ++- .../quant_reader/table_reformatter.py | 3 +- .../quant_reader/wideformat_reader.py | 4 +-- alphabase/spectral_library/base.py | 30 ++++++++-------- alphabase/spectral_library/decoy.py | 8 +++-- alphabase/spectral_library/flat.py | 8 ++--- alphabase/spectral_library/reader.py | 8 ++--- alphabase/spectral_library/translate.py | 11 +++--- alphabase/spectral_library/validate.py | 6 ++-- alphabase/utils.py | 9 ++--- docs/conf.py | 4 +-- pyproject.toml | 19 +++++++++-- release/pyinstaller/alphabase_pyinstaller.py | 5 +-- setup.py | 5 +-- 38 files changed, 209 insertions(+), 189 deletions(-) diff --git a/alphabase/constants/_const.py b/alphabase/constants/_const.py index 5fa3fed3..d7d5da91 100644 --- a/alphabase/constants/_const.py +++ b/alphabase/constants/_const.py @@ -1,4 +1,5 @@ import os + import numpy as np from alphabase.yaml_utils import load_yaml diff --git a/alphabase/constants/aa.py b/alphabase/constants/aa.py index a8c49a92..b8b27e7c 100644 --- a/alphabase/constants/aa.py +++ b/alphabase/constants/aa.py @@ -1,18 +1,17 @@ import os -import pandas as pd -import numpy as np import typing -from alphabase.yaml_utils import load_yaml +import numpy as np +import pandas as pd +from alphabase.constants._const import CONST_FILE_FOLDER from alphabase.constants.atom import ( - calc_mass_from_formula, MASS_H2O, + calc_mass_from_formula, parse_formula, reset_elements, ) - -from alphabase.constants._const import CONST_FILE_FOLDER +from alphabase.yaml_utils import load_yaml # We use all 128 ASCII code to represent amino acids for flexible extensions in the future. # The amino acid masses are stored in 128-lengh array :py:data:`AA_ASCII_MASS`. diff --git a/alphabase/constants/atom.py b/alphabase/constants/atom.py index b53b5e38..4d8e5f98 100644 --- a/alphabase/constants/atom.py +++ b/alphabase/constants/atom.py @@ -1,11 +1,11 @@ import os -import numpy as np -import numba import typing -from alphabase.yaml_utils import load_yaml +import numba +import numpy as np from alphabase.constants._const import CONST_FILE_FOLDER, common_const_dict +from alphabase.yaml_utils import load_yaml MASS_PROTON: float = common_const_dict["MASS_PROTON"] MASS_ISOTOPE: float = common_const_dict["MASS_ISOTOPE"] diff --git a/alphabase/constants/element.py b/alphabase/constants/element.py index d3803609..9d34ebaf 100644 --- a/alphabase/constants/element.py +++ b/alphabase/constants/element.py @@ -1,7 +1,7 @@ -from alphabase.constants.atom import * # noqa: F403 TODO remove in the next release - import warnings +from alphabase.constants.atom import * # noqa: F403 TODO remove in the next release + warnings.warn( "The module `alphabase.constants.element` is deprecated, " "it will be removed in alphabase>=1.3.0. " diff --git a/alphabase/constants/isotope.py b/alphabase/constants/isotope.py index a0c432ff..8feecc93 100644 --- a/alphabase/constants/isotope.py +++ b/alphabase/constants/isotope.py @@ -1,14 +1,15 @@ +import typing + import numba import numpy as np -import typing from alphabase.constants.atom import ( - MAX_ISOTOPE_LEN, - EMPTY_DIST, CHEM_ISOTOPE_DIST, CHEM_MONO_IDX, - truncate_isotope, + EMPTY_DIST, + MAX_ISOTOPE_LEN, parse_formula, + truncate_isotope, ) diff --git a/alphabase/constants/modification.py b/alphabase/constants/modification.py index a1627e7c..279ee6f0 100644 --- a/alphabase/constants/modification.py +++ b/alphabase/constants/modification.py @@ -1,17 +1,16 @@ import os +from typing import List, Union + import numba import numpy as np import pandas as pd -from typing import Union, List +from alphabase.constants._const import CONST_FILE_FOLDER from alphabase.constants.atom import ( calc_mass_from_formula, parse_formula, ) -from alphabase.constants._const import CONST_FILE_FOLDER - - #: Main entry of modification infomation (DataFrame fotmat). MOD_DF: pd.DataFrame = pd.DataFrame() @@ -138,9 +137,7 @@ def calc_modification_mass( """ masses = np.zeros(nAA) for site, mod in zip(mod_sites, mod_names): - if site == 0: - masses[site] += MOD_MASS[mod] - elif site == -1: + if site == 0 or site == -1: masses[site] += MOD_MASS[mod] else: masses[site - 1] += MOD_MASS[mod] @@ -178,9 +175,7 @@ def calc_mod_masses_for_same_len_seqs( masses = np.zeros((len(mod_names_list), nAA)) for i, (mod_names, mod_sites) in enumerate(zip(mod_names_list, mod_sites_list)): for mod, site in zip(mod_names, mod_sites): - if site == 0: - masses[i, site] += MOD_MASS[mod] - elif site == -1: + if site == 0 or site == -1: masses[i, site] += MOD_MASS[mod] else: masses[i, site - 1] += MOD_MASS[mod] diff --git a/alphabase/io/hdf.py b/alphabase/io/hdf.py index 26f12a8f..a9b41446 100644 --- a/alphabase/io/hdf.py +++ b/alphabase/io/hdf.py @@ -1,12 +1,13 @@ +import contextlib +import re +import time + import h5py import numpy as np import pandas as pd -import re -import contextlib -import time -class HDF_Object(object): +class HDF_Object: """ A generic class to access HDF components. """ diff --git a/alphabase/io/tempmmap.py b/alphabase/io/tempmmap.py index f8be53bc..7dfac298 100644 --- a/alphabase/io/tempmmap.py +++ b/alphabase/io/tempmmap.py @@ -2,16 +2,17 @@ """This module allows to create temporary mmapped arrays.""" # builtin -import os -import logging import atexit +import logging +import mmap +import os +import shutil +import tempfile + +import h5py # external import numpy as np -import mmap -import h5py -import tempfile -import shutil _TEMP_DIR = tempfile.TemporaryDirectory(prefix="temp_mmap_") TEMP_DIR_NAME = _TEMP_DIR.name diff --git a/alphabase/peptide/fragment.py b/alphabase/peptide/fragment.py index 39b5d912..ba0ff3c9 100644 --- a/alphabase/peptide/fragment.py +++ b/alphabase/peptide/fragment.py @@ -1,22 +1,21 @@ +from typing import Dict, List, Tuple, Union + +import numba as nb import numpy as np import pandas as pd -from typing import List, Union, Tuple, Dict -import numba as nb -from alphabase.constants._const import PEAK_MZ_DTYPE, PEAK_INTENSITY_DTYPE - -from alphabase.constants.modification import calc_modloss_mass +from alphabase.constants._const import PEAK_INTENSITY_DTYPE, PEAK_MZ_DTYPE from alphabase.constants.atom import ( MASS_PROTON, + calc_mass_from_formula, ) +from alphabase.constants.modification import calc_modloss_mass from alphabase.peptide.mass_calc import calc_b_y_and_peptide_masses_for_same_len_seqs from alphabase.peptide.precursor import ( - refine_precursor_df, is_precursor_refined, + refine_precursor_df, ) -from alphabase.constants.atom import calc_mass_from_formula - frag_type_representation_dict = { "c": "b+N(1)H(3)", "z": "y+N(-1)H(-2)", diff --git a/alphabase/peptide/mass_calc.py b/alphabase/peptide/mass_calc.py index b2ae9610..a1a60c70 100644 --- a/alphabase/peptide/mass_calc.py +++ b/alphabase/peptide/mass_calc.py @@ -1,17 +1,18 @@ -import numpy as np from typing import List, Tuple +import numpy as np + from alphabase.constants.aa import ( calc_AA_masses, calc_AA_masses_for_same_len_seqs, calc_sequence_masses_for_same_len_seqs, ) +from alphabase.constants.atom import MASS_H2O from alphabase.constants.modification import ( + calc_mod_masses_for_same_len_seqs, calc_modification_mass, calc_modification_mass_sum, - calc_mod_masses_for_same_len_seqs, ) -from alphabase.constants.atom import MASS_H2O def calc_diff_modification_mass( @@ -42,9 +43,7 @@ def calc_diff_modification_mass( """ masses = np.zeros(pep_len) for site, mass in zip(mass_diff_sites, mass_diffs): - if site == 0: - masses[site] += mass - elif site == -1: + if site == 0 or site == -1: masses[site] += mass else: masses[site - 1] += mass @@ -87,9 +86,7 @@ def calc_mod_diff_masses_for_same_len_seqs( zip(aa_mass_diffs_list, mod_sites_list) ): for mod_diff, site in zip(aa_mass_diffs, mod_sites): - if site == 0: - masses[i, site] += mod_diff - elif site == -1: + if site == 0 or site == -1: masses[i, site] += mod_diff else: masses[i, site - 1] += mod_diff diff --git a/alphabase/peptide/mobility.py b/alphabase/peptide/mobility.py index be4a443d..5326c9a1 100644 --- a/alphabase/peptide/mobility.py +++ b/alphabase/peptide/mobility.py @@ -1,8 +1,8 @@ import numpy as np import pandas as pd -from alphabase.peptide.precursor import update_precursor_mz from alphabase.constants.atom import common_const_dict +from alphabase.peptide.precursor import update_precursor_mz CCS_IM_COEF = common_const_dict["MOBILITY"]["CCS_IM_COEF"] IM_GAS_MASS = common_const_dict["MOBILITY"]["IM_GAS_MASS"] diff --git a/alphabase/peptide/precursor.py b/alphabase/peptide/precursor.py index 5e4e4125..c45bf968 100644 --- a/alphabase/peptide/precursor.py +++ b/alphabase/peptide/precursor.py @@ -1,17 +1,17 @@ -import pandas as pd -import numpy as np -import numba -import typing import multiprocessing as mp -from tqdm import tqdm +import typing +from functools import partial +import numba +import numpy as np +import pandas as pd +from tqdm import tqdm from xxhash import xxh64_intdigest -from functools import partial -from alphabase.constants.atom import MASS_PROTON, MASS_ISOTOPE from alphabase.constants.aa import AA_Composition -from alphabase.constants.modification import MOD_Composition +from alphabase.constants.atom import MASS_ISOTOPE, MASS_PROTON from alphabase.constants.isotope import IsotopeDistribution +from alphabase.constants.modification import MOD_Composition from alphabase.peptide.mass_calc import calc_peptide_masses_for_same_len_seqs @@ -586,7 +586,7 @@ def calc_precursor_isotope_intensity( isotope_dist = IsotopeDistribution() - col_names = ["i_{}".format(i) for i in range(max_isotope)] + col_names = [f"i_{i}" for i in range(max_isotope)] precursor_dist = np.zeros((len(precursor_df), max_isotope), dtype=np.float32) diff --git a/alphabase/protein/fasta.py b/alphabase/protein/fasta.py index a7e7f9df..174edffb 100644 --- a/alphabase/protein/fasta.py +++ b/alphabase/protein/fasta.py @@ -1,25 +1,22 @@ -import regex as re -import numpy as np -import pandas as pd -import numba -import os -import itertools import copy -import ahocorasick -from tqdm import tqdm - +import itertools +import os import warnings - -from Bio import SeqIO from typing import Union -from alphabase.yaml_utils import load_yaml -from alphabase.io.hdf import HDF_File -from alphabase.utils import explode_multiple_columns +import ahocorasick +import numba +import numpy as np +import pandas as pd +import regex as re +from Bio import SeqIO +from tqdm import tqdm from alphabase.constants._const import CONST_FILE_FOLDER - +from alphabase.io.hdf import HDF_File from alphabase.spectral_library.base import SpecLibBase +from alphabase.utils import explode_multiple_columns +from alphabase.yaml_utils import load_yaml def get_uniprot_gene_name(description: str): @@ -46,7 +43,7 @@ def read_fasta_file(fasta_filename: str = ""): protein information, {protein_id:str, full_name:str, gene_name:str, description:str, sequence:str} """ - with open(fasta_filename, "rt") as handle: + with open(fasta_filename) as handle: iterator = SeqIO.parse(handle, "fasta") while iterator: try: @@ -180,7 +177,7 @@ def cleave_sequence_with_cut_pos( return seq_list, miss_list, nterm_list, cterm_list -class Digest(object): +class Digest: def __init__( self, protease: str = "trypsin", diff --git a/alphabase/protein/protein_level_decoy.py b/alphabase/protein/protein_level_decoy.py index eadac7e6..3727c11a 100644 --- a/alphabase/protein/protein_level_decoy.py +++ b/alphabase/protein/protein_level_decoy.py @@ -1,7 +1,7 @@ import pandas as pd from alphabase.protein.fasta import SpecLibFasta -from alphabase.spectral_library.decoy import decoy_lib_provider, SpecLibDecoy +from alphabase.spectral_library.decoy import SpecLibDecoy, decoy_lib_provider class ProteinReverseDecoy(SpecLibDecoy): diff --git a/alphabase/psm_reader/__init__.py b/alphabase/psm_reader/__init__.py index 30e431ba..1c7f9579 100644 --- a/alphabase/psm_reader/__init__.py +++ b/alphabase/psm_reader/__init__.py @@ -15,38 +15,50 @@ "SageReaderParquet", ] -from alphabase.psm_reader.psm_reader import ( - psm_reader_provider, - psm_reader_yaml, - PSMReaderBase, -) from alphabase.psm_reader.alphapept_reader import ( AlphaPeptReader, +) +from alphabase.psm_reader.alphapept_reader import ( register_readers as register_ap_readers, ) from alphabase.psm_reader.dia_psm_reader import ( DiannReader, SpectronautReader, - SwathReader, SpectronautReportReader, + SwathReader, +) +from alphabase.psm_reader.dia_psm_reader import ( register_readers as register_dia_readers, ) from alphabase.psm_reader.maxquant_reader import ( MaxQuantReader, - register_readers as register_mq_readers, ) -from alphabase.psm_reader.pfind_reader import ( - pFindReader, - register_readers as register_pf_readers, +from alphabase.psm_reader.maxquant_reader import ( + register_readers as register_mq_readers, ) from alphabase.psm_reader.msfragger_reader import ( MSFragger_PSM_TSV_Reader, MSFraggerPepXML, +) +from alphabase.psm_reader.msfragger_reader import ( register_readers as register_fragger_readers, ) +from alphabase.psm_reader.pfind_reader import ( + pFindReader, +) +from alphabase.psm_reader.pfind_reader import ( + register_readers as register_pf_readers, +) +from alphabase.psm_reader.psm_reader import ( + PSMReaderBase, + psm_reader_provider, + psm_reader_yaml, +) from alphabase.psm_reader.sage_reader import ( - SageReaderTSV, SageReaderParquet, + SageReaderTSV, +) +from alphabase.psm_reader.sage_reader import ( register_readers as register_sage_readers, ) diff --git a/alphabase/psm_reader/alphapept_reader.py b/alphabase/psm_reader/alphapept_reader.py index 7b0e2ca5..0327fabc 100644 --- a/alphabase/psm_reader/alphapept_reader.py +++ b/alphabase/psm_reader/alphapept_reader.py @@ -1,8 +1,9 @@ -import numba import os -import pandas as pd -import numpy as np + import h5py +import numba +import numpy as np +import pandas as pd from alphabase.psm_reader.psm_reader import ( PSMReaderBase, diff --git a/alphabase/psm_reader/dia_psm_reader.py b/alphabase/psm_reader/dia_psm_reader.py index 0f651b2d..310f4485 100644 --- a/alphabase/psm_reader/dia_psm_reader.py +++ b/alphabase/psm_reader/dia_psm_reader.py @@ -1,9 +1,8 @@ -import pandas as pd import numpy as np - -from alphabase.psm_reader.psm_reader import psm_reader_provider, psm_reader_yaml +import pandas as pd from alphabase.psm_reader.maxquant_reader import MaxQuantReader +from alphabase.psm_reader.psm_reader import psm_reader_provider, psm_reader_yaml class SpectronautReader(MaxQuantReader): diff --git a/alphabase/psm_reader/maxquant_reader.py b/alphabase/psm_reader/maxquant_reader.py index 49e8202a..6087b02f 100644 --- a/alphabase/psm_reader/maxquant_reader.py +++ b/alphabase/psm_reader/maxquant_reader.py @@ -1,16 +1,16 @@ -import pandas as pd -import numpy as np -import numba import copy +import numba +import numpy as np +import pandas as pd + +from alphabase.constants.modification import MOD_DF from alphabase.psm_reader.psm_reader import ( PSMReaderBase, psm_reader_provider, psm_reader_yaml, ) -from alphabase.constants.modification import MOD_DF - mod_to_unimod_dict = {} for mod_name, unimod_id in MOD_DF[["mod_name", "unimod_id"]].values: unimod_id = int(unimod_id) diff --git a/alphabase/psm_reader/msfragger_reader.py b/alphabase/psm_reader/msfragger_reader.py index fde27480..56f9ef9c 100644 --- a/alphabase/psm_reader/msfragger_reader.py +++ b/alphabase/psm_reader/msfragger_reader.py @@ -1,16 +1,15 @@ import numpy as np import pandas as pd +import pyteomics.pepxml as pepxml +from alphabase.constants.aa import AA_ASCII_MASS +from alphabase.constants.atom import MASS_H, MASS_O +from alphabase.constants.modification import MOD_MASS from alphabase.psm_reader.psm_reader import ( PSMReaderBase, - psm_reader_yaml, psm_reader_provider, + psm_reader_yaml, ) -from alphabase.constants.aa import AA_ASCII_MASS -from alphabase.constants.atom import MASS_H, MASS_O -from alphabase.constants.modification import MOD_MASS - -import pyteomics.pepxml as pepxml def _is_fragger_decoy(proteins): diff --git a/alphabase/psm_reader/pfind_reader.py b/alphabase/psm_reader/pfind_reader.py index 6253d5fc..c5c61d4d 100644 --- a/alphabase/psm_reader/pfind_reader.py +++ b/alphabase/psm_reader/pfind_reader.py @@ -1,8 +1,7 @@ -import pandas as pd import numpy as np +import pandas as pd import alphabase.constants.modification as ap_mod - from alphabase.psm_reader.psm_reader import ( PSMReaderBase, psm_reader_provider, @@ -48,9 +47,7 @@ def translate_pFind_mod(mod_str): ret_mods = [] for mod in mod_str.split(";"): mod = convert_one_pFind_mod(mod) - if not mod: - return pd.NA - elif mod not in ap_mod.MOD_INFO_DICT: + if not mod or mod not in ap_mod.MOD_INFO_DICT: return pd.NA else: ret_mods.append(mod) diff --git a/alphabase/psm_reader/psm_reader.py b/alphabase/psm_reader/psm_reader.py index 53ed84f4..e57c1d92 100644 --- a/alphabase/psm_reader/psm_reader.py +++ b/alphabase/psm_reader/psm_reader.py @@ -1,13 +1,13 @@ -import os import copy -import pandas as pd -import numpy as np +import os import warnings +import numpy as np +import pandas as pd + import alphabase.peptide.mobility as mobility -from alphabase.peptide.precursor import update_precursor_mz, reset_precursor_df from alphabase.constants._const import CONST_FILE_FOLDER - +from alphabase.peptide.precursor import reset_precursor_df, update_precursor_mz from alphabase.utils import get_delimiter from alphabase.yaml_utils import load_yaml @@ -78,7 +78,7 @@ def keep_modifications(mod_str: str, mod_set: set) -> str: psm_reader_yaml = load_yaml(os.path.join(CONST_FILE_FOLDER, "psm_reader.yaml")) -class PSMReaderBase(object): +class PSMReaderBase: def __init__( self, *, diff --git a/alphabase/psm_reader/sage_reader.py b/alphabase/psm_reader/sage_reader.py index 71b7187f..9a47983d 100644 --- a/alphabase/psm_reader/sage_reader.py +++ b/alphabase/psm_reader/sage_reader.py @@ -1,17 +1,17 @@ -import numpy as np -import pandas as pd -import typing import re +import typing from functools import partial +import numpy as np +import pandas as pd + +from alphabase.constants.modification import MOD_DF from alphabase.psm_reader.psm_reader import ( PSMReaderBase, psm_reader_provider, psm_reader_yaml, ) -from alphabase.constants.modification import MOD_DF - def sage_spec_idx_from_scannr(scannr: str) -> int: """Extract the spectrum index from the scannr field in Sage output. diff --git a/alphabase/quantification/quant_reader/config_dict_loader.py b/alphabase/quantification/quant_reader/config_dict_loader.py index 70fe78e7..2cdf4aa1 100644 --- a/alphabase/quantification/quant_reader/config_dict_loader.py +++ b/alphabase/quantification/quant_reader/config_dict_loader.py @@ -1,11 +1,12 @@ +import itertools import os -import yaml -import pandas as pd import os.path import pathlib -import itertools import re +import pandas as pd +import yaml + INTABLE_CONFIG = os.path.join( pathlib.Path(__file__).parent.absolute(), "../../../alphabase/constants/const_files/quant_reader_config.yaml", @@ -57,7 +58,7 @@ def _get_seperator(input_file): def _load_config(config_yaml): - with open(config_yaml, "r") as stream: + with open(config_yaml) as stream: config_all = yaml.safe_load(stream) return config_all diff --git a/alphabase/quantification/quant_reader/longformat_reader.py b/alphabase/quantification/quant_reader/longformat_reader.py index 2301879c..88a31db7 100644 --- a/alphabase/quantification/quant_reader/longformat_reader.py +++ b/alphabase/quantification/quant_reader/longformat_reader.py @@ -1,14 +1,17 @@ -import pandas as pd +import glob import os +import os.path import shutil -import glob + import dask.dataframe as dd -import os.path +import pandas as pd -from . import config_dict_loader -from . import quantreader_utils -from . import table_reformatter -from . import plexdia_reformatter +from . import ( + config_dict_loader, + plexdia_reformatter, + quantreader_utils, + table_reformatter, +) def reformat_and_write_longtable_according_to_config( diff --git a/alphabase/quantification/quant_reader/quant_reader_manager.py b/alphabase/quantification/quant_reader/quant_reader_manager.py index 98dcb0b3..469c0821 100644 --- a/alphabase/quantification/quant_reader/quant_reader_manager.py +++ b/alphabase/quantification/quant_reader/quant_reader_manager.py @@ -1,7 +1,6 @@ import pandas as pd -from . import config_dict_loader -from . import longformat_reader -from . import wideformat_reader + +from . import config_dict_loader, longformat_reader, wideformat_reader def import_data( diff --git a/alphabase/quantification/quant_reader/table_reformatter.py b/alphabase/quantification/quant_reader/table_reformatter.py index 9f4b8bbe..70527265 100644 --- a/alphabase/quantification/quant_reader/table_reformatter.py +++ b/alphabase/quantification/quant_reader/table_reformatter.py @@ -1,6 +1,7 @@ -import pandas as pd import copy +import pandas as pd + def merge_protein_cols_and_config_dict( input_df, config_dict, use_alphaquant_format=False diff --git a/alphabase/quantification/quant_reader/wideformat_reader.py b/alphabase/quantification/quant_reader/wideformat_reader.py index b1fdaa66..52ce7cdf 100644 --- a/alphabase/quantification/quant_reader/wideformat_reader.py +++ b/alphabase/quantification/quant_reader/wideformat_reader.py @@ -1,6 +1,6 @@ import pandas as pd -from . import quantreader_utils -from . import table_reformatter + +from . import quantreader_utils, table_reformatter def reformat_and_write_wideformat_table(peptides_tsv, outfile_name, config_dict): diff --git a/alphabase/spectral_library/base.py b/alphabase/spectral_library/base.py index 972db75c..ba687112 100644 --- a/alphabase/spectral_library/base.py +++ b/alphabase/spectral_library/base.py @@ -1,31 +1,32 @@ -import pandas as pd -import numpy as np -import typing -import logging import copy -import warnings +import logging import re +import typing +import warnings + +import numpy as np +import pandas as pd +from alphabase.io.hdf import HDF_File from alphabase.peptide.fragment import ( - create_fragment_mz_dataframe, calc_fragment_count, + create_fragment_mz_dataframe, filter_fragment_number, join_left, remove_unused_fragments, ) from alphabase.peptide.precursor import ( - update_precursor_mz, - refine_precursor_df, - calc_precursor_isotope_intensity_mp, - calc_precursor_isotope_intensity, - calc_precursor_isotope_info_mp, calc_precursor_isotope_info, + calc_precursor_isotope_info_mp, + calc_precursor_isotope_intensity, + calc_precursor_isotope_intensity_mp, hash_precursor_df, + refine_precursor_df, + update_precursor_mz, ) -from alphabase.io.hdf import HDF_File -class SpecLibBase(object): +class SpecLibBase: """ Base spectral library in alphabase and alphapeptdeep. @@ -320,10 +321,9 @@ def append_decoy_sequence(self): ... ``` """ - from alphabase.spectral_library.decoy import decoy_lib_provider - # register 'protein_reverse' to the decoy_lib_provider from alphabase.protein.protein_level_decoy import register_decoy + from alphabase.spectral_library.decoy import decoy_lib_provider register_decoy() diff --git a/alphabase/spectral_library/decoy.py b/alphabase/spectral_library/decoy.py index 2f3e4dc2..76a02409 100644 --- a/alphabase/spectral_library/decoy.py +++ b/alphabase/spectral_library/decoy.py @@ -1,7 +1,9 @@ import copy +import multiprocessing as mp from typing import Any + import pandas as pd -import multiprocessing as mp + from alphabase.spectral_library.base import SpecLibBase @@ -11,7 +13,7 @@ def _batchify_series(series, mp_batch_size): yield series.iloc[i : i + mp_batch_size] -class BaseDecoyGenerator(object): +class BaseDecoyGenerator: """ Base class for decoy generator. A class is used instead of a function to make as it needs to be pickled for multiprocessing. @@ -208,7 +210,7 @@ def _remove_target_seqs(self): ) -class SpecLibDecoyProvider(object): +class SpecLibDecoyProvider: def __init__(self): self.decoy_dict = {} diff --git a/alphabase/spectral_library/flat.py b/alphabase/spectral_library/flat.py index 3257eb00..62e9db7c 100644 --- a/alphabase/spectral_library/flat.py +++ b/alphabase/spectral_library/flat.py @@ -1,11 +1,11 @@ -import pandas as pd -import numpy as np import warnings -from alphabase.spectral_library.base import SpecLibBase -from alphabase.peptide.fragment import flatten_fragments, remove_unused_fragments +import numpy as np +import pandas as pd from alphabase.io.hdf import HDF_File +from alphabase.peptide.fragment import flatten_fragments, remove_unused_fragments +from alphabase.spectral_library.base import SpecLibBase class SpecLibFlat(SpecLibBase): diff --git a/alphabase/spectral_library/reader.py b/alphabase/spectral_library/reader.py index d5d8c349..f5dd209a 100644 --- a/alphabase/spectral_library/reader.py +++ b/alphabase/spectral_library/reader.py @@ -1,15 +1,15 @@ import typing + import numpy as np import pandas as pd from tqdm import tqdm +from alphabase.constants._const import PEAK_INTENSITY_DTYPE from alphabase.peptide.mobility import mobility_to_ccs_for_df +from alphabase.psm_reader import psm_reader_provider from alphabase.psm_reader.maxquant_reader import MaxQuantReader -from alphabase.spectral_library.base import SpecLibBase from alphabase.psm_reader.psm_reader import psm_reader_yaml -from alphabase.psm_reader import psm_reader_provider - -from alphabase.constants._const import PEAK_INTENSITY_DTYPE +from alphabase.spectral_library.base import SpecLibBase class LibraryReaderBase(MaxQuantReader, SpecLibBase): diff --git a/alphabase/spectral_library/translate.py b/alphabase/spectral_library/translate.py index 5e710200..6a8f460c 100644 --- a/alphabase/spectral_library/translate.py +++ b/alphabase/spectral_library/translate.py @@ -1,14 +1,13 @@ -import pandas as pd -import numpy as np -import tqdm +import multiprocessing as mp import typing + import numba -import multiprocessing as mp +import numpy as np +import pandas as pd +import tqdm from alphabase.constants.modification import MOD_DF - from alphabase.spectral_library.base import SpecLibBase - from alphabase.utils import explode_multiple_columns diff --git a/alphabase/spectral_library/validate.py b/alphabase/spectral_library/validate.py index c4b9ac38..4c869322 100644 --- a/alphabase/spectral_library/validate.py +++ b/alphabase/spectral_library/validate.py @@ -1,7 +1,7 @@ -import pandas as pd -import numpy as np +from typing import List, Union -from typing import Union, List +import numpy as np +import pandas as pd class Column: diff --git a/alphabase/utils.py b/alphabase/utils.py index adc1d4a4..adb00faf 100644 --- a/alphabase/utils.py +++ b/alphabase/utils.py @@ -1,7 +1,8 @@ -import tqdm -import pandas as pd -import itertools import io +import itertools + +import pandas as pd +import tqdm # from alphatims @@ -39,7 +40,7 @@ def get_delimiter(tsv_file: str): line = tsv_file.readline().strip() tsv_file.seek(0) else: - with open(tsv_file, "r") as f: + with open(tsv_file) as f: line = f.readline().strip() if "\t" in line: return "\t" diff --git a/docs/conf.py b/docs/conf.py index 58851c17..597637c4 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -10,10 +10,10 @@ # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # -import os -import sys import importlib import inspect +import os +import sys sys.path.insert(0, os.path.abspath("..")) diff --git a/pyproject.toml b/pyproject.toml index 7f5d25d4..ebe33c6e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,19 @@ - [tool.ruff.lint] -select = ["E", "F"] +select = [ + # pycodestyle + "E", + # Pyflakes + "F", +# # pyupgrade +# "UP", +# # flake8-bugbear +# "B", +# # flake8-simplify +# "SIM", +# # isort +# "I", +] ignore = [ - "E501" # Line too long (ruff wraps code, but not docstrings) + "E501", # Line too long (ruff wraps code, but not docstrings) + "B028" # No explicit `stacklevel` keyword argument found (for warnings) ] diff --git a/release/pyinstaller/alphabase_pyinstaller.py b/release/pyinstaller/alphabase_pyinstaller.py index f4d40f19..74a4af7d 100644 --- a/release/pyinstaller/alphabase_pyinstaller.py +++ b/release/pyinstaller/alphabase_pyinstaller.py @@ -1,13 +1,14 @@ if __name__ == "__main__": try: - import alphabase.gui import multiprocessing + import alphabase.gui + multiprocessing.freeze_support() alphabase.gui.run() except Exception: - import traceback import sys + import traceback exc_info = sys.exc_info() # Display the *original* exception diff --git a/setup.py b/setup.py index e2859fc3..d3e36c2b 100644 --- a/setup.py +++ b/setup.py @@ -1,15 +1,16 @@ #!python # builtin -import setuptools import re +import setuptools + # local import alphabase as package2install def get_long_description(): - with open("README.md", "r") as readme_file: + with open("README.md") as readme_file: long_description = readme_file.read() return long_description From a8e12383348b4d7f2d230505b22e6becdf328cfe Mon Sep 17 00:00:00 2001 From: mschwoerer <82171591+mschwoer@users.noreply.github.com> Date: Wed, 22 May 2024 16:51:41 +0200 Subject: [PATCH 02/30] auto-fix more linting issues --- alphabase/constants/aa.py | 6 +- alphabase/constants/isotope.py | 18 +++--- alphabase/constants/modification.py | 5 +- alphabase/io/hdf.py | 5 +- alphabase/peptide/fragment.py | 59 ++++++++++--------- alphabase/peptide/precursor.py | 24 ++++---- alphabase/protein/fasta.py | 29 +++++---- alphabase/psm_reader/alphapept_reader.py | 7 +-- alphabase/psm_reader/maxquant_reader.py | 9 ++- alphabase/psm_reader/msfragger_reader.py | 5 +- alphabase/psm_reader/psm_reader.py | 22 +++---- .../quant_reader/config_dict_loader.py | 6 +- .../quant_reader/longformat_reader.py | 6 +- .../quant_reader/quantreader_utils.py | 7 ++- .../quant_reader/table_reformatter.py | 10 ++-- .../quant_reader/wideformat_reader.py | 2 +- alphabase/spectral_library/base.py | 31 ++++++---- alphabase/spectral_library/flat.py | 20 ++++--- alphabase/spectral_library/reader.py | 44 +++++++------- alphabase/spectral_library/translate.py | 2 +- alphabase/spectral_library/validate.py | 18 +++--- setup.py | 5 +- 22 files changed, 175 insertions(+), 165 deletions(-) diff --git a/alphabase/constants/aa.py b/alphabase/constants/aa.py index b8b27e7c..8cae7d7e 100644 --- a/alphabase/constants/aa.py +++ b/alphabase/constants/aa.py @@ -69,7 +69,7 @@ def reset_AA_df(): def reset_AA_Composition(): global AA_Composition AA_Composition = {} - for aa, formula, mass in AA_DF.values: + for aa, formula, _mass in AA_DF.values: AA_Composition[aa] = dict(parse_formula(formula)) return AA_Composition @@ -77,7 +77,9 @@ def reset_AA_Composition(): reset_AA_Composition() -def reset_AA_atoms(atom_replace_dict: typing.Dict = {}): +def reset_AA_atoms(atom_replace_dict: typing.Dict = None): + if atom_replace_dict is None: + atom_replace_dict = {} reset_elements() replace_atoms(atom_replace_dict) reset_AA_mass() diff --git a/alphabase/constants/isotope.py b/alphabase/constants/isotope.py index 8feecc93..82528fa0 100644 --- a/alphabase/constants/isotope.py +++ b/alphabase/constants/isotope.py @@ -155,14 +155,7 @@ def _calc_one_elem_cum_dist(element_cum_dist: np.ndarray, element_cum_mono: np.n class IsotopeDistribution: def __init__( self, - max_elem_num_dict: dict = { - "C": 2000, - "H": 5000, - "N": 1000, - "O": 1000, - "S": 200, - "P": 200, - }, + max_elem_num_dict: dict = None, ): """Faster calculation of isotope abundance distribution by pre-building isotope distribution tables for most common elements. @@ -193,6 +186,15 @@ def __init__( {element: mono position array of cumulated isotope distribution}, and mono position array is a 1-D int np.ndarray. """ + if max_elem_num_dict is None: + max_elem_num_dict = { + "C": 2000, + "H": 5000, + "N": 1000, + "O": 1000, + "S": 200, + "P": 200, + } self.element_to_cum_dist_dict = {} self.element_to_cum_mono_idx = {} for elem, n in max_elem_num_dict.items(): diff --git a/alphabase/constants/modification.py b/alphabase/constants/modification.py index 279ee6f0..6a3d9805 100644 --- a/alphabase/constants/modification.py +++ b/alphabase/constants/modification.py @@ -276,10 +276,7 @@ def calc_modloss_mass_with_importance( mod_losses = np.zeros(nAA + 2) mod_losses[mod_sites] = [MOD_LOSS_MASS[mod] for mod in mod_names] _loss_importance = np.zeros(nAA + 2) - _loss_importance[mod_sites] = [ - MOD_LOSS_IMPORTANCE[mod] if mod in MOD_LOSS_IMPORTANCE else 0 - for mod in mod_names - ] + _loss_importance[mod_sites] = [MOD_LOSS_IMPORTANCE.get(mod, 0) for mod in mod_names] # Will not consider the modloss if the corresponding modloss_importance is 0 mod_losses[_loss_importance == 0] = 0 diff --git a/alphabase/io/hdf.py b/alphabase/io/hdf.py index a9b41446..d4ffcc61 100644 --- a/alphabase/io/hdf.py +++ b/alphabase/io/hdf.py @@ -496,10 +496,7 @@ def __init__( >>> hdf_file.dfs.df1.data_from "colleagues" """ - if delete_existing: - mode = "w" - else: - mode = "a" + mode = "w" if delete_existing else "a" with h5py.File(file_name, mode): # , swmr=True): pass super().__init__( diff --git a/alphabase/peptide/fragment.py b/alphabase/peptide/fragment.py index ba0ff3c9..c65e079e 100644 --- a/alphabase/peptide/fragment.py +++ b/alphabase/peptide/fragment.py @@ -494,10 +494,12 @@ def mask_fragments_for_charge_greater_than_precursor_charge( precursor_charge_array: np.ndarray, nAA_array: np.ndarray, *, - candidate_fragment_charges: list = [2, 3, 4], + candidate_fragment_charges: list = None, ): """Mask the fragment dataframe when the fragment charge is larger than the precursor charge""" + if candidate_fragment_charges is None: + candidate_fragment_charges = [2, 3, 4] precursor_charge_array = np.repeat(precursor_charge_array, nAA_array - 1) for col in fragment_df.columns: for charge in candidate_fragment_charges: @@ -681,8 +683,8 @@ def flatten_fragments( fragment_intensity_df: pd.DataFrame, min_fragment_intensity: float = -1, keep_top_k_fragments: int = 1000, - custom_columns: list = ["type", "number", "position", "charge", "loss_type"], - custom_df: Dict[str, pd.DataFrame] = {}, + custom_columns: list = None, + custom_df: Dict[str, pd.DataFrame] = None, ) -> Tuple[pd.DataFrame, pd.DataFrame]: """ Converts the tabular fragment format consisting of @@ -750,6 +752,10 @@ def flatten_fragments( - charge: uint8, fragment charge - loss_type: int16, fragment loss type, 0=noloss, 17=NH3, 18=H2O, 98=H3PO4 (phos), ... """ + if custom_df is None: + custom_df = {} + if custom_columns is None: + custom_columns = ["type", "number", "position", "charge", "loss_type"] if len(precursor_df) == 0: return precursor_df, pd.DataFrame() # new dataframes for fragments and precursors are created @@ -1047,25 +1053,24 @@ def create_fragment_mz_dataframe( pd.DataFrame `fragment_mz_df` with given `charged_frag_types` """ - if reference_fragment_df is None: - if "frag_start_idx" in precursor_df.columns: - # raise ValueError( - # "`precursor_df` contains 'frag_start_idx' column, "\ - # "please provide `reference_fragment_df` argument" - # ) - fragment_mz_df = init_fragment_by_precursor_dataframe( - precursor_df, - charged_frag_types, - dtype=dtype, - ) - return create_fragment_mz_dataframe( - precursor_df=precursor_df, - charged_frag_types=charged_frag_types, - reference_fragment_df=fragment_mz_df, - inplace_in_reference=True, - batch_size=batch_size, - dtype=dtype, - ) + if reference_fragment_df is None and "frag_start_idx" in precursor_df.columns: + # raise ValueError( + # "`precursor_df` contains 'frag_start_idx' column, "\ + # "please provide `reference_fragment_df` argument" + # ) + fragment_mz_df = init_fragment_by_precursor_dataframe( + precursor_df, + charged_frag_types, + dtype=dtype, + ) + return create_fragment_mz_dataframe( + precursor_df=precursor_df, + charged_frag_types=charged_frag_types, + reference_fragment_df=fragment_mz_df, + inplace_in_reference=True, + batch_size=batch_size, + dtype=dtype, + ) if "nAA" not in precursor_df.columns: # fast return create_fragment_mz_dataframe_by_sort_precursor( @@ -1255,12 +1260,10 @@ def filter_fragment_number( if not set(["frag_start_idx", "frag_stop_idx"]).issubset(precursor_df.columns): raise KeyError("frag_start_idx and frag_stop_idx not in dataframe") - for i, (start_idx, stop_idx, n_allowed_lib) in enumerate( - zip( - precursor_df["frag_start_idx"].values, - precursor_df["frag_stop_idx"].values, - precursor_df[n_fragments_allowed_column_name].values, - ) + for start_idx, stop_idx, n_allowed_lib in zip( + precursor_df["frag_start_idx"].values, + precursor_df["frag_stop_idx"].values, + precursor_df[n_fragments_allowed_column_name].values, ): _allowed = min(n_allowed_lib, n_allowed) diff --git a/alphabase/peptide/precursor.py b/alphabase/peptide/precursor.py index c45bf968..9f7ccfa3 100644 --- a/alphabase/peptide/precursor.py +++ b/alphabase/peptide/precursor.py @@ -25,18 +25,16 @@ def refine_precursor_df( """ if ensure_data_validity: df.fillna("", inplace=True) - if "charge" in df.columns: - if df.charge.dtype not in [ - "int", - "int8", - "int64", - "int32", - # np.int64, np.int32, np.int8, - ]: - df["charge"] = df["charge"].astype(np.int8) - if "mod_sites" in df.columns: - if df.mod_sites.dtype not in ["O", "U"]: - df["mod_sites"] = df.mod_sites.astype("U") + if "charge" in df.columns and df.charge.dtype not in [ + "int", + "int8", + "int64", + "int32", + # np.int64, np.int32, np.int8, + ]: + df["charge"] = df["charge"].astype(np.int8) + if "mod_sites" in df.columns and df.mod_sites.dtype not in ["O", "U"]: + df["mod_sites"] = df.mod_sites.astype("U") if "nAA" not in df.columns: df["nAA"] = df.sequence.str.len().astype(np.int32) @@ -107,7 +105,7 @@ def update_precursor_mz( # precursor_mz_idx = precursor_df.columns.get_loc( # 'precursor_mz' # ) - for nAA, big_df_group in _grouped: + for _, big_df_group in _grouped: for i in range(0, len(big_df_group), batch_size): batch_end = i + batch_size diff --git a/alphabase/protein/fasta.py b/alphabase/protein/fasta.py index 174edffb..3c5e6dc6 100644 --- a/alphabase/protein/fasta.py +++ b/alphabase/protein/fasta.py @@ -429,8 +429,8 @@ def add_single_peptide_labeling( nterm_label_mod: str, cterm_label_mod: str, ): - add_nterm_label = True if nterm_label_mod else False - add_cterm_label = True if cterm_label_mod else False + add_nterm_label = bool(nterm_label_mod) + add_cterm_label = bool(cterm_label_mod) if mod_sites: _sites = mod_sites.split(";") if "0" in _sites: @@ -478,10 +478,7 @@ def create_labeling_peptide_df( if len(peptide_df) == 0: return peptide_df - if inplace: - df = peptide_df - else: - df = peptide_df.copy() + df = peptide_df if inplace else peptide_df.copy() (label_aas, label_mod_dict, nterm_label_mod, cterm_label_mod) = parse_labels(labels) @@ -507,7 +504,7 @@ def protein_idxes_to_names(protein_idxes: str, protein_names: list): def append_special_modifications( df: pd.DataFrame, - var_mods: list = ["Phospho@S", "Phospho@T", "Phospho@Y"], + var_mods: list = None, min_mod_num: int = 0, max_mod_num: int = 1, max_peptidoform_num: int = 100, @@ -553,6 +550,8 @@ def append_special_modifications( pd.DataFrame The precursor_df with new modification added. """ + if var_mods is None: + var_mods = ["Phospho@S", "Phospho@T", "Phospho@Y"] if len(var_mods) == 0 or len(df) == 0: return df @@ -644,7 +643,7 @@ class SpecLibFasta(SpecLibBase): def __init__( self, - charged_frag_types: list = ["b_z1", "b_z2", "y_z1", "y_z2"], + charged_frag_types: list = None, *, protease: str = "trypsin", max_missed_cleavages: int = 2, @@ -654,12 +653,12 @@ def __init__( precursor_charge_max: int = 4, precursor_mz_min: float = 400.0, precursor_mz_max: float = 2000.0, - var_mods: list = ["Acetyl@Protein_N-term", "Oxidation@M"], + var_mods: list = None, min_var_mod_num: int = 0, max_var_mod_num: int = 2, - fix_mods: list = ["Carbamidomethyl@C"], + fix_mods: list = None, labeling_channels: dict = None, - special_mods: list = [], + special_mods: list = None, min_special_mod_num: int = 0, max_special_mod_num: int = 1, special_mods_cannot_modify_pep_n_term: bool = False, @@ -758,6 +757,14 @@ def __init__( include_contaminants : bool, optional If include contaminants.fasta, by default False """ + if special_mods is None: + special_mods = [] + if fix_mods is None: + fix_mods = ["Carbamidomethyl@C"] + if var_mods is None: + var_mods = ["Acetyl@Protein_N-term", "Oxidation@M"] + if charged_frag_types is None: + charged_frag_types = ["b_z1", "b_z2", "y_z1", "y_z2"] super().__init__( charged_frag_types=charged_frag_types, precursor_mz_min=precursor_mz_min, diff --git a/alphabase/psm_reader/alphapept_reader.py b/alphabase/psm_reader/alphapept_reader.py index 0327fabc..df59f8fa 100644 --- a/alphabase/psm_reader/alphapept_reader.py +++ b/alphabase/psm_reader/alphapept_reader.py @@ -18,10 +18,7 @@ def parse_ap(precursor): Parser to parse peptide strings """ items = precursor.split("_") - if len(items) == 3: - decoy = 1 - else: - decoy = 0 + decoy = 1 if len(items) == 3 else 0 modseq = items[0] charge = items[-1] @@ -81,7 +78,7 @@ def _init_modification_mapping(self): def _load_file(self, filename): with h5py.File(filename, "r") as _hdf: dataset = _hdf[self.hdf_dataset] - df = pd.DataFrame({col: dataset[col] for col in dataset.keys()}) + df = pd.DataFrame({col: dataset[col] for col in dataset}) df["raw_name"] = os.path.basename(filename)[: -len(".ms_data.hdf")] df["precursor"] = df["precursor"].str.decode("utf-8") # df['naked_sequence'] = df['naked_sequence'].str.decode('utf-8') diff --git a/alphabase/psm_reader/maxquant_reader.py b/alphabase/psm_reader/maxquant_reader.py index 6087b02f..96c5a67c 100644 --- a/alphabase/psm_reader/maxquant_reader.py +++ b/alphabase/psm_reader/maxquant_reader.py @@ -75,10 +75,7 @@ def parse_mod_seq( 0 for N-term; -1 for C-term; 1 to N for normal modifications. """ PeptideModSeq = modseq - if modseq[0] == "_": - underscore_for_ncterm = True - else: - underscore_for_ncterm = False + underscore_for_ncterm = modseq[0] == "_" mod_list = [] site_list = [] site = PeptideModSeq.find(mod_sep[0]) @@ -136,7 +133,7 @@ def __init__( fdr=0.01, keep_decoy=False, fixed_C57=True, - mod_seq_columns=["Modified sequence"], + mod_seq_columns=None, **kwargs, ): """Reader for MaxQuant msms.txt and evidence.txt @@ -168,6 +165,8 @@ def __init__( The columns to find modified sequences, by default ['Modified sequence'] """ + if mod_seq_columns is None: + mod_seq_columns = ["Modified sequence"] super().__init__( column_mapping=column_mapping, modification_mapping=modification_mapping, diff --git a/alphabase/psm_reader/msfragger_reader.py b/alphabase/psm_reader/msfragger_reader.py index 56f9ef9c..005f23d8 100644 --- a/alphabase/psm_reader/msfragger_reader.py +++ b/alphabase/psm_reader/msfragger_reader.py @@ -13,10 +13,7 @@ def _is_fragger_decoy(proteins): - for prot in proteins: - if not prot.lower().startswith("rev_"): - return False - return True + return all(prot.lower().startswith("rev_") for prot in proteins) mass_mapped_mods = psm_reader_yaml["msfragger_pepxml"]["mass_mapped_mods"] diff --git a/alphabase/psm_reader/psm_reader.py b/alphabase/psm_reader/psm_reader.py index e57c1d92..9721cdc8 100644 --- a/alphabase/psm_reader/psm_reader.py +++ b/alphabase/psm_reader/psm_reader.py @@ -344,7 +344,7 @@ def normalize_rt_by_raw_name(self): self.norm_rt() if "raw_name" not in self.psm_df.columns: return - for raw_name, df_group in self.psm_df.groupby("raw_name"): + for _, df_group in self.psm_df.groupby("raw_name"): self.psm_df.loc[df_group.index, "rt_norm"] = ( df_group.rt_norm / df_group.rt_norm.max() ) @@ -510,19 +510,21 @@ def _post_process(self, origin_df: pd.DataFrame): def filter_psm_by_modifications( self, - include_mod_set=set( - [ - "Oxidation@M", - "Phospho@S", - "Phospho@T", - "Phospho@Y", - "Acetyl@Protein N-term", - ] - ), + include_mod_set=None, ): """ Only keeps peptides with modifications in `include_mod_list`. """ + if include_mod_set is None: + include_mod_set = set( + [ + "Oxidation@M", + "Phospho@S", + "Phospho@T", + "Phospho@Y", + "Acetyl@Protein N-term", + ] + ) self._psm_df.mods = self._psm_df.mods.apply( keep_modifications, mod_set=include_mod_set ) diff --git a/alphabase/quantification/quant_reader/config_dict_loader.py b/alphabase/quantification/quant_reader/config_dict_loader.py index 2cdf4aa1..1f37adbc 100644 --- a/alphabase/quantification/quant_reader/config_dict_loader.py +++ b/alphabase/quantification/quant_reader/config_dict_loader.py @@ -24,7 +24,7 @@ def get_input_type_and_config_dict(input_file, input_type_to_use=None): uploaded_data_columns = set(pd.read_csv(input_file, sep=sep, nrows=1).columns) - for input_type in type2relevant_columns.keys(): + for input_type in type2relevant_columns: if (input_type_to_use is not None) and (input_type != input_type_to_use): continue relevant_columns = type2relevant_columns.get(input_type) @@ -65,7 +65,7 @@ def _load_config(config_yaml): def _get_type2relevant_cols(config_all): type2relcols = {} - for type in config_all.keys(): + for type in config_all: config_typedict = config_all.get(type) relevant_cols = get_relevant_columns_config_dict(config_typedict) type2relcols[type] = relevant_cols @@ -78,7 +78,7 @@ def get_relevant_columns_config_dict(config_typedict): for filtconf in config_typedict.get("filters", {}).values(): filtcols.append(filtconf.get("param")) - if "ion_hierarchy" in config_typedict.keys(): + if "ion_hierarchy" in config_typedict: for headr in config_typedict.get("ion_hierarchy").values(): ioncols = list(itertools.chain.from_iterable(headr.get("mapping").values())) dict_ioncols.extend(ioncols) diff --git a/alphabase/quantification/quant_reader/longformat_reader.py b/alphabase/quantification/quant_reader/longformat_reader.py index 88a31db7..a89c9952 100644 --- a/alphabase/quantification/quant_reader/longformat_reader.py +++ b/alphabase/quantification/quant_reader/longformat_reader.py @@ -153,7 +153,7 @@ def adapt_subtable(input_df_subset, config_dict, use_alphaquant_format): input_df_subset = quantreader_utils.filter_input( config_dict.get("filters", {}), input_df_subset ) - if "ion_hierarchy" in config_dict.keys(): + if "ion_hierarchy" in config_dict: return table_reformatter.merge_protein_cols_and_config_dict( input_df_subset, config_dict, use_alphaquant_format ) @@ -240,9 +240,9 @@ def process_with_dask( def get_hierarchy_names_from_config_dict(config_dict_for_type): hierarchy_names = [] - if "ion_hierarchy" in config_dict_for_type.keys(): + if "ion_hierarchy" in config_dict_for_type: ion_hierarchy = config_dict_for_type.get("ion_hierarchy") - for hierarchy_type in ion_hierarchy.keys(): + for hierarchy_type in ion_hierarchy: hierarchy_names += ion_hierarchy.get(hierarchy_type).get("order") return list(set(hierarchy_names)) else: diff --git a/alphabase/quantification/quant_reader/quantreader_utils.py b/alphabase/quantification/quant_reader/quantreader_utils.py index 49c094fc..9c01071e 100644 --- a/alphabase/quantification/quant_reader/quantreader_utils.py +++ b/alphabase/quantification/quant_reader/quantreader_utils.py @@ -1,3 +1,6 @@ +import contextlib + + def filter_input(filter_dict, input): if filter_dict is None: return input @@ -14,10 +17,8 @@ def filter_input(filter_dict, input): if comparator == "==": input = input[input[param] == value] continue - try: + with contextlib.suppress(Exception): input = input.astype({f"{param}": "float"}) - except Exception: - pass if comparator == ">": input = input[input[param].astype(type(value)) > value] diff --git a/alphabase/quantification/quant_reader/table_reformatter.py b/alphabase/quantification/quant_reader/table_reformatter.py index 70527265..4c221f1d 100644 --- a/alphabase/quantification/quant_reader/table_reformatter.py +++ b/alphabase/quantification/quant_reader/table_reformatter.py @@ -25,7 +25,7 @@ def merge_protein_cols_and_config_dict( input_df = input_df.drop(columns=[x for x in protein_cols if x != "protein"]) index_names = [] - for hierarchy_type in ion_hierarchy.keys(): + for hierarchy_type in ion_hierarchy: df_subset = input_df.copy() ion_hierarchy_local = ion_hierarchy.get(hierarchy_type).get("order") ion_headers_merged, ion_headers_grouped = get_ionname_columns( @@ -35,13 +35,13 @@ def merge_protein_cols_and_config_dict( df_subset, hierarchy_type, config_dict, ion_headers_merged ) headers = list(set(ion_headers_merged + quant_columns + ["protein"])) - if "sample_ID" in config_dict.keys(): + if "sample_ID" in config_dict: headers += [config_dict.get("sample_ID")] df_subset = df_subset[headers].drop_duplicates() if splitcol2sep is not None: if ( - quant_columns[0] in splitcol2sep.keys() + quant_columns[0] in splitcol2sep ): # in the case that quantitative values are stored grouped in one column (e.g. msiso1,msiso2,msiso3, etc.), reformat accordingly df_subset = split_extend_df(df_subset, splitcol2sep) ion_headers_grouped = adapt_headers_on_extended_df( @@ -97,7 +97,7 @@ def get_quantitative_columns(input_df, hierarchy_type, config_dict, ion_headers_ quantcolumn_candidates = [ x for x in input_df.columns if x not in naming_columns ] - if "quant_pre_or_suffix" in config_dict.keys(): + if "quant_pre_or_suffix" in config_dict: return [ x for x in quantcolumn_candidates @@ -147,7 +147,7 @@ def adapt_headers_on_extended_df(ion_headers_grouped, splitcol2sep): for vals in ion_headers_grouped_copy: if splitcol2sep is not None: for idx in range(len(vals)): - if vals[idx] in splitcol2sep.keys(): + if vals[idx] in splitcol2sep: vals[idx] = vals[idx] + "_idxs" return ion_headers_grouped_copy diff --git a/alphabase/quantification/quant_reader/wideformat_reader.py b/alphabase/quantification/quant_reader/wideformat_reader.py index 52ce7cdf..1e7c03a3 100644 --- a/alphabase/quantification/quant_reader/wideformat_reader.py +++ b/alphabase/quantification/quant_reader/wideformat_reader.py @@ -12,7 +12,7 @@ def reformat_and_write_wideformat_table(peptides_tsv, outfile_name, config_dict) input_df = table_reformatter.merge_protein_cols_and_config_dict( input_df, config_dict ) - if "quant_pre_or_suffix" in config_dict.keys(): + if "quant_pre_or_suffix" in config_dict: quant_pre_or_suffix = config_dict.get("quant_pre_or_suffix") headers = ["protein", "quant_id"] + list( filter( diff --git a/alphabase/spectral_library/base.py b/alphabase/spectral_library/base.py index ba687112..fc84404f 100644 --- a/alphabase/spectral_library/base.py +++ b/alphabase/spectral_library/base.py @@ -80,7 +80,7 @@ def __init__( # ['b_z1','b_z2','y_z1','y_modloss_z1', ...]; # 'b_z1': 'b' is the fragment type and # 'z1' is the charge state z=1. - charged_frag_types: typing.List[str] = ["b_z1", "b_z2", "y_z1", "y_z2"], + charged_frag_types: typing.List[str] = None, precursor_mz_min=400, precursor_mz_max=6000, decoy: str = None, @@ -104,7 +104,11 @@ def __init__( Decoy methods, could be "pseudo_reverse" or "diann". Defaults to None. """ - self.charged_frag_types = charged_frag_types + self.charged_frag_types = ( + ["b_z1", "b_z2", "y_z1", "y_z2"] + if charged_frag_types is None + else charged_frag_types + ) self._precursor_df = pd.DataFrame() self._fragment_intensity_df = pd.DataFrame() self._fragment_mz_df = pd.DataFrame() @@ -190,12 +194,7 @@ def copy(self): def append( self, other: "SpecLibBase", - dfs_to_append: typing.List[str] = [ - "_precursor_df", - "_fragment_intensity_df", - "_fragment_mz_df", - "_fragment_intensity_predicted_df", - ], + dfs_to_append: typing.List[str] = None, remove_unused_dfs: bool = True, ): """ @@ -223,6 +222,13 @@ def append( None """ + if dfs_to_append is None: + dfs_to_append = [ + "_precursor_df", + "_fragment_intensity_df", + "_fragment_mz_df", + "_fragment_intensity_predicted_df", + ] if remove_unused_dfs: current_frag_dfs = self.available_dense_fragment_dfs() for attr in current_frag_dfs: @@ -265,11 +271,10 @@ def check_matching_columns(df1, df2): n_fragments = [] # get subset of dfs_to_append starting with _fragment for attr in dfs_to_append: - if attr.startswith("_fragment"): - if hasattr(self, attr): - n_current_fragments = len(getattr(self, attr)) - if n_current_fragments > 0: - n_fragments += [n_current_fragments] + if attr.startswith("_fragment") and hasattr(self, attr): + n_current_fragments = len(getattr(self, attr)) + if n_current_fragments > 0: + n_fragments += [n_current_fragments] if not np.all(np.array(n_fragments) == n_fragments[0]): raise ValueError( diff --git a/alphabase/spectral_library/flat.py b/alphabase/spectral_library/flat.py index 62e9db7c..3af62c78 100644 --- a/alphabase/spectral_library/flat.py +++ b/alphabase/spectral_library/flat.py @@ -38,16 +38,10 @@ class SpecLibFlat(SpecLibBase): def __init__( self, - charged_frag_types: list = ["b_z1", "b_z2", "y_z1", "y_z2"], + charged_frag_types: list = None, min_fragment_intensity: float = 0.001, keep_top_k_fragments: int = 1000, - custom_fragment_df_columns: list = [ - "type", - "number", - "position", - "charge", - "loss_type", - ], + custom_fragment_df_columns: list = None, **kwargs, ): """ @@ -63,6 +57,16 @@ def __init__( See :attr:`custom_fragment_df_columns`, defaults to ['type','number','position','charge','loss_type'] """ + if custom_fragment_df_columns is None: + custom_fragment_df_columns = [ + "type", + "number", + "position", + "charge", + "loss_type", + ] + if charged_frag_types is None: + charged_frag_types = ["b_z1", "b_z2", "y_z1", "y_z2"] super().__init__(charged_frag_types=charged_frag_types) self.min_fragment_intensity = min_fragment_intensity self.keep_top_k_fragments = keep_top_k_fragments diff --git a/alphabase/spectral_library/reader.py b/alphabase/spectral_library/reader.py index f5dd209a..ed5e5975 100644 --- a/alphabase/spectral_library/reader.py +++ b/alphabase/spectral_library/reader.py @@ -15,16 +15,7 @@ class LibraryReaderBase(MaxQuantReader, SpecLibBase): def __init__( self, - charged_frag_types: typing.List[str] = [ - "b_z1", - "b_z2", - "y_z1", - "y_z2", - "b_modloss_z1", - "b_modloss_z2", - "y_modloss_z1", - "y_modloss_z2", - ], + charged_frag_types: typing.List[str] = None, column_mapping: dict = None, modification_mapping: dict = None, fdr=0.01, @@ -79,6 +70,17 @@ def __init__( Can be either `pseudo_reverse` or `diann` """ + if charged_frag_types is None: + charged_frag_types = [ + "b_z1", + "b_z2", + "y_z1", + "y_z2", + "b_modloss_z1", + "b_modloss_z2", + "y_modloss_z1", + "y_modloss_z2", + ] SpecLibBase.__init__( self, charged_frag_types=charged_frag_types, @@ -293,21 +295,23 @@ def _post_process( class LibraryReaderFromRawData(SpecLibBase): def __init__( self, - charged_frag_types: typing.List[str] = [ - "b_z1", - "b_z2", - "y_z1", - "y_z2", - "b_modloss_z1", - "b_modloss_z2", - "y_modloss_z1", - "y_modloss_z2", - ], + charged_frag_types: typing.List[str] = None, precursor_mz_min: float = 400, precursor_mz_max: float = 2000, decoy: str = None, **kwargs, ): + if charged_frag_types is None: + charged_frag_types = [ + "b_z1", + "b_z2", + "y_z1", + "y_z2", + "b_modloss_z1", + "b_modloss_z2", + "y_modloss_z1", + "y_modloss_z2", + ] super().__init__( charged_frag_types=charged_frag_types, precursor_mz_min=precursor_mz_min, diff --git a/alphabase/spectral_library/translate.py b/alphabase/spectral_library/translate.py index 6a8f460c..b163a37d 100644 --- a/alphabase/spectral_library/translate.py +++ b/alphabase/spectral_library/translate.py @@ -120,7 +120,7 @@ def merge_precursor_fragment_df( iters = enumerate(df[["frag_start_idx", "frag_stop_idx"]].values) if verbose: iters = tqdm.tqdm(iters) - for i, (start, end) in iters: + for _i, (start, end) in iters: intens = fragment_inten_df.iloc[start:end, :].to_numpy( copy=True ) # is loc[start:end-1,:] faster? diff --git a/alphabase/spectral_library/validate.py b/alphabase/spectral_library/validate.py index 4c869322..3396d577 100644 --- a/alphabase/spectral_library/validate.py +++ b/alphabase/spectral_library/validate.py @@ -72,17 +72,15 @@ def __call__(self, df: pd.DataFrame): f"Validation failed: Column {self.name} of type {_get_type_name(df[self.name].dtype)} cannot be cast to {_get_type_name(self.type)}" ) - if not self.allow_NaN: - if df[self.name].isna().any(): - raise ValueError( - f"Validation failed: Column {self.name} contains NaN values" - ) + if not self.allow_NaN and df[self.name].isna().any(): + raise ValueError( + f"Validation failed: Column {self.name} contains NaN values" + ) - if not self.allow_inf: - if not np.isfinite(df[self.name]).all(): - raise ValueError( - f"Validation failed: Column {self.name} contains inf values" - ) + if not self.allow_inf and not np.isfinite(df[self.name]).all(): + raise ValueError( + f"Validation failed: Column {self.name} contains inf values" + ) class Optional(Column): diff --git a/setup.py b/setup.py index d3e36c2b..b803c302 100644 --- a/setup.py +++ b/setup.py @@ -21,10 +21,7 @@ def get_requirements(): requirement_file_names[""] = "requirements.txt" for extra, requirement_file_name in requirement_file_names.items(): with open(requirement_file_name) as requirements_file: - if extra != "": - extra_stable = f"{extra}-stable" - else: - extra_stable = "stable" + extra_stable = f"{extra}-stable" if extra != "" else "stable" extra_requirements[extra_stable] = [] extra_requirements[extra] = [] for line in requirements_file: From dae9f9527f38d80ed4c91e42a618de1f0a6e30c7 Mon Sep 17 00:00:00 2001 From: mschwoerer <82171591+mschwoer@users.noreply.github.com> Date: Wed, 22 May 2024 16:54:57 +0200 Subject: [PATCH 03/30] fix more linting issues --- alphabase/io/hdf.py | 16 +++++++++------- alphabase/io/tempmmap.py | 9 ++++----- alphabase/psm_reader/psm_reader.py | 7 ++++--- alphabase/spectral_library/base.py | 12 +++++++----- alphabase/utils.py | 2 +- pyproject.toml | 16 ++++++++-------- 6 files changed, 33 insertions(+), 29 deletions(-) diff --git a/alphabase/io/hdf.py b/alphabase/io/hdf.py index d4ffcc61..8262d9e1 100644 --- a/alphabase/io/hdf.py +++ b/alphabase/io/hdf.py @@ -199,14 +199,16 @@ def set_truncate(self, truncate: bool = True): def __setattr__(self, name, value): try: super().__setattr__(name, value) - except NotImplementedError: + except NotImplementedError as e: if not self.truncate: if name in self.group_names: - raise KeyError(f"Group name '{name}' cannot be truncated") + raise KeyError(f"Group name '{name}' cannot be truncated") from e elif name in self.dataset_names: - raise KeyError(f"Dataset name '{name}' cannot be truncated") + raise KeyError(f"Dataset name '{name}' cannot be truncated") from e elif name in self.dataframe_names: - raise KeyError(f"Dataframe name '{name}' cannot be truncated") + raise KeyError( + f"Dataframe name '{name}' cannot be truncated" + ) from e if isinstance(value, (np.ndarray, pd.core.series.Series)): self.add_dataset(name, value) elif isinstance(value, (dict, pd.DataFrame)): @@ -217,7 +219,7 @@ def __setattr__(self, name, value): "Only (str, bool, int, float, np.ndarray, " "pd.core.series.Series, dict pd.DataFrame) types are " "accepted.", - ) + ) from e def add_dataset( self, @@ -252,12 +254,12 @@ def add_dataset( # chunks=array.shape, maxshape=tuple([None for i in array.shape]), ) - except TypeError: + except TypeError as e: raise NotImplementedError( f"Type {array.dtype} is not understood. " "If this is a string format, try to cast it to " "np.dtype('O') as possible solution." - ) + ) from e dataset = HDF_Dataset( file_name=self.file_name, name=f"{self.name}/{name}", diff --git a/alphabase/io/tempmmap.py b/alphabase/io/tempmmap.py index 7dfac298..a4d7b0d8 100644 --- a/alphabase/io/tempmmap.py +++ b/alphabase/io/tempmmap.py @@ -119,11 +119,10 @@ def create_empty_mmap(shape: tuple, dtype: np.dtype, path: str = None, overwrite ) else: # check that if overwrite is false the file does not already exist - if not overwrite: - if os.path.exists(path): - raise ValueError( - "The file already exists. Set overwrite to True to overwrite the file or choose a different name." - ) + if not overwrite and os.path.exists(path): + raise ValueError( + "The file already exists. Set overwrite to True to overwrite the file or choose a different name." + ) if not os.path.basename.endswith(".hdf"): raise ValueError("The chosen file name needs to end with .hdf") if os.path.isdir(os.path.commonpath(path)): diff --git a/alphabase/psm_reader/psm_reader.py b/alphabase/psm_reader/psm_reader.py index 9721cdc8..0ff51dbb 100644 --- a/alphabase/psm_reader/psm_reader.py +++ b/alphabase/psm_reader/psm_reader.py @@ -240,9 +240,10 @@ def _reverse_mod_mapping(self): for this_mod, other_mod in self.modification_mapping.items(): if isinstance(other_mod, (list, tuple)): for _mod in other_mod: - if _mod in self.rev_mod_mapping: - if this_mod.endswith("Protein N-term"): - continue + if _mod in self.rev_mod_mapping and this_mod.endswith( + "Protein N-term" + ): + continue self.rev_mod_mapping[_mod] = this_mod else: self.rev_mod_mapping[other_mod] = this_mod diff --git a/alphabase/spectral_library/base.py b/alphabase/spectral_library/base.py index fc84404f..47a31b20 100644 --- a/alphabase/spectral_library/base.py +++ b/alphabase/spectral_library/base.py @@ -281,19 +281,21 @@ def check_matching_columns(df1, df2): "The libraries can't be appended as the number of fragments in the current libraries are not the same." ) - for attr, matching_columns in zip(dfs_to_append, matching_columns): + for attr, column in zip(dfs_to_append, matching_columns): if hasattr(self, attr) and hasattr(other, attr): current_df = getattr(self, attr) # copy dataframes to avoid changing the original ones - other_df = getattr(other, attr)[matching_columns].copy() + other_df = getattr(other, attr)[column].copy() if attr.startswith("_precursor"): frag_idx_increment = 0 for fragment_df in ["_fragment_intensity_df", "_fragment_mz_df"]: - if hasattr(self, fragment_df): - if len(getattr(self, fragment_df)) > 0: - frag_idx_increment = len(getattr(self, fragment_df)) + if ( + hasattr(self, fragment_df) + and len(getattr(self, fragment_df)) > 0 + ): + frag_idx_increment = len(getattr(self, fragment_df)) if "frag_start_idx" in other_df.columns: other_df["frag_start_idx"] += frag_idx_increment diff --git a/alphabase/utils.py b/alphabase/utils.py index adb00faf..7bb7fa3c 100644 --- a/alphabase/utils.py +++ b/alphabase/utils.py @@ -9,7 +9,7 @@ def process_bar(iterator, len_iter): with tqdm.tqdm(total=len_iter) as bar: i = 0 - for i, iter in enumerate(iterator): + for i, iter in enumerate(iterator): # noqa: B007 yield iter bar.update() bar.update(len_iter - i - 1) diff --git a/pyproject.toml b/pyproject.toml index ebe33c6e..4847eeee 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,14 +4,14 @@ select = [ "E", # Pyflakes "F", -# # pyupgrade -# "UP", -# # flake8-bugbear -# "B", -# # flake8-simplify -# "SIM", -# # isort -# "I", + # pyupgrade + "UP", + # flake8-bugbear + "B", + # flake8-simplify + "SIM", + # isort + "I", ] ignore = [ "E501", # Line too long (ruff wraps code, but not docstrings) From fd03c81662f2245c3240922d748728fe0b4ea193 Mon Sep 17 00:00:00 2001 From: mschwoerer <82171591+mschwoer@users.noreply.github.com> Date: Wed, 12 Jun 2024 09:11:29 +0200 Subject: [PATCH 04/30] revert back tp mutable arguments --- alphabase/constants/aa.py | 4 +--- alphabase/constants/isotope.py | 18 ++++++++---------- alphabase/peptide/fragment.py | 12 +++--------- alphabase/protein/fasta.py | 20 +++++--------------- alphabase/spectral_library/base.py | 22 ++++++++-------------- alphabase/spectral_library/flat.py | 20 ++++++++------------ alphabase/spectral_library/reader.py | 22 ++++++++++------------ pyproject.toml | 3 ++- 8 files changed, 45 insertions(+), 76 deletions(-) diff --git a/alphabase/constants/aa.py b/alphabase/constants/aa.py index 8cae7d7e..c2334e9e 100644 --- a/alphabase/constants/aa.py +++ b/alphabase/constants/aa.py @@ -77,9 +77,7 @@ def reset_AA_Composition(): reset_AA_Composition() -def reset_AA_atoms(atom_replace_dict: typing.Dict = None): - if atom_replace_dict is None: - atom_replace_dict = {} +def reset_AA_atoms(atom_replace_dict: typing.Dict = {}): reset_elements() replace_atoms(atom_replace_dict) reset_AA_mass() diff --git a/alphabase/constants/isotope.py b/alphabase/constants/isotope.py index 82528fa0..8feecc93 100644 --- a/alphabase/constants/isotope.py +++ b/alphabase/constants/isotope.py @@ -155,7 +155,14 @@ def _calc_one_elem_cum_dist(element_cum_dist: np.ndarray, element_cum_mono: np.n class IsotopeDistribution: def __init__( self, - max_elem_num_dict: dict = None, + max_elem_num_dict: dict = { + "C": 2000, + "H": 5000, + "N": 1000, + "O": 1000, + "S": 200, + "P": 200, + }, ): """Faster calculation of isotope abundance distribution by pre-building isotope distribution tables for most common elements. @@ -186,15 +193,6 @@ def __init__( {element: mono position array of cumulated isotope distribution}, and mono position array is a 1-D int np.ndarray. """ - if max_elem_num_dict is None: - max_elem_num_dict = { - "C": 2000, - "H": 5000, - "N": 1000, - "O": 1000, - "S": 200, - "P": 200, - } self.element_to_cum_dist_dict = {} self.element_to_cum_mono_idx = {} for elem, n in max_elem_num_dict.items(): diff --git a/alphabase/peptide/fragment.py b/alphabase/peptide/fragment.py index c65e079e..2eb4a6d9 100644 --- a/alphabase/peptide/fragment.py +++ b/alphabase/peptide/fragment.py @@ -494,12 +494,10 @@ def mask_fragments_for_charge_greater_than_precursor_charge( precursor_charge_array: np.ndarray, nAA_array: np.ndarray, *, - candidate_fragment_charges: list = None, + candidate_fragment_charges: list = [2, 3, 4], ): """Mask the fragment dataframe when the fragment charge is larger than the precursor charge""" - if candidate_fragment_charges is None: - candidate_fragment_charges = [2, 3, 4] precursor_charge_array = np.repeat(precursor_charge_array, nAA_array - 1) for col in fragment_df.columns: for charge in candidate_fragment_charges: @@ -683,8 +681,8 @@ def flatten_fragments( fragment_intensity_df: pd.DataFrame, min_fragment_intensity: float = -1, keep_top_k_fragments: int = 1000, - custom_columns: list = None, - custom_df: Dict[str, pd.DataFrame] = None, + custom_columns: list = ["type", "number", "position", "charge", "loss_type"], + custom_df: Dict[str, pd.DataFrame] = {}, ) -> Tuple[pd.DataFrame, pd.DataFrame]: """ Converts the tabular fragment format consisting of @@ -752,10 +750,6 @@ def flatten_fragments( - charge: uint8, fragment charge - loss_type: int16, fragment loss type, 0=noloss, 17=NH3, 18=H2O, 98=H3PO4 (phos), ... """ - if custom_df is None: - custom_df = {} - if custom_columns is None: - custom_columns = ["type", "number", "position", "charge", "loss_type"] if len(precursor_df) == 0: return precursor_df, pd.DataFrame() # new dataframes for fragments and precursors are created diff --git a/alphabase/protein/fasta.py b/alphabase/protein/fasta.py index 3c5e6dc6..5de7670b 100644 --- a/alphabase/protein/fasta.py +++ b/alphabase/protein/fasta.py @@ -504,7 +504,7 @@ def protein_idxes_to_names(protein_idxes: str, protein_names: list): def append_special_modifications( df: pd.DataFrame, - var_mods: list = None, + var_mods: list = ["Phospho@S", "Phospho@T", "Phospho@Y"], min_mod_num: int = 0, max_mod_num: int = 1, max_peptidoform_num: int = 100, @@ -550,8 +550,6 @@ def append_special_modifications( pd.DataFrame The precursor_df with new modification added. """ - if var_mods is None: - var_mods = ["Phospho@S", "Phospho@T", "Phospho@Y"] if len(var_mods) == 0 or len(df) == 0: return df @@ -643,7 +641,7 @@ class SpecLibFasta(SpecLibBase): def __init__( self, - charged_frag_types: list = None, + charged_frag_types: list = ["b_z1", "b_z2", "y_z1", "y_z2"], *, protease: str = "trypsin", max_missed_cleavages: int = 2, @@ -653,12 +651,12 @@ def __init__( precursor_charge_max: int = 4, precursor_mz_min: float = 400.0, precursor_mz_max: float = 2000.0, - var_mods: list = None, + var_mods: list = ["Acetyl@Protein_N-term", "Oxidation@M"], min_var_mod_num: int = 0, max_var_mod_num: int = 2, - fix_mods: list = None, + fix_mods: list = ["Carbamidomethyl@C"], labeling_channels: dict = None, - special_mods: list = None, + special_mods: list = [], min_special_mod_num: int = 0, max_special_mod_num: int = 1, special_mods_cannot_modify_pep_n_term: bool = False, @@ -757,14 +755,6 @@ def __init__( include_contaminants : bool, optional If include contaminants.fasta, by default False """ - if special_mods is None: - special_mods = [] - if fix_mods is None: - fix_mods = ["Carbamidomethyl@C"] - if var_mods is None: - var_mods = ["Acetyl@Protein_N-term", "Oxidation@M"] - if charged_frag_types is None: - charged_frag_types = ["b_z1", "b_z2", "y_z1", "y_z2"] super().__init__( charged_frag_types=charged_frag_types, precursor_mz_min=precursor_mz_min, diff --git a/alphabase/spectral_library/base.py b/alphabase/spectral_library/base.py index 47a31b20..cf605207 100644 --- a/alphabase/spectral_library/base.py +++ b/alphabase/spectral_library/base.py @@ -80,7 +80,7 @@ def __init__( # ['b_z1','b_z2','y_z1','y_modloss_z1', ...]; # 'b_z1': 'b' is the fragment type and # 'z1' is the charge state z=1. - charged_frag_types: typing.List[str] = None, + charged_frag_types: typing.List[str] = ["b_z1", "b_z2", "y_z1", "y_z2"], precursor_mz_min=400, precursor_mz_max=6000, decoy: str = None, @@ -104,11 +104,7 @@ def __init__( Decoy methods, could be "pseudo_reverse" or "diann". Defaults to None. """ - self.charged_frag_types = ( - ["b_z1", "b_z2", "y_z1", "y_z2"] - if charged_frag_types is None - else charged_frag_types - ) + self.charged_frag_types = charged_frag_types self._precursor_df = pd.DataFrame() self._fragment_intensity_df = pd.DataFrame() self._fragment_mz_df = pd.DataFrame() @@ -194,7 +190,12 @@ def copy(self): def append( self, other: "SpecLibBase", - dfs_to_append: typing.List[str] = None, + dfs_to_append: typing.List[str] = [ + "_precursor_df", + "_fragment_intensity_df", + "_fragment_mz_df", + "_fragment_intensity_predicted_df", + ], remove_unused_dfs: bool = True, ): """ @@ -222,13 +223,6 @@ def append( None """ - if dfs_to_append is None: - dfs_to_append = [ - "_precursor_df", - "_fragment_intensity_df", - "_fragment_mz_df", - "_fragment_intensity_predicted_df", - ] if remove_unused_dfs: current_frag_dfs = self.available_dense_fragment_dfs() for attr in current_frag_dfs: diff --git a/alphabase/spectral_library/flat.py b/alphabase/spectral_library/flat.py index 3af62c78..62e9db7c 100644 --- a/alphabase/spectral_library/flat.py +++ b/alphabase/spectral_library/flat.py @@ -38,10 +38,16 @@ class SpecLibFlat(SpecLibBase): def __init__( self, - charged_frag_types: list = None, + charged_frag_types: list = ["b_z1", "b_z2", "y_z1", "y_z2"], min_fragment_intensity: float = 0.001, keep_top_k_fragments: int = 1000, - custom_fragment_df_columns: list = None, + custom_fragment_df_columns: list = [ + "type", + "number", + "position", + "charge", + "loss_type", + ], **kwargs, ): """ @@ -57,16 +63,6 @@ def __init__( See :attr:`custom_fragment_df_columns`, defaults to ['type','number','position','charge','loss_type'] """ - if custom_fragment_df_columns is None: - custom_fragment_df_columns = [ - "type", - "number", - "position", - "charge", - "loss_type", - ] - if charged_frag_types is None: - charged_frag_types = ["b_z1", "b_z2", "y_z1", "y_z2"] super().__init__(charged_frag_types=charged_frag_types) self.min_fragment_intensity = min_fragment_intensity self.keep_top_k_fragments = keep_top_k_fragments diff --git a/alphabase/spectral_library/reader.py b/alphabase/spectral_library/reader.py index ed5e5975..6461ef00 100644 --- a/alphabase/spectral_library/reader.py +++ b/alphabase/spectral_library/reader.py @@ -15,7 +15,16 @@ class LibraryReaderBase(MaxQuantReader, SpecLibBase): def __init__( self, - charged_frag_types: typing.List[str] = None, + charged_frag_types: typing.List[str] = [ + "b_z1", + "b_z2", + "y_z1", + "y_z2", + "b_modloss_z1", + "b_modloss_z2", + "y_modloss_z1", + "y_modloss_z2", + ], column_mapping: dict = None, modification_mapping: dict = None, fdr=0.01, @@ -70,17 +79,6 @@ def __init__( Can be either `pseudo_reverse` or `diann` """ - if charged_frag_types is None: - charged_frag_types = [ - "b_z1", - "b_z2", - "y_z1", - "y_z2", - "b_modloss_z1", - "b_modloss_z2", - "y_modloss_z1", - "y_modloss_z2", - ] SpecLibBase.__init__( self, charged_frag_types=charged_frag_types, diff --git a/pyproject.toml b/pyproject.toml index 4847eeee..565e4a72 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,5 +15,6 @@ select = [ ] ignore = [ "E501", # Line too long (ruff wraps code, but not docstrings) - "B028" # No explicit `stacklevel` keyword argument found (for warnings) + "B028", # No explicit `stacklevel` keyword argument found (for warnings) + "B006", # Do not use mutable data structures for argument defaults # TODO: fix this! ] From 6a574602fb38755fd074db4928f52ff887fc3156 Mon Sep 17 00:00:00 2001 From: mschwoerer <82171591+mschwoer@users.noreply.github.com> Date: Wed, 12 Jun 2024 14:28:05 +0200 Subject: [PATCH 05/30] tolerate mutable arguments in ruff --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 565e4a72..659c6123 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,5 +16,5 @@ select = [ ignore = [ "E501", # Line too long (ruff wraps code, but not docstrings) "B028", # No explicit `stacklevel` keyword argument found (for warnings) - "B006", # Do not use mutable data structures for argument defaults # TODO: fix this! + #"B006", # Do not use mutable data structures for argument defaults # TODO: fix this! ] From 7811213fba89b2522b4514d4bacd3a6eb3408d4d Mon Sep 17 00:00:00 2001 From: mschwoerer <82171591+mschwoer@users.noreply.github.com> Date: Wed, 12 Jun 2024 14:28:18 +0200 Subject: [PATCH 06/30] tolerate mutable arguments in ruff --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 659c6123..565e4a72 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,5 +16,5 @@ select = [ ignore = [ "E501", # Line too long (ruff wraps code, but not docstrings) "B028", # No explicit `stacklevel` keyword argument found (for warnings) - #"B006", # Do not use mutable data structures for argument defaults # TODO: fix this! + "B006", # Do not use mutable data structures for argument defaults # TODO: fix this! ] From 894e4a2615d808583c2f8b607f0a3a80a2f4b2e0 Mon Sep 17 00:00:00 2001 From: mschwoerer <82171591+mschwoer@users.noreply.github.com> Date: Mon, 24 Jun 2024 13:48:06 +0200 Subject: [PATCH 07/30] test --- nbs_tests/psm_reader/sage_reader.ipynb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/nbs_tests/psm_reader/sage_reader.ipynb b/nbs_tests/psm_reader/sage_reader.ipynb index cb1f90f5..b19b901a 100644 --- a/nbs_tests/psm_reader/sage_reader.ipynb +++ b/nbs_tests/psm_reader/sage_reader.ipynb @@ -58,7 +58,9 @@ "outputs": [], "source": [ "#| hide\n", - "assert capture_modifications('Q[-17.026548]DQSANEKNK[+42.010567]LEM[+15.9949]NK[+42.010567]', annotated_mod_df) == ('0;9;12;14', 'Gln->pyro-Glu@Q^Any N-term;Acetyl@K;Oxidation@M;Acetyl@K')" + "result = capture_modifications('Q[-17.026548]DQSANEKNK[+42.010567]LEM[+15.9949]NK[+42.010567]', annotated_mod_df) \n", + "expected = ('0;9;12;14', 'Gln->pyro-Glu@Q^Any N-term;Acetyl@K;Oxidation@M;Acetyl@K') \n", + "assert result ==expected, f\"Expected: {expected}, got: {result}\"" ] }, { From 3f38a892f3e468217538ed766ca7d1edf6a0a5ee Mon Sep 17 00:00:00 2001 From: mschwoerer <82171591+mschwoer@users.noreply.github.com> Date: Tue, 25 Jun 2024 13:57:27 +0200 Subject: [PATCH 08/30] remove modification names with whitespaces --- .../constants/const_files/modification.tsv | 602 +++++++++--------- scripts/unimod_to_tsv.ipynb | 188 +++--- 2 files changed, 410 insertions(+), 380 deletions(-) diff --git a/alphabase/constants/const_files/modification.tsv b/alphabase/constants/const_files/modification.tsv index 49ed5d0e..8ba1b0cc 100644 --- a/alphabase/constants/const_files/modification.tsv +++ b/alphabase/constants/const_files/modification.tsv @@ -1,16 +1,16 @@ mod_name unimod_mass unimod_avge_mass composition unimod_modloss modloss_composition classification unimod_id modloss_importance Acetyl@T 42.010565 42.0367 H(2)C(2)O(1) 0.0 Post-translational 1 0.0 -Acetyl@Protein N-term 42.010565 42.0367 H(2)C(2)O(1) 0.0 Post-translational 1 0.0 +Acetyl@Protein_N-term 42.010565 42.0367 H(2)C(2)O(1) 0.0 Post-translational 1 0.0 Acetyl@S 42.010565 42.0367 H(2)C(2)O(1) 0.0 Post-translational 1 0.0 Acetyl@C 42.010565 42.0367 H(2)C(2)O(1) 0.0 Post-translational 1 0.0 -Acetyl@Any N-term 42.010565 42.0367 H(2)C(2)O(1) 0.0 Multiple 1 0.0 +Acetyl@Any_N-term 42.010565 42.0367 H(2)C(2)O(1) 0.0 Multiple 1 0.0 Acetyl@K 42.010565 42.0367 H(2)C(2)O(1) 0.0 Multiple 1 0.0 Acetyl@Y 42.010565 42.0367 H(2)C(2)O(1) 0.0 Chemical derivative 1 0.0 Acetyl@H 42.010565 42.0367 H(2)C(2)O(1) 0.0 Chemical derivative 1 0.0 Acetyl@R 42.010565 42.0367 H(2)C(2)O(1) 0.0 Artefact 1 0.0 -Amidated@Any C-term -0.984016 -0.9848 H(1)N(1)O(-1) 0.0 Artefact 2 0.0 -Amidated@Protein C-term -0.984016 -0.9848 H(1)N(1)O(-1) 0.0 Post-translational 2 0.0 -Biotin@Any N-term 226.077598 226.2954 H(14)C(10)N(2)O(2)S(1) 0.0 Chemical derivative 3 0.0 +Amidated@Any_C-term -0.984016 -0.9848 H(1)N(1)O(-1) 0.0 Artefact 2 0.0 +Amidated@Protein_C-term -0.984016 -0.9848 H(1)N(1)O(-1) 0.0 Post-translational 2 0.0 +Biotin@Any_N-term 226.077598 226.2954 H(14)C(10)N(2)O(2)S(1) 0.0 Chemical derivative 3 0.0 Biotin@K 226.077598 226.2954 H(14)C(10)N(2)O(2)S(1) 0.0 Post-translational 3 0.0 Carbamidomethyl@Y 57.021464 57.0513 H(3)C(2)N(1)O(1) 0.0 Artefact 4 0.0 Carbamidomethyl@T 57.021464 57.0513 H(3)C(2)N(1)O(1) 0.0 Artefact 4 0.0 @@ -18,7 +18,7 @@ Carbamidomethyl@S 57.021464 57.0513 H(3)C(2)N(1)O(1) 0.0 Artefact 4 0.0 Carbamidomethyl@E 57.021464 57.0513 H(3)C(2)N(1)O(1) 0.0 Artefact 4 0.0 Carbamidomethyl@D 57.021464 57.0513 H(3)C(2)N(1)O(1) 0.0 Artefact 4 0.0 Carbamidomethyl@H 57.021464 57.0513 H(3)C(2)N(1)O(1) 0.0 Artefact 4 0.0 -Carbamidomethyl@Any N-term 57.021464 57.0513 H(3)C(2)N(1)O(1) 0.0 Artefact 4 0.0 +Carbamidomethyl@Any_N-term 57.021464 57.0513 H(3)C(2)N(1)O(1) 0.0 Artefact 4 0.0 Carbamidomethyl@K 57.021464 57.0513 H(3)C(2)N(1)O(1) 0.0 Artefact 4 0.0 Carbamidomethyl@C 57.021464 57.0513 H(3)C(2)N(1)O(1) 0.0 Chemical derivative 4 0.0 Carbamidomethyl@U 57.021464 57.0513 H(3)C(2)N(1)O(1) 0.0 Chemical derivative 4 0.0 @@ -29,10 +29,10 @@ Carbamyl@S 43.005814 43.0247 H(1)C(1)N(1)O(1) 0.0 Chemical derivative 5 0.0 Carbamyl@M 43.005814 43.0247 H(1)C(1)N(1)O(1) 0.0 Artefact 5 0.0 Carbamyl@C 43.005814 43.0247 H(1)C(1)N(1)O(1) 0.0 Artefact 5 0.0 Carbamyl@R 43.005814 43.0247 H(1)C(1)N(1)O(1) 0.0 Artefact 5 0.0 -Carbamyl@Any N-term 43.005814 43.0247 H(1)C(1)N(1)O(1) 0.0 Multiple 5 0.0 +Carbamyl@Any_N-term 43.005814 43.0247 H(1)C(1)N(1)O(1) 0.0 Multiple 5 0.0 Carbamyl@K 43.005814 43.0247 H(1)C(1)N(1)O(1) 0.0 Multiple 5 0.0 -Carbamyl@Protein N-term 43.005814 43.0247 H(1)C(1)N(1)O(1) 0.0 Post-translational 5 0.0 -Carboxymethyl@Any N-term 58.005479 58.0361 H(2)C(2)O(2) 0.0 Artefact 6 0.0 +Carbamyl@Protein_N-term 43.005814 43.0247 H(1)C(1)N(1)O(1) 0.0 Post-translational 5 0.0 +Carboxymethyl@Any_N-term 58.005479 58.0361 H(2)C(2)O(2) 0.0 Artefact 6 0.0 Carboxymethyl@K 58.005479 58.0361 H(2)C(2)O(2) 0.0 Artefact 6 0.0 Carboxymethyl@C 58.005479 58.0361 H(2)C(2)O(2) 0.0 Chemical derivative 6 0.0 Carboxymethyl@W 58.005479 58.0361 H(2)C(2)O(2) 0.0 Chemical derivative 6 0.0 @@ -40,11 +40,11 @@ Carboxymethyl@U 58.005479 58.0361 H(2)C(2)O(2) 0.0 Chemical derivative 6 0.0 Deamidated@Q 0.984016 0.9848 H(-1)N(-1)O(1) 0.0 Artefact 7 0.0 Deamidated@R 0.984016 0.9848 H(-1)N(-1)O(1) 43.005814 H(1)C(1)N(1)O(1) Post-translational 7 0.5 Deamidated@N 0.984016 0.9848 H(-1)N(-1)O(1) 0.0 Artefact 7 0.0 -Deamidated@F^Protein N-term 0.984016 0.9848 H(-1)N(-1)O(1) 0.0 Post-translational 7 0.0 +Deamidated@F^Protein_N-term 0.984016 0.9848 H(-1)N(-1)O(1) 0.0 Post-translational 7 0.0 ICAT-G@C 486.251206 486.6253 H(38)C(22)N(4)O(6)S(1) 0.0 Isotopic label 8 0.0 ICAT-G:2H(8)@C 494.30142 494.6746 H(30)2H(8)C(22)N(4)O(6)S(1) 0.0 Isotopic label 9 0.0 -Met->Hse@M^Any C-term -29.992806 -30.0922 H(-2)C(-1)O(1)S(-1) 0.0 Chemical derivative 10 0.0 -Met->Hsl@M^Any C-term -48.003371 -48.1075 H(-4)C(-1)S(-1) 0.0 Chemical derivative 11 0.0 +Met->Hse@M^Any_C-term -29.992806 -30.0922 H(-2)C(-1)O(1)S(-1) 0.0 Chemical derivative 10 0.0 +Met->Hsl@M^Any_C-term -48.003371 -48.1075 H(-4)C(-1)S(-1) 0.0 Chemical derivative 11 0.0 ICAT-D:2H(8)@C 450.275205 450.6221 H(26)2H(8)C(20)N(4)O(5)S(1) 0.0 Isotopic label 12 0.0 ICAT-D@C 442.224991 442.5728 H(34)C(20)N(4)O(5)S(1) 0.0 Isotopic label 13 0.0 NIPCAM@C 99.068414 99.1311 H(9)C(5)N(1)O(1) 0.0 Chemical derivative 17 0.0 @@ -68,32 +68,32 @@ Dehydrated@D -18.010565 -18.0153 H(-2)O(-1) 0.0 Chemical derivative 23 0.0 Dehydrated@Y -18.010565 -18.0153 H(-2)O(-1) 0.0 Post-translational 23 0.0 Dehydrated@T -18.010565 -18.0153 H(-2)O(-1) 0.0 Post-translational 23 0.0 Dehydrated@S -18.010565 -18.0153 H(-2)O(-1) 0.0 Post-translational 23 0.0 -Dehydrated@N^Protein C-term -18.010565 -18.0153 H(-2)O(-1) 0.0 Post-translational 23 0.0 -Dehydrated@Q^Protein C-term -18.010565 -18.0153 H(-2)O(-1) 0.0 Post-translational 23 0.0 -Dehydrated@C^Any N-term -18.010565 -18.0153 H(-2)O(-1) 0.0 Artefact 23 0.0 +Dehydrated@N^Protein_C-term -18.010565 -18.0153 H(-2)O(-1) 0.0 Post-translational 23 0.0 +Dehydrated@Q^Protein_C-term -18.010565 -18.0153 H(-2)O(-1) 0.0 Post-translational 23 0.0 +Dehydrated@C^Any_N-term -18.010565 -18.0153 H(-2)O(-1) 0.0 Artefact 23 0.0 Propionamide@C 71.037114 71.0779 H(5)C(3)N(1)O(1) 0.0 Artefact 24 0.0 Propionamide@K 71.037114 71.0779 H(5)C(3)N(1)O(1) 0.0 Chemical derivative 24 0.0 -Propionamide@Any N-term 71.037114 71.0779 H(5)C(3)N(1)O(1) 0.0 Chemical derivative 24 0.0 -Pyridylacetyl@Any N-term 119.037114 119.1207 H(5)C(7)N(1)O(1) 0.0 Chemical derivative 25 0.0 +Propionamide@Any_N-term 71.037114 71.0779 H(5)C(3)N(1)O(1) 0.0 Chemical derivative 24 0.0 +Pyridylacetyl@Any_N-term 119.037114 119.1207 H(5)C(7)N(1)O(1) 0.0 Chemical derivative 25 0.0 Pyridylacetyl@K 119.037114 119.1207 H(5)C(7)N(1)O(1) 0.0 Chemical derivative 25 0.0 -Pyro-carbamidomethyl@C^Any N-term 39.994915 40.0208 C(2)O(1) 0.0 Artefact 26 0.0 -Glu->pyro-Glu@E^Any N-term -18.010565 -18.0153 H(-2)O(-1) 0.0 Artefact 27 0.0 -Gln->pyro-Glu@Q^Any N-term -17.026549 -17.0305 H(-3)N(-1) 0.0 Artefact 28 0.0 -SMA@Any N-term 127.063329 127.1412 H(9)C(6)N(1)O(2) 0.0 Chemical derivative 29 0.0 +Pyro-carbamidomethyl@C^Any_N-term 39.994915 40.0208 C(2)O(1) 0.0 Artefact 26 0.0 +Glu->pyro-Glu@E^Any_N-term -18.010565 -18.0153 H(-2)O(-1) 0.0 Artefact 27 0.0 +Gln->pyro-Glu@Q^Any_N-term -17.026549 -17.0305 H(-3)N(-1) 0.0 Artefact 28 0.0 +SMA@Any_N-term 127.063329 127.1412 H(9)C(6)N(1)O(2) 0.0 Chemical derivative 29 0.0 SMA@K 127.063329 127.1412 H(9)C(6)N(1)O(2) 0.0 Chemical derivative 29 0.0 Cation:Na@D 21.981943 21.9818 H(-1)Na(1) 0.0 Artefact 30 0.0 -Cation:Na@Any C-term 21.981943 21.9818 H(-1)Na(1) 0.0 Artefact 30 0.0 +Cation:Na@Any_C-term 21.981943 21.9818 H(-1)Na(1) 0.0 Artefact 30 0.0 Cation:Na@E 21.981943 21.9818 H(-1)Na(1) 0.0 Artefact 30 0.0 Pyridylethyl@C 105.057849 105.1372 H(7)C(7)N(1) 0.0 Chemical derivative 31 0.0 Methyl@E 14.01565 14.0266 H(2)C(1) 0.0 Post-translational 34 0.0 Methyl@D 14.01565 14.0266 H(2)C(1) 0.0 Post-translational 34 0.0 -Methyl@Any C-term 14.01565 14.0266 H(2)C(1) 0.0 Multiple 34 0.0 -Methyl@Protein N-term 14.01565 14.0266 H(2)C(1) 0.0 Post-translational 34 0.0 +Methyl@Any_C-term 14.01565 14.0266 H(2)C(1) 0.0 Multiple 34 0.0 +Methyl@Protein_N-term 14.01565 14.0266 H(2)C(1) 0.0 Post-translational 34 0.0 Methyl@L 14.01565 14.0266 H(2)C(1) 0.0 Post-translational 34 0.0 Methyl@I 14.01565 14.0266 H(2)C(1) 0.0 Post-translational 34 0.0 Methyl@R 14.01565 14.0266 H(2)C(1) 0.0 Post-translational 34 0.0 Methyl@Q 14.01565 14.0266 H(2)C(1) 0.0 Post-translational 34 0.0 -Methyl@Any N-term 14.01565 14.0266 H(2)C(1) 0.0 Chemical derivative 34 0.0 +Methyl@Any_N-term 14.01565 14.0266 H(2)C(1) 0.0 Chemical derivative 34 0.0 Methyl@N 14.01565 14.0266 H(2)C(1) 0.0 Post-translational 34 0.0 Methyl@K 14.01565 14.0266 H(2)C(1) 0.0 Post-translational 34 0.0 Methyl@H 14.01565 14.0266 H(2)C(1) 0.0 Post-translational 34 0.0 @@ -107,7 +107,7 @@ Oxidation@Q 15.994915 15.9994 O(1) 0.0 Chemical derivative 35 0.0 Oxidation@L 15.994915 15.9994 O(1) 0.0 Chemical derivative 35 0.0 Oxidation@I 15.994915 15.9994 O(1) 0.0 Chemical derivative 35 0.0 Oxidation@U 15.994915 15.9994 O(1) 0.0 Multiple 35 0.0 -Oxidation@G^Any C-term 15.994915 15.9994 O(1) 0.0 Pre-translational 35 0.0 +Oxidation@G^Any_C-term 15.994915 15.9994 O(1) 0.0 Pre-translational 35 0.0 Oxidation@W 15.994915 15.9994 O(1) 0.0 Artefact 35 0.0 Oxidation@C 15.994915 15.9994 O(1) 0.0 Post-translational 35 0.0 Oxidation@H 15.994915 15.9994 O(1) 0.0 Artefact 35 0.0 @@ -120,20 +120,20 @@ Oxidation@P 15.994915 15.9994 O(1) 0.0 Post-translational 35 0.0 Oxidation@N 15.994915 15.9994 O(1) 0.0 Post-translational 35 0.0 Oxidation@K 15.994915 15.9994 O(1) 0.0 Post-translational 35 0.0 Oxidation@D 15.994915 15.9994 O(1) 0.0 Post-translational 35 0.0 -Dimethyl@Protein N-term 28.0313 28.0532 H(4)C(2) 0.0 Isotopic label 36 0.0 -Dimethyl@P^Protein N-term 28.0313 28.0532 H(4)C(2) 0.0 Post-translational 36 0.0 +Dimethyl@Protein_N-term 28.0313 28.0532 H(4)C(2) 0.0 Isotopic label 36 0.0 +Dimethyl@P^Protein_N-term 28.0313 28.0532 H(4)C(2) 0.0 Post-translational 36 0.0 Dimethyl@N 28.0313 28.0532 H(4)C(2) 0.0 Post-translational 36 0.0 -Dimethyl@Any N-term 28.0313 28.0532 H(4)C(2) 0.0 Isotopic label 36 0.0 +Dimethyl@Any_N-term 28.0313 28.0532 H(4)C(2) 0.0 Isotopic label 36 0.0 Dimethyl@K 28.0313 28.0532 H(4)C(2) 0.0 Multiple 36 0.0 Dimethyl@R 28.0313 28.0532 H(4)C(2) 0.0 Post-translational 36 0.0 -Trimethyl@A^Protein N-term 42.04695 42.0797 H(6)C(3) 0.0 Post-translational 37 0.0 +Trimethyl@A^Protein_N-term 42.04695 42.0797 H(6)C(3) 0.0 Post-translational 37 0.0 Trimethyl@R 42.04695 42.0797 H(6)C(3) 0.0 Chemical derivative 37 0.0 Trimethyl@K 42.04695 42.0797 H(6)C(3) 59.073499 H(9)C(3)N(1) Post-translational 37 0.5 Methylthio@C 45.987721 46.0916 H(2)C(1)S(1) 0.0 Multiple 39 0.0 Methylthio@N 45.987721 46.0916 H(2)C(1)S(1) 0.0 Post-translational 39 0.0 Methylthio@D 45.987721 46.0916 H(2)C(1)S(1) 0.0 Post-translational 39 0.0 Methylthio@K 45.987721 46.0916 H(2)C(1)S(1) 0.0 Artefact 39 0.0 -Methylthio@Any N-term 45.987721 46.0916 H(2)C(1)S(1) 0.0 Artefact 39 0.0 +Methylthio@Any_N-term 45.987721 46.0916 H(2)C(1)S(1) 0.0 Artefact 39 0.0 Sulfo@S 79.956815 80.0632 O(3)S(1) 79.956815 O(3)S(1) Post-translational 40 0.5 Sulfo@T 79.956815 80.0632 O(3)S(1) 79.956815 O(3)S(1) Post-translational 40 0.5 Sulfo@Y 79.956815 80.0632 O(3)S(1) 79.956815 O(3)S(1) Post-translational 40 0.5 @@ -142,7 +142,7 @@ Hex@C 162.052824 162.1406 H(10)C(6)O(5) 0.0 Other glycosylation 41 0.0 Hex@W 162.052824 162.1406 H(10)C(6)O(5) 0.0 Other glycosylation 41 0.0 Hex@T 162.052824 162.1406 H(10)C(6)O(5) 162.052824 H(10)C(6)O(5) O-linked glycosylation 41 0.5 Hex@S 162.052824 162.1406 H(10)C(6)O(5) 162.052824 H(10)C(6)O(5) O-linked glycosylation 41 0.5 -Hex@Any N-term 162.052824 162.1406 H(10)C(6)O(5) 54.031694 H(6)O(3) Other glycosylation 41 0.5 +Hex@Any_N-term 162.052824 162.1406 H(10)C(6)O(5) 54.031694 H(6)O(3) Other glycosylation 41 0.5 Hex@N 162.052824 162.1406 H(10)C(6)O(5) 162.052824 H(10)C(6)O(5) N-linked glycosylation 41 0.5 Hex@R 162.052824 162.1406 H(10)C(6)O(5) 54.031694 H(6)O(3) Other glycosylation 41 0.5 Hex@K 162.052824 162.1406 H(10)C(6)O(5) 54.031694 H(6)O(3) Other glycosylation 41 0.5 @@ -155,21 +155,21 @@ HexNAc@N 203.079373 203.1925 H(13)C(8)N(1)O(5) 203.079373 H(13)C(8)N(1)O(5) N-li Farnesyl@C 204.187801 204.3511 H(24)C(15) 0.0 Post-translational 44 0.0 Myristoyl@C 210.198366 210.3556 H(26)C(14)O(1) 0.0 Post-translational 45 0.0 Myristoyl@K 210.198366 210.3556 H(26)C(14)O(1) 0.0 Post-translational 45 0.0 -Myristoyl@G^Any N-term 210.198366 210.3556 H(26)C(14)O(1) 0.0 Post-translational 45 0.0 +Myristoyl@G^Any_N-term 210.198366 210.3556 H(26)C(14)O(1) 0.0 Post-translational 45 0.0 PyridoxalPhosphate@K 229.014009 229.1266 H(8)C(8)N(1)O(5)P(1) 0.0 Post-translational 46 0.0 Palmitoyl@T 238.229666 238.4088 H(30)C(16)O(1) 0.0 Post-translational 47 0.0 Palmitoyl@S 238.229666 238.4088 H(30)C(16)O(1) 0.0 Post-translational 47 0.0 Palmitoyl@K 238.229666 238.4088 H(30)C(16)O(1) 0.0 Post-translational 47 0.0 Palmitoyl@C 238.229666 238.4088 H(30)C(16)O(1) 0.0 Post-translational 47 0.0 -Palmitoyl@Protein N-term 238.229666 238.4088 H(30)C(16)O(1) 0.0 Post-translational 47 0.0 +Palmitoyl@Protein_N-term 238.229666 238.4088 H(30)C(16)O(1) 0.0 Post-translational 47 0.0 GeranylGeranyl@C 272.250401 272.4681 H(32)C(20) 0.0 Post-translational 48 0.0 Phosphopantetheine@S 340.085794 340.333 H(21)C(11)N(2)O(6)P(1)S(1) 0.0 Post-translational 49 0.0 FAD@Y 783.141486 783.5339 H(31)C(27)N(9)O(15)P(2) 0.0 Post-translational 50 0.0 FAD@H 783.141486 783.5339 H(31)C(27)N(9)O(15)P(2) 0.0 Post-translational 50 0.0 FAD@C 783.141486 783.5339 H(31)C(27)N(9)O(15)P(2) 0.0 Post-translational 50 0.0 -Tripalmitate@C^Protein N-term 788.725777 789.3049 H(96)C(51)O(5) 0.0 Post-translational 51 0.0 +Tripalmitate@C^Protein_N-term 788.725777 789.3049 H(96)C(51)O(5) 0.0 Post-translational 51 0.0 Guanidinyl@K 42.021798 42.04 H(2)C(1)N(2) 0.0 Chemical derivative 52 0.0 -Guanidinyl@Any N-term 42.021798 42.04 H(2)C(1)N(2) 0.0 Chemical derivative 52 0.0 +Guanidinyl@Any_N-term 42.021798 42.04 H(2)C(1)N(2) 0.0 Chemical derivative 52 0.0 HNE@K 156.11503 156.2221 H(16)C(9)O(2) 0.0 Post-translational 53 0.0 HNE@H 156.11503 156.2221 H(16)C(9)O(2) 0.0 Post-translational 53 0.0 HNE@C 156.11503 156.2221 H(16)C(9)O(2) 0.0 Post-translational 53 0.0 @@ -177,36 +177,36 @@ HNE@A 156.11503 156.2221 H(16)C(9)O(2) 0.0 Post-translational 53 0.0 HNE@L 156.11503 156.2221 H(16)C(9)O(2) 0.0 Post-translational 53 0.0 Glucuronyl@T 176.032088 176.1241 H(8)C(6)O(6) 176.032088 H(8)C(6)O(6) O-linked glycosylation 54 0.5 Glucuronyl@S 176.032088 176.1241 H(8)C(6)O(6) 176.032088 H(8)C(6)O(6) O-linked glycosylation 54 0.5 -Glucuronyl@Protein N-term 176.032088 176.1241 H(8)C(6)O(6) 0.0 Other glycosylation 54 0.0 +Glucuronyl@Protein_N-term 176.032088 176.1241 H(8)C(6)O(6) 0.0 Other glycosylation 54 0.0 Glutathione@C 305.068156 305.3076 H(15)C(10)N(3)O(6)S(1) 0.0 Post-translational 55 0.0 Acetyl:2H(3)@T 45.029395 45.0552 H(-1)2H(3)C(2)O(1) 0.0 Isotopic label 56 0.0 Acetyl:2H(3)@S 45.029395 45.0552 H(-1)2H(3)C(2)O(1) 0.0 Isotopic label 56 0.0 Acetyl:2H(3)@H 45.029395 45.0552 H(-1)2H(3)C(2)O(1) 0.0 Isotopic label 56 0.0 -Acetyl:2H(3)@Any N-term 45.029395 45.0552 H(-1)2H(3)C(2)O(1) 0.0 Isotopic label 56 0.0 +Acetyl:2H(3)@Any_N-term 45.029395 45.0552 H(-1)2H(3)C(2)O(1) 0.0 Isotopic label 56 0.0 Acetyl:2H(3)@K 45.029395 45.0552 H(-1)2H(3)C(2)O(1) 0.0 Isotopic label 56 0.0 Acetyl:2H(3)@Y 45.029395 45.0552 H(-1)2H(3)C(2)O(1) 0.0 Isotopic label 56 0.0 -Acetyl:2H(3)@Protein N-term 45.029395 45.0552 H(-1)2H(3)C(2)O(1) 0.0 Isotopic label 56 0.0 -Propionyl@Any N-term 56.026215 56.0633 H(4)C(3)O(1) 0.0 Isotopic label 58 0.0 +Acetyl:2H(3)@Protein_N-term 45.029395 45.0552 H(-1)2H(3)C(2)O(1) 0.0 Isotopic label 56 0.0 +Propionyl@Any_N-term 56.026215 56.0633 H(4)C(3)O(1) 0.0 Isotopic label 58 0.0 Propionyl@K 56.026215 56.0633 H(4)C(3)O(1) 0.0 Isotopic label 58 0.0 Propionyl@S 56.026215 56.0633 H(4)C(3)O(1) 0.0 Chemical derivative 58 0.0 Propionyl@T 56.026215 56.0633 H(4)C(3)O(1) 0.0 Isotopic label 58 0.0 -Propionyl@Protein N-term 56.026215 56.0633 H(4)C(3)O(1) 0.0 Multiple 58 0.0 -Propionyl:13C(3)@Any N-term 59.036279 59.0412 H(4)13C(3)O(1) 0.0 Isotopic label 59 0.0 +Propionyl@Protein_N-term 56.026215 56.0633 H(4)C(3)O(1) 0.0 Multiple 58 0.0 +Propionyl:13C(3)@Any_N-term 59.036279 59.0412 H(4)13C(3)O(1) 0.0 Isotopic label 59 0.0 Propionyl:13C(3)@K 59.036279 59.0412 H(4)13C(3)O(1) 0.0 Isotopic label 59 0.0 -GIST-Quat@Any N-term 127.099714 127.1842 H(13)C(7)N(1)O(1) 59.073499 H(9)C(3)N(1) Isotopic label 60 0.5 +GIST-Quat@Any_N-term 127.099714 127.1842 H(13)C(7)N(1)O(1) 59.073499 H(9)C(3)N(1) Isotopic label 60 0.5 GIST-Quat@K 127.099714 127.1842 H(13)C(7)N(1)O(1) 59.073499 H(9)C(3)N(1) Isotopic label 60 0.5 -GIST-Quat:2H(3)@Any N-term 130.118544 130.2027 H(10)2H(3)C(7)N(1)O(1) 62.09233 H(6)2H(3)C(3)N(1) Isotopic label 61 0.5 +GIST-Quat:2H(3)@Any_N-term 130.118544 130.2027 H(10)2H(3)C(7)N(1)O(1) 62.09233 H(6)2H(3)C(3)N(1) Isotopic label 61 0.5 GIST-Quat:2H(3)@K 130.118544 130.2027 H(10)2H(3)C(7)N(1)O(1) 62.09233 H(6)2H(3)C(3)N(1) Isotopic label 61 0.5 -GIST-Quat:2H(6)@Any N-term 133.137375 133.2212 H(7)2H(6)C(7)N(1)O(1) 65.11116 H(3)2H(6)C(3)N(1) Isotopic label 62 0.5 +GIST-Quat:2H(6)@Any_N-term 133.137375 133.2212 H(7)2H(6)C(7)N(1)O(1) 65.11116 H(3)2H(6)C(3)N(1) Isotopic label 62 0.5 GIST-Quat:2H(6)@K 133.137375 133.2212 H(7)2H(6)C(7)N(1)O(1) 65.11116 H(3)2H(6)C(3)N(1) Isotopic label 62 0.5 -GIST-Quat:2H(9)@Any N-term 136.156205 136.2397 H(4)2H(9)C(7)N(1)O(1) 68.12999 2H(9)C(3)N(1) Isotopic label 63 0.5 +GIST-Quat:2H(9)@Any_N-term 136.156205 136.2397 H(4)2H(9)C(7)N(1)O(1) 68.12999 2H(9)C(3)N(1) Isotopic label 63 0.5 GIST-Quat:2H(9)@K 136.156205 136.2397 H(4)2H(9)C(7)N(1)O(1) 68.12999 2H(9)C(3)N(1) Isotopic label 63 0.5 -Succinyl@Protein N-term 100.016044 100.0728 H(4)C(4)O(3) 0.0 Post-translational 64 0.0 -Succinyl@Any N-term 100.016044 100.0728 H(4)C(4)O(3) 0.0 Isotopic label 64 0.0 +Succinyl@Protein_N-term 100.016044 100.0728 H(4)C(4)O(3) 0.0 Post-translational 64 0.0 +Succinyl@Any_N-term 100.016044 100.0728 H(4)C(4)O(3) 0.0 Isotopic label 64 0.0 Succinyl@K 100.016044 100.0728 H(4)C(4)O(3) 0.0 Isotopic label 64 0.0 -Succinyl:2H(4)@Any N-term 104.041151 104.0974 2H(4)C(4)O(3) 0.0 Isotopic label 65 0.0 +Succinyl:2H(4)@Any_N-term 104.041151 104.0974 2H(4)C(4)O(3) 0.0 Isotopic label 65 0.0 Succinyl:2H(4)@K 104.041151 104.0974 2H(4)C(4)O(3) 0.0 Isotopic label 65 0.0 -Succinyl:13C(4)@Any N-term 104.029463 104.0434 H(4)13C(4)O(3) 0.0 Isotopic label 66 0.0 +Succinyl:13C(4)@Any_N-term 104.029463 104.0434 H(4)13C(4)O(3) 0.0 Isotopic label 66 0.0 Succinyl:13C(4)@K 104.029463 104.0434 H(4)13C(4)O(3) 0.0 Isotopic label 66 0.0 probiotinhydrazide@P 258.115047 258.3405 H(18)C(10)N(4)O(2)S(1) 0.0 Chemical derivative 357 0.0 Pro->pyro-Glu@P 13.979265 13.9835 H(-2)O(1) 0.0 Chemical derivative 359 0.0 @@ -215,23 +215,23 @@ His->Asp@H -22.031969 -22.0519 H(-2)C(-2)N(-2)O(2) 0.0 AA substitution 349 0.0 Trp->Hydroxykynurenin@W 19.989829 19.9881 C(-1)O(2) 0.0 Chemical derivative 350 0.0 Delta:H(4)C(3)@K 40.0313 40.0639 H(4)C(3) 0.0 Other 256 0.0 Delta:H(4)C(3)@H 40.0313 40.0639 H(4)C(3) 0.0 Other 256 0.0 -Delta:H(4)C(3)@Protein N-term 40.0313 40.0639 H(4)C(3) 0.0 Other 256 0.0 +Delta:H(4)C(3)@Protein_N-term 40.0313 40.0639 H(4)C(3) 0.0 Other 256 0.0 Delta:H(4)C(2)@K 28.0313 28.0532 H(4)C(2) 0.0 Other 255 0.0 Delta:H(4)C(2)@H 28.0313 28.0532 H(4)C(2) 0.0 Other 255 0.0 -Delta:H(4)C(2)@Any N-term 28.0313 28.0532 H(4)C(2) 0.0 Other 255 0.0 +Delta:H(4)C(2)@Any_N-term 28.0313 28.0532 H(4)C(2) 0.0 Other 255 0.0 Cys->Dha@C -33.987721 -34.0809 H(-2)S(-1) 0.0 Chemical derivative 368 0.0 Arg->GluSA@R -43.053433 -43.0711 H(-5)C(-1)N(-3)O(1) 0.0 Chemical derivative 344 0.0 Trioxidation@Y 47.984744 47.9982 O(3) 0.0 Chemical derivative 345 0.0 Trioxidation@W 47.984744 47.9982 O(3) 0.0 Chemical derivative 345 0.0 Trioxidation@C 47.984744 47.9982 O(3) 0.0 Chemical derivative 345 0.0 Trioxidation@F 47.984744 47.9982 O(3) 0.0 Artefact 345 0.0 -Iminobiotin@Any N-term 225.093583 225.3106 H(15)C(10)N(3)O(1)S(1) 0.0 Chemical derivative 89 0.0 +Iminobiotin@Any_N-term 225.093583 225.3106 H(15)C(10)N(3)O(1)S(1) 0.0 Chemical derivative 89 0.0 Iminobiotin@K 225.093583 225.3106 H(15)C(10)N(3)O(1)S(1) 0.0 Chemical derivative 89 0.0 -ESP@Any N-term 338.177647 338.4682 H(26)C(16)N(4)O(2)S(1) 0.0 Isotopic label 90 0.0 +ESP@Any_N-term 338.177647 338.4682 H(26)C(16)N(4)O(2)S(1) 0.0 Isotopic label 90 0.0 ESP@K 338.177647 338.4682 H(26)C(16)N(4)O(2)S(1) 0.0 Isotopic label 90 0.0 -ESP:2H(10)@Any N-term 348.240414 348.5299 H(16)2H(10)C(16)N(4)O(2)S(1) 0.0 Isotopic label 91 0.0 +ESP:2H(10)@Any_N-term 348.240414 348.5299 H(16)2H(10)C(16)N(4)O(2)S(1) 0.0 Isotopic label 91 0.0 ESP:2H(10)@K 348.240414 348.5299 H(16)2H(10)C(16)N(4)O(2)S(1) 0.0 Isotopic label 91 0.0 -NHS-LC-Biotin@Any N-term 339.161662 339.453 H(25)C(16)N(3)O(3)S(1) 0.0 Chemical derivative 92 0.0 +NHS-LC-Biotin@Any_N-term 339.161662 339.453 H(25)C(16)N(3)O(3)S(1) 0.0 Chemical derivative 92 0.0 NHS-LC-Biotin@K 339.161662 339.453 H(25)C(16)N(3)O(3)S(1) 0.0 Chemical derivative 92 0.0 EDT-maleimide-PEO-biotin@T 601.206246 601.8021 H(39)C(25)N(5)O(6)S(3) 0.0 Chemical derivative 93 0.0 EDT-maleimide-PEO-biotin@S 601.206246 601.8021 H(39)C(25)N(5)O(6)S(3) 0.0 Chemical derivative 93 0.0 @@ -243,14 +243,14 @@ Nitro@Y 44.985078 44.9976 H(-1)N(1)O(2) 0.0 Chemical derivative 354 0.0 Nitro@W 44.985078 44.9976 H(-1)N(1)O(2) 0.0 Chemical derivative 354 0.0 Nitro@F 44.985078 44.9976 H(-1)N(1)O(2) 0.0 Artefact 354 0.0 ICAT-C@C 227.126991 227.2603 H(17)C(10)N(3)O(3) 0.0 Isotopic label 105 0.0 -Delta:H(2)C(2)@Protein N-term 26.01565 26.0373 H(2)C(2) 0.0 Other 254 0.0 +Delta:H(2)C(2)@Protein_N-term 26.01565 26.0373 H(2)C(2) 0.0 Other 254 0.0 Delta:H(2)C(2)@K 26.01565 26.0373 H(2)C(2) 0.0 Other 254 0.0 Delta:H(2)C(2)@H 26.01565 26.0373 H(2)C(2) 0.0 Other 254 0.0 -Delta:H(2)C(2)@Any N-term 26.01565 26.0373 H(2)C(2) 0.0 Other 254 0.0 +Delta:H(2)C(2)@Any_N-term 26.01565 26.0373 H(2)C(2) 0.0 Other 254 0.0 Trp->Kynurenin@W 3.994915 3.9887 C(-1)O(1) 0.0 Chemical derivative 351 0.0 Lys->Allysine@K -1.031634 -1.0311 H(-3)N(-1)O(1) 0.0 Post-translational 352 0.0 ICAT-C:13C(9)@C 236.157185 236.1942 H(17)C(1)13C(9)N(3)O(3) 0.0 Isotopic label 106 0.0 -FormylMet@Protein N-term 159.035399 159.2062 H(9)C(6)N(1)O(2)S(1) 0.0 Pre-translational 107 0.0 +FormylMet@Protein_N-term 159.035399 159.2062 H(9)C(6)N(1)O(2)S(1) 0.0 Pre-translational 107 0.0 Nethylmaleimide@C 125.047679 125.1253 H(7)C(6)N(1)O(2) 0.0 Chemical derivative 108 0.0 OxLysBiotinRed@K 354.172562 354.4676 H(26)C(16)N(4)O(3)S(1) 0.0 Chemical derivative 112 0.0 IBTP@C 316.138088 316.3759 H(21)C(22)P(1) 0.0 Chemical derivative 119 0.0 @@ -265,21 +265,21 @@ GG@C 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Other 121 0.0 GG@T 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Other 121 0.0 GG@S 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Other 121 0.0 GG@K 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Other 121 1000000.0 -GG@Protein N-term 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Post-translational 121 0.0 -Formyl@Protein N-term 27.994915 28.0101 C(1)O(1) 0.0 Post-translational 122 0.0 +GG@Protein_N-term 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Post-translational 121 0.0 +Formyl@Protein_N-term 27.994915 28.0101 C(1)O(1) 0.0 Post-translational 122 0.0 Formyl@T 27.994915 28.0101 C(1)O(1) 0.0 Artefact 122 0.0 Formyl@K 27.994915 28.0101 C(1)O(1) 0.0 Artefact 122 0.0 -Formyl@Any N-term 27.994915 28.0101 C(1)O(1) 0.0 Artefact 122 0.0 +Formyl@Any_N-term 27.994915 28.0101 C(1)O(1) 0.0 Artefact 122 0.0 Formyl@S 27.994915 28.0101 C(1)O(1) 0.0 Artefact 122 0.0 ICAT-H@C 345.097915 345.7754 H(20)C(15)N(1)O(6)Cl(1) 0.0 Isotopic label 123 0.0 ICAT-H:13C(6)@C 351.118044 351.7313 H(20)C(9)13C(6)N(1)O(6)Cl(1) 0.0 Isotopic label 124 0.0 -Cation:K@Any C-term 37.955882 38.0904 H(-1)K(1) 0.0 Artefact 530 0.0 +Cation:K@Any_C-term 37.955882 38.0904 H(-1)K(1) 0.0 Artefact 530 0.0 Cation:K@E 37.955882 38.0904 H(-1)K(1) 0.0 Artefact 530 0.0 Cation:K@D 37.955882 38.0904 H(-1)K(1) 0.0 Artefact 530 0.0 -Xlink:DTSSP[88]@Protein N-term 87.998285 88.1283 H(4)C(3)O(1)S(1) 0.0 Chemical derivative 126 0.0 +Xlink:DTSSP[88]@Protein_N-term 87.998285 88.1283 H(4)C(3)O(1)S(1) 0.0 Chemical derivative 126 0.0 Xlink:DTSSP[88]@K 87.998285 88.1283 H(4)C(3)O(1)S(1) 0.0 Chemical derivative 126 0.0 Xlink:EGS[226]@K 226.047738 226.1828 H(10)C(10)O(6) 0.0 Chemical derivative 1897 0.0 -Xlink:EGS[226]@Protein N-term 226.047738 226.1828 H(10)C(10)O(6) 0.0 Chemical derivative 1897 0.0 +Xlink:EGS[226]@Protein_N-term 226.047738 226.1828 H(10)C(10)O(6) 0.0 Chemical derivative 1897 0.0 Fluoro@Y 17.990578 17.9905 H(-1)F(1) 0.0 Non-standard residue 127 0.0 Fluoro@W 17.990578 17.9905 H(-1)F(1) 0.0 Non-standard residue 127 0.0 Fluoro@F 17.990578 17.9905 H(-1)F(1) 0.0 Non-standard residue 127 0.0 @@ -290,16 +290,16 @@ Iodo@Y 125.896648 125.8965 H(-1)I(1) 0.0 Chemical derivative 129 0.0 Diiodo@Y 251.793296 251.7931 H(-2)I(2) 0.0 Chemical derivative 130 0.0 Diiodo@H 251.793296 251.7931 H(-2)I(2) 0.0 Chemical derivative 130 0.0 Triiodo@Y 377.689944 377.6896 H(-3)I(3) 0.0 Chemical derivative 131 0.0 -Myristoleyl@G^Protein N-term 208.182715 208.3398 H(24)C(14)O(1) 0.0 Co-translational 134 0.0 +Myristoleyl@G^Protein_N-term 208.182715 208.3398 H(24)C(14)O(1) 0.0 Co-translational 134 0.0 Pro->Pyrrolidinone@P -30.010565 -30.026 H(-2)C(-1)O(-1) 0.0 Chemical derivative 360 0.0 -Myristoyl+Delta:H(-4)@G^Protein N-term 206.167065 206.3239 H(22)C(14)O(1) 0.0 Co-translational 135 0.0 -Benzoyl@Any N-term 104.026215 104.1061 H(4)C(7)O(1) 0.0 Isotopic label 136 0.0 +Myristoyl+Delta:H(-4)@G^Protein_N-term 206.167065 206.3239 H(22)C(14)O(1) 0.0 Co-translational 135 0.0 +Benzoyl@Any_N-term 104.026215 104.1061 H(4)C(7)O(1) 0.0 Isotopic label 136 0.0 Benzoyl@K 104.026215 104.1061 H(4)C(7)O(1) 0.0 Isotopic label 136 0.0 Hex(5)HexNAc(2)@N 1216.422863 1217.088 H(76)C(46)N(2)O(35) 1216.422863 H(76)C(46)N(2)O(35) N-linked glycosylation 137 0.5 -Dansyl@Any N-term 233.051049 233.2862 H(11)C(12)N(1)O(2)S(1) 0.0 Chemical derivative 139 0.0 +Dansyl@Any_N-term 233.051049 233.2862 H(11)C(12)N(1)O(2)S(1) 0.0 Chemical derivative 139 0.0 Dansyl@K 233.051049 233.2862 H(11)C(12)N(1)O(2)S(1) 0.0 Chemical derivative 139 0.0 -a-type-ion@Any C-term -46.005479 -46.0254 H(-2)C(-1)O(-2) 0.0 Other 140 0.0 -Amidine@Any N-term 41.026549 41.0519 H(3)C(2)N(1) 0.0 Chemical derivative 141 0.0 +a-type-ion@Any_C-term -46.005479 -46.0254 H(-2)C(-1)O(-2) 0.0 Other 140 0.0 +Amidine@Any_N-term 41.026549 41.0519 H(3)C(2)N(1) 0.0 Chemical derivative 141 0.0 Amidine@K 41.026549 41.0519 H(3)C(2)N(1) 0.0 Chemical derivative 141 0.0 HexNAc(1)dHex(1)@T 349.137281 349.3337 H(23)C(14)N(1)O(9) 349.137281 H(23)C(14)N(1)O(9) O-linked glycosylation 142 0.5 HexNAc(1)dHex(1)@S 349.137281 349.3337 H(23)C(14)N(1)O(9) 349.137281 H(23)C(14)N(1)O(9) O-linked glycosylation 142 0.5 @@ -350,9 +350,9 @@ Delta:S(-1)Se(1)@C 47.944449 46.895 S(-1)Se(1) 0.0 Non-standard residue 162 0.0 NBS:13C(6)@W 159.008578 159.1144 H(3)13C(6)N(1)O(2)S(1) 0.0 Chemical derivative 171 0.0 Methyl:2H(3)13C(1)@K 18.037835 18.0377 H(-1)2H(3)13C(1) 0.0 Isotopic label 329 0.0 Methyl:2H(3)13C(1)@R 18.037835 18.0377 H(-1)2H(3)13C(1) 0.0 Isotopic label 329 0.0 -Methyl:2H(3)13C(1)@Any N-term 18.037835 18.0377 H(-1)2H(3)13C(1) 0.0 Isotopic label 329 0.0 -Dimethyl:2H(6)13C(2)@Protein N-term 36.07567 36.0754 H(-2)2H(6)13C(2) 0.0 Isotopic label 330 0.0 -Dimethyl:2H(6)13C(2)@Any N-term 36.07567 36.0754 H(-2)2H(6)13C(2) 0.0 Isotopic label 330 0.0 +Methyl:2H(3)13C(1)@Any_N-term 18.037835 18.0377 H(-1)2H(3)13C(1) 0.0 Isotopic label 329 0.0 +Dimethyl:2H(6)13C(2)@Protein_N-term 36.07567 36.0754 H(-2)2H(6)13C(2) 0.0 Isotopic label 330 0.0 +Dimethyl:2H(6)13C(2)@Any_N-term 36.07567 36.0754 H(-2)2H(6)13C(2) 0.0 Isotopic label 330 0.0 Dimethyl:2H(6)13C(2)@R 36.07567 36.0754 H(-2)2H(6)13C(2) 0.0 Isotopic label 330 0.0 Dimethyl:2H(6)13C(2)@K 36.07567 36.0754 H(-2)2H(6)13C(2) 0.0 Isotopic label 330 0.0 NBS@W 152.988449 153.1585 H(3)C(6)N(1)O(2)S(1) 0.0 Chemical derivative 172 0.0 @@ -375,11 +375,11 @@ Label:13C(6)@R 6.020129 5.9559 C(-6)13C(6) 0.0 Isotopic label 188 0.0 HPG@R 132.021129 132.1162 H(4)C(8)O(2) 0.0 Chemical derivative 186 0.0 2HPG@R 282.052824 282.2476 H(10)C(16)O(5) 0.0 Chemical derivative 187 0.0 QAT:2H(3)@C 174.168569 174.2784 H(16)2H(3)C(9)N(2)O(1) 0.0 Isotopic label 196 0.0 -Label:18O(2)@Any C-term 4.008491 3.9995 O(-2)18O(2) 0.0 Isotopic label 193 0.0 -AccQTag@Any N-term 170.048013 170.1674 H(6)C(10)N(2)O(1) 0.0 Chemical derivative 194 0.0 +Label:18O(2)@Any_C-term 4.008491 3.9995 O(-2)18O(2) 0.0 Isotopic label 193 0.0 +AccQTag@Any_N-term 170.048013 170.1674 H(6)C(10)N(2)O(1) 0.0 Chemical derivative 194 0.0 AccQTag@K 170.048013 170.1674 H(6)C(10)N(2)O(1) 0.0 Chemical derivative 194 0.0 -Dimethyl:2H(4)@Protein N-term 32.056407 32.0778 2H(4)C(2) 0.0 Isotopic label 199 0.0 -Dimethyl:2H(4)@Any N-term 32.056407 32.0778 2H(4)C(2) 0.0 Isotopic label 199 0.0 +Dimethyl:2H(4)@Protein_N-term 32.056407 32.0778 2H(4)C(2) 0.0 Isotopic label 199 0.0 +Dimethyl:2H(4)@Any_N-term 32.056407 32.0778 2H(4)C(2) 0.0 Isotopic label 199 0.0 Dimethyl:2H(4)@K 32.056407 32.0778 2H(4)C(2) 0.0 Isotopic label 199 0.0 Dimethyl:2H(4)@R 32.056407 32.0778 2H(4)C(2) 0.0 Isotopic label 199 0.0 EQAT@C 184.157563 184.2786 H(20)C(10)N(2)O(1) 0.0 Chemical derivative 197 0.0 @@ -408,11 +408,11 @@ NEIAA@Y 85.052764 85.1045 H(7)C(4)N(1)O(1) 0.0 Isotopic label 211 0.0 NEIAA@C 85.052764 85.1045 H(7)C(4)N(1)O(1) 0.0 Isotopic label 211 0.0 iTRAQ4plex@C 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 214 0.0 iTRAQ4plex@T 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 214 0.0 -iTRAQ4plex@Protein N-term 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 214 0.0 +iTRAQ4plex@Protein_N-term 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 214 0.0 iTRAQ4plex@S 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 214 0.0 iTRAQ4plex@H 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 214 0.0 iTRAQ4plex@Y 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 214 0.0 -iTRAQ4plex@Any N-term 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 214 0.0 +iTRAQ4plex@Any_N-term 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 214 0.0 iTRAQ4plex@K 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 214 0.0 Crotonaldehyde@K 70.041865 70.0898 H(6)C(4)O(1) 0.0 Other 253 0.0 Crotonaldehyde@H 70.041865 70.0898 H(6)C(4)O(1) 0.0 Other 253 0.0 @@ -426,26 +426,26 @@ Argbiotinhydrazide@R 199.066699 199.27 H(13)C(9)N(1)O(2)S(1) 0.0 Chemical deriv Label:18O(1)@Y 2.004246 1.9998 O(-1)18O(1) 0.0 Isotopic label 258 0.0 Label:18O(1)@T 2.004246 1.9998 O(-1)18O(1) 0.0 Isotopic label 258 0.0 Label:18O(1)@S 2.004246 1.9998 O(-1)18O(1) 0.0 Isotopic label 258 0.0 -Label:18O(1)@Any C-term 2.004246 1.9998 O(-1)18O(1) 0.0 Isotopic label 258 0.0 +Label:18O(1)@Any_C-term 2.004246 1.9998 O(-1)18O(1) 0.0 Isotopic label 258 0.0 Label:13C(6)15N(2)@K 8.014199 7.9427 C(-6)13C(6)N(-2)15N(2) 0.0 Isotopic label 259 0.0 Thiophospho@Y 95.943487 96.0455 H(1)O(2)P(1)S(1) 0.0 Other 260 0.0 Thiophospho@T 95.943487 96.0455 H(1)O(2)P(1)S(1) 0.0 Other 260 0.0 Thiophospho@S 95.943487 96.0455 H(1)O(2)P(1)S(1) 0.0 Other 260 0.0 SPITC@K 214.971084 215.2495 H(5)C(7)N(1)O(3)S(2) 0.0 Chemical derivative 261 0.0 -SPITC@Any N-term 214.971084 215.2495 H(5)C(7)N(1)O(3)S(2) 0.0 Chemical derivative 261 0.0 +SPITC@Any_N-term 214.971084 215.2495 H(5)C(7)N(1)O(3)S(2) 0.0 Chemical derivative 261 0.0 IGBP@C 296.016039 297.1478 H(13)C(12)N(2)O(2)Br(1) 0.0 Isotopic label 243 0.0 Cytopiloyne@Y 362.136553 362.3738 H(22)C(19)O(7) 0.0 Chemical derivative 270 0.0 Cytopiloyne@S 362.136553 362.3738 H(22)C(19)O(7) 0.0 Chemical derivative 270 0.0 Cytopiloyne@R 362.136553 362.3738 H(22)C(19)O(7) 0.0 Chemical derivative 270 0.0 Cytopiloyne@P 362.136553 362.3738 H(22)C(19)O(7) 0.0 Chemical derivative 270 0.0 -Cytopiloyne@Any N-term 362.136553 362.3738 H(22)C(19)O(7) 0.0 Chemical derivative 270 0.0 +Cytopiloyne@Any_N-term 362.136553 362.3738 H(22)C(19)O(7) 0.0 Chemical derivative 270 0.0 Cytopiloyne@K 362.136553 362.3738 H(22)C(19)O(7) 0.0 Chemical derivative 270 0.0 Cytopiloyne@C 362.136553 362.3738 H(22)C(19)O(7) 0.0 Chemical derivative 270 0.0 Cytopiloyne+water@Y 380.147118 380.3891 H(24)C(19)O(8) 0.0 Chemical derivative 271 0.0 Cytopiloyne+water@T 380.147118 380.3891 H(24)C(19)O(8) 0.0 Chemical derivative 271 0.0 Cytopiloyne+water@S 380.147118 380.3891 H(24)C(19)O(8) 0.0 Chemical derivative 271 0.0 Cytopiloyne+water@R 380.147118 380.3891 H(24)C(19)O(8) 0.0 Chemical derivative 271 0.0 -Cytopiloyne+water@Any N-term 380.147118 380.3891 H(24)C(19)O(8) 0.0 Chemical derivative 271 0.0 +Cytopiloyne+water@Any_N-term 380.147118 380.3891 H(24)C(19)O(8) 0.0 Chemical derivative 271 0.0 Cytopiloyne+water@K 380.147118 380.3891 H(24)C(19)O(8) 0.0 Chemical derivative 271 0.0 Cytopiloyne+water@C 380.147118 380.3891 H(24)C(19)O(8) 0.0 Chemical derivative 271 0.0 Label:13C(6)15N(4)@R 10.008269 9.9296 C(-6)13C(6)N(-4)15N(4) 0.0 Isotopic label 267 0.0 @@ -458,8 +458,8 @@ Label:13C(5)15N(1)@V 6.013809 5.9567 C(-5)13C(5)N(-1)15N(1) 0.0 Isotopic label Label:13C(5)15N(1)@E 6.013809 5.9567 C(-5)13C(5)N(-1)15N(1) 0.0 Isotopic label 268 0.0 PET@T 121.035005 121.2028 H(7)C(7)N(1)O(-1)S(1) 0.0 Chemical derivative 264 0.0 PET@S 121.035005 121.2028 H(7)C(7)N(1)O(-1)S(1) 0.0 Chemical derivative 264 0.0 -CAF@Any N-term 135.983029 136.1265 H(4)C(3)O(4)S(1) 0.0 Chemical derivative 272 0.0 -Xlink:BS2G[96]@Protein N-term 96.021129 96.0841 H(4)C(5)O(2) 0.0 Chemical derivative 1905 0.0 +CAF@Any_N-term 135.983029 136.1265 H(4)C(3)O(4)S(1) 0.0 Chemical derivative 272 0.0 +Xlink:BS2G[96]@Protein_N-term 96.021129 96.0841 H(4)C(5)O(2) 0.0 Chemical derivative 1905 0.0 Xlink:BS2G[96]@K 96.021129 96.0841 H(4)C(5)O(2) 0.0 Chemical derivative 1905 0.0 Nitrosyl@C 28.990164 28.9982 H(-1)N(1)O(1) 0.0 Post-translational 275 0.0 Nitrosyl@Y 28.990164 28.9982 H(-1)N(1)O(1) 0.0 Chemical derivative 275 0.0 @@ -467,7 +467,7 @@ Kdo@T 220.058303 220.1767 H(12)C(8)O(7) 220.058303 H(12)C(8)O(7) O-linked glycos Kdo@S 220.058303 220.1767 H(12)C(8)O(7) 220.058303 H(12)C(8)O(7) O-linked glycosylation 2022 0.5 AEBS@Y 183.035399 183.2276 H(9)C(8)N(1)O(2)S(1) 0.0 Artefact 276 0.0 AEBS@S 183.035399 183.2276 H(9)C(8)N(1)O(2)S(1) 0.0 Artefact 276 0.0 -AEBS@Protein N-term 183.035399 183.2276 H(9)C(8)N(1)O(2)S(1) 0.0 Artefact 276 0.0 +AEBS@Protein_N-term 183.035399 183.2276 H(9)C(8)N(1)O(2)S(1) 0.0 Artefact 276 0.0 AEBS@K 183.035399 183.2276 H(9)C(8)N(1)O(2)S(1) 0.0 Artefact 276 0.0 AEBS@H 183.035399 183.2276 H(9)C(8)N(1)O(2)S(1) 0.0 Artefact 276 0.0 Ethanolyl@K 44.026215 44.0526 H(4)C(2)O(1) 0.0 Chemical derivative 278 0.0 @@ -475,10 +475,10 @@ Ethanolyl@C 44.026215 44.0526 H(4)C(2)O(1) 0.0 Chemical derivative 278 0.0 Ethanolyl@R 44.026215 44.0526 H(4)C(2)O(1) 0.0 Chemical derivative 278 0.0 Label:13C(6)15N(2)+Dimethyl@K 36.045499 35.9959 H(4)C(-4)13C(6)N(-2)15N(2) 0.0 Isotopic label 987 0.0 HMVK@C 86.036779 86.0892 H(6)C(4)O(2) 0.0 Chemical derivative 371 0.0 -Ethyl@Any C-term 28.0313 28.0532 H(4)C(2) 0.0 Chemical derivative 280 0.0 -Ethyl@Protein N-term 28.0313 28.0532 H(4)C(2) 0.0 Chemical derivative 280 0.0 +Ethyl@Any_C-term 28.0313 28.0532 H(4)C(2) 0.0 Chemical derivative 280 0.0 +Ethyl@Protein_N-term 28.0313 28.0532 H(4)C(2) 0.0 Chemical derivative 280 0.0 Ethyl@E 28.0313 28.0532 H(4)C(2) 0.0 Artefact 280 0.0 -Ethyl@Any N-term 28.0313 28.0532 H(4)C(2) 0.0 Multiple 280 0.0 +Ethyl@Any_N-term 28.0313 28.0532 H(4)C(2) 0.0 Multiple 280 0.0 Ethyl@K 28.0313 28.0532 H(4)C(2) 0.0 Multiple 280 0.0 Ethyl@D 28.0313 28.0532 H(4)C(2) 0.0 Chemical derivative 280 0.0 CoenzymeA@C 765.09956 765.5182 H(34)C(21)N(7)O(16)P(3)S(1) 0.0 Post-translational 281 0.0 @@ -486,15 +486,15 @@ Methyl+Deamidated@Q 14.999666 15.0113 H(1)C(1)N(-1)O(1) 0.0 Post-translational Methyl+Deamidated@N 14.999666 15.0113 H(1)C(1)N(-1)O(1) 0.0 Chemical derivative 528 0.0 Delta:H(5)C(2)@P 29.039125 29.0611 H(5)C(2) 0.0 Post-translational 529 0.0 Methyl:2H(2)@K 16.028204 16.0389 2H(2)C(1) 0.0 Isotopic label 284 0.0 -Methyl:2H(2)@Any N-term 16.028204 16.0389 2H(2)C(1) 0.0 Isotopic label 284 0.0 +Methyl:2H(2)@Any_N-term 16.028204 16.0389 2H(2)C(1) 0.0 Isotopic label 284 0.0 SulfanilicAcid@E 155.004099 155.1744 H(5)C(6)N(1)O(2)S(1) 0.0 Isotopic label 285 0.0 SulfanilicAcid@D 155.004099 155.1744 H(5)C(6)N(1)O(2)S(1) 0.0 Isotopic label 285 0.0 -SulfanilicAcid@Any C-term 155.004099 155.1744 H(5)C(6)N(1)O(2)S(1) 0.0 Isotopic label 285 0.0 +SulfanilicAcid@Any_C-term 155.004099 155.1744 H(5)C(6)N(1)O(2)S(1) 0.0 Isotopic label 285 0.0 SulfanilicAcid:13C(6)@E 161.024228 161.1303 H(5)13C(6)N(1)O(2)S(1) 0.0 Chemical derivative 286 0.0 SulfanilicAcid:13C(6)@D 161.024228 161.1303 H(5)13C(6)N(1)O(2)S(1) 0.0 Chemical derivative 286 0.0 -SulfanilicAcid:13C(6)@Any C-term 161.024228 161.1303 H(5)13C(6)N(1)O(2)S(1) 0.0 Chemical derivative 286 0.0 +SulfanilicAcid:13C(6)@Any_C-term 161.024228 161.1303 H(5)13C(6)N(1)O(2)S(1) 0.0 Chemical derivative 286 0.0 Biotin-PEO-Amine@D 356.188212 356.4835 H(28)C(16)N(4)O(3)S(1) 0.0 Chemical derivative 289 0.0 -Biotin-PEO-Amine@Protein C-term 356.188212 356.4835 H(28)C(16)N(4)O(3)S(1) 0.0 Chemical derivative 289 0.0 +Biotin-PEO-Amine@Protein_C-term 356.188212 356.4835 H(28)C(16)N(4)O(3)S(1) 0.0 Chemical derivative 289 0.0 Biotin-PEO-Amine@E 356.188212 356.4835 H(28)C(16)N(4)O(3)S(1) 0.0 Chemical derivative 289 0.0 Trp->Oxolactone@W 13.979265 13.9835 H(-2)O(1) 0.0 Chemical derivative 288 0.0 Biotin-HPDP@C 428.191582 428.6124 H(32)C(19)N(4)O(3)S(2) 0.0 Chemical derivative 290 0.0 @@ -502,7 +502,7 @@ Delta:Hg(1)@C 201.970617 200.59 Hg(1) 0.0 Chemical derivative 291 0.0 IodoU-AMP@Y 322.020217 322.1654 H(11)C(9)N(2)O(9)P(1) 0.0 Chemical derivative 292 0.0 IodoU-AMP@W 322.020217 322.1654 H(11)C(9)N(2)O(9)P(1) 0.0 Chemical derivative 292 0.0 IodoU-AMP@F 322.020217 322.1654 H(11)C(9)N(2)O(9)P(1) 0.0 Chemical derivative 292 0.0 -CAMthiopropanoyl@Protein N-term 145.019749 145.1796 H(7)C(5)N(1)O(2)S(1) 0.0 Chemical derivative 293 0.0 +CAMthiopropanoyl@Protein_N-term 145.019749 145.1796 H(7)C(5)N(1)O(2)S(1) 0.0 Chemical derivative 293 0.0 CAMthiopropanoyl@K 145.019749 145.1796 H(7)C(5)N(1)O(2)S(1) 0.0 Chemical derivative 293 0.0 IED-Biotin@C 326.141261 326.4145 H(22)C(14)N(4)O(3)S(1) 0.0 Chemical derivative 294 0.0 dHex@N 146.057909 146.1412 H(10)C(6)O(4) 146.057909 H(10)C(6)O(4) N-linked glycosylation 295 0.5 @@ -517,7 +517,7 @@ Carboxy@E 43.989829 44.0095 C(1)O(2) 0.0 Post-translational 299 0.0 Carboxy@D 43.989829 44.0095 C(1)O(2) 0.0 Post-translational 299 0.0 Carboxy@K 43.989829 44.0095 C(1)O(2) 0.0 Post-translational 299 0.0 Carboxy@W 43.989829 44.0095 C(1)O(2) 0.0 Chemical derivative 299 0.0 -Carboxy@M^Protein N-term 43.989829 44.0095 C(1)O(2) 0.0 Post-translational 299 0.0 +Carboxy@M^Protein_N-term 43.989829 44.0095 C(1)O(2) 0.0 Post-translational 299 0.0 Bromobimane@C 190.074228 190.1986 H(10)C(10)N(2)O(2) 0.0 Chemical derivative 301 0.0 Menadione@K 170.036779 170.1641 H(6)C(11)O(2) 0.0 Chemical derivative 302 0.0 Menadione@C 170.036779 170.1641 H(6)C(11)O(2) 0.0 Chemical derivative 302 0.0 @@ -539,7 +539,7 @@ Hex(5)HexNAc(4)@S 1622.581608 1623.4731 H(102)C(62)N(4)O(45) 1622.581608 H(102)C Hex(5)HexNAc(4)@N 1622.581608 1623.4731 H(102)C(62)N(4)O(45) 1622.581608 H(102)C(62)N(4)O(45) N-linked glycosylation 311 0.5 Hex(5)HexNAc(4)@T 1622.581608 1623.4731 H(102)C(62)N(4)O(45) 1622.581608 H(102)C(62)N(4)O(45) O-linked glycosylation 311 0.5 Cysteinyl@C 119.004099 119.1423 H(5)C(3)N(1)O(2)S(1) 0.0 Multiple 312 0.0 -Lys-loss@K^Protein C-term -128.094963 -128.1723 H(-12)C(-6)N(-2)O(-1) 0.0 Post-translational 313 0.0 +Lys-loss@K^Protein_C-term -128.094963 -128.1723 H(-12)C(-6)N(-2)O(-1) 0.0 Post-translational 313 0.0 Nmethylmaleimide@K 111.032028 111.0987 H(5)C(5)N(1)O(2) 0.0 Chemical derivative 314 0.0 Nmethylmaleimide@C 111.032028 111.0987 H(5)C(5)N(1)O(2) 0.0 Chemical derivative 314 0.0 CyDye-Cy3@C 672.298156 672.8335 H(44)C(37)N(4)O(6)S(1) 0.0 Chemical derivative 494 0.0 @@ -551,7 +551,7 @@ Nethylmaleimide+water@K 143.058243 143.1406 H(9)C(6)N(1)O(3) 0.0 Chemical deriv Nethylmaleimide+water@C 143.058243 143.1406 H(9)C(6)N(1)O(3) 0.0 Chemical derivative 320 0.0 Methyl+Acetyl:2H(3)@K 59.045045 59.0817 H(1)2H(3)C(3)O(1) 0.0 Isotopic label 768 0.0 Xlink:B10621@C 713.093079 713.5626 H(30)C(31)N(4)O(6)S(1)I(1) 0.0 Chemical derivative 323 0.0 -Xlink:DTBP[87]@Protein N-term 87.01427 87.1435 H(5)C(3)N(1)S(1) 0.0 Chemical derivative 324 0.0 +Xlink:DTBP[87]@Protein_N-term 87.01427 87.1435 H(5)C(3)N(1)S(1) 0.0 Chemical derivative 324 0.0 Xlink:DTBP[87]@K 87.01427 87.1435 H(5)C(3)N(1)S(1) 0.0 Chemical derivative 324 0.0 FP-Biotin@K 572.316129 572.7405 H(49)C(27)N(4)O(5)P(1)S(1) 0.0 Chemical derivative 325 0.0 FP-Biotin@T 572.316129 572.7405 H(49)C(27)N(4)O(5)P(1)S(1) 0.0 Chemical derivative 325 0.0 @@ -573,21 +573,21 @@ Diisopropylphosphate@K 164.060231 164.1394 H(13)C(6)O(3)P(1) 0.0 Chemical deriv Diisopropylphosphate@Y 164.060231 164.1394 H(13)C(6)O(3)P(1) 0.0 Chemical derivative 362 0.0 Diisopropylphosphate@T 164.060231 164.1394 H(13)C(6)O(3)P(1) 0.0 Chemical derivative 362 0.0 Diisopropylphosphate@S 164.060231 164.1394 H(13)C(6)O(3)P(1) 0.0 Chemical derivative 362 0.0 -Diisopropylphosphate@Any N-term 164.060231 164.1394 H(13)C(6)O(3)P(1) 0.0 Chemical derivative 362 0.0 +Diisopropylphosphate@Any_N-term 164.060231 164.1394 H(13)C(6)O(3)P(1) 0.0 Chemical derivative 362 0.0 Isopropylphospho@Y 122.013281 122.0596 H(7)C(3)O(3)P(1) 0.0 Chemical derivative 363 0.0 Isopropylphospho@T 122.013281 122.0596 H(7)C(3)O(3)P(1) 0.0 Chemical derivative 363 0.0 Isopropylphospho@S 122.013281 122.0596 H(7)C(3)O(3)P(1) 0.0 Chemical derivative 363 0.0 -ICPL:13C(6)@Any N-term 111.041593 111.05 H(3)13C(6)N(1)O(1) 0.0 Isotopic label 364 0.0 -ICPL:13C(6)@Protein N-term 111.041593 111.05 H(3)13C(6)N(1)O(1) 0.0 Isotopic label 364 0.0 +ICPL:13C(6)@Any_N-term 111.041593 111.05 H(3)13C(6)N(1)O(1) 0.0 Isotopic label 364 0.0 +ICPL:13C(6)@Protein_N-term 111.041593 111.05 H(3)13C(6)N(1)O(1) 0.0 Isotopic label 364 0.0 ICPL:13C(6)@K 111.041593 111.05 H(3)13C(6)N(1)O(1) 0.0 Isotopic label 364 0.0 CarbamidomethylDTT@C 209.018035 209.2864 H(11)C(6)N(1)O(3)S(2) 0.0 Artefact 893 0.0 -ICPL@Protein N-term 105.021464 105.0941 H(3)C(6)N(1)O(1) 0.0 Isotopic label 365 0.0 +ICPL@Protein_N-term 105.021464 105.0941 H(3)C(6)N(1)O(1) 0.0 Isotopic label 365 0.0 ICPL@K 105.021464 105.0941 H(3)C(6)N(1)O(1) 0.0 Isotopic label 365 0.0 -ICPL@Any N-term 105.021464 105.0941 H(3)C(6)N(1)O(1) 0.0 Isotopic label 365 0.0 +ICPL@Any_N-term 105.021464 105.0941 H(3)C(6)N(1)O(1) 0.0 Isotopic label 365 0.0 Deamidated:18O(1)@Q 2.988261 2.9845 H(-1)N(-1)18O(1) 0.0 Isotopic label 366 0.0 Deamidated:18O(1)@N 2.988261 2.9845 H(-1)N(-1)18O(1) 0.0 Isotopic label 366 0.0 Arg->Orn@R -42.021798 -42.04 H(-2)C(-1)N(-2) 0.0 Artefact 372 0.0 -Cation:Cu[I]@Any C-term 61.921774 62.5381 H(-1)Cu(1) 0.0 Artefact 531 0.0 +Cation:Cu[I]@Any_C-term 61.921774 62.5381 H(-1)Cu(1) 0.0 Artefact 531 0.0 Cation:Cu[I]@E 61.921774 62.5381 H(-1)Cu(1) 0.0 Artefact 531 0.0 Cation:Cu[I]@D 61.921774 62.5381 H(-1)Cu(1) 0.0 Artefact 531 0.0 Cation:Cu[I]@H 61.921774 62.5381 H(-1)Cu(1) 0.0 Artefact 531 0.0 @@ -600,10 +600,10 @@ Carboxyethyl@H 72.021129 72.0627 H(4)C(3)O(2) 0.0 Chemical derivative 378 0.0 Hypusine@K 87.068414 87.1204 H(9)C(4)N(1)O(1) 0.0 Post-translational 379 0.0 Retinylidene@K 266.203451 266.4204 H(26)C(20) 0.0 Post-translational 380 0.0 Lys->AminoadipicAcid@K 14.96328 14.9683 H(-3)N(-1)O(2) 0.0 Post-translational 381 0.0 -Cys->PyruvicAcid@C^Protein N-term -33.003705 -33.0961 H(-3)N(-1)O(1)S(-1) 0.0 Post-translational 382 0.0 -Ammonia-loss@C^Any N-term -17.026549 -17.0305 H(-3)N(-1) 0.0 Artefact 385 0.0 -Ammonia-loss@S^Protein N-term -17.026549 -17.0305 H(-3)N(-1) 0.0 Post-translational 385 0.0 -Ammonia-loss@T^Protein N-term -17.026549 -17.0305 H(-3)N(-1) 0.0 Post-translational 385 0.0 +Cys->PyruvicAcid@C^Protein_N-term -33.003705 -33.0961 H(-3)N(-1)O(1)S(-1) 0.0 Post-translational 382 0.0 +Ammonia-loss@C^Any_N-term -17.026549 -17.0305 H(-3)N(-1) 0.0 Artefact 385 0.0 +Ammonia-loss@S^Protein_N-term -17.026549 -17.0305 H(-3)N(-1) 0.0 Post-translational 385 0.0 +Ammonia-loss@T^Protein_N-term -17.026549 -17.0305 H(-3)N(-1) 0.0 Post-translational 385 0.0 Ammonia-loss@N -17.026549 -17.0305 H(-3)N(-1) 0.0 Chemical derivative 385 0.0 Phycocyanobilin@C 586.279135 586.678 H(38)C(33)N(4)O(6) 0.0 Post-translational 387 0.0 Phycoerythrobilin@C 588.294785 588.6939 H(40)C(33)N(4)O(6) 0.0 Post-translational 388 0.0 @@ -614,7 +614,7 @@ Molybdopterin@C 521.884073 520.2668 H(11)C(10)N(5)O(8)P(1)S(2)Mo(1) 0.0 Post-tr Quinone@W 29.974179 29.9829 H(-2)O(2) 0.0 Post-translational 392 0.0 Quinone@Y 29.974179 29.9829 H(-2)O(2) 0.0 Post-translational 392 0.0 Glucosylgalactosyl@K 340.100562 340.2806 H(20)C(12)O(11) 340.100562 H(20)C(12)O(11) Other glycosylation 393 0.5 -GPIanchor@Protein C-term 123.00853 123.0477 H(6)C(2)N(1)O(3)P(1) 0.0 Post-translational 394 0.0 +GPIanchor@Protein_C-term 123.00853 123.0477 H(6)C(2)N(1)O(3)P(1) 0.0 Post-translational 394 0.0 PhosphoribosyldephosphoCoA@S 881.146904 881.6335 H(42)C(26)N(7)O(19)P(3)S(1) 0.0 Post-translational 395 0.0 GlycerylPE@E 197.04531 197.1262 H(12)C(5)N(1)O(5)P(1) 0.0 Post-translational 396 0.0 Triiodothyronine@Y 469.716159 469.785 H(1)C(6)O(1)I(3) 0.0 Post-translational 397 0.0 @@ -623,25 +623,25 @@ Tyr->Dha@Y -94.041865 -94.1112 H(-6)C(-6)O(-1) 0.0 Post-translational 400 0.0 Didehydro@S -2.01565 -2.0159 H(-2) 0.0 Post-translational 401 0.0 Didehydro@Y -2.01565 -2.0159 H(-2) 0.0 Post-translational 401 0.0 Didehydro@T -2.01565 -2.0159 H(-2) 0.0 Chemical derivative 401 0.0 -Didehydro@K^Any C-term -2.01565 -2.0159 H(-2) 0.0 Artefact 401 0.0 +Didehydro@K^Any_C-term -2.01565 -2.0159 H(-2) 0.0 Artefact 401 0.0 Cys->Oxoalanine@C -17.992806 -18.0815 H(-2)O(1)S(-1) 0.0 Post-translational 402 0.0 -Ser->LacticAcid@S^Protein N-term -15.010899 -15.0146 H(-1)N(-1) 0.0 Post-translational 403 0.0 +Ser->LacticAcid@S^Protein_N-term -15.010899 -15.0146 H(-1)N(-1) 0.0 Post-translational 403 0.0 GluGlu@E 258.085186 258.228 H(14)C(10)N(2)O(6) 0.0 Post-translational 451 0.0 -GluGlu@Protein C-term 258.085186 258.228 H(14)C(10)N(2)O(6) 0.0 Post-translational 451 0.0 +GluGlu@Protein_C-term 258.085186 258.228 H(14)C(10)N(2)O(6) 0.0 Post-translational 451 0.0 Phosphoadenosine@H 329.05252 329.2059 H(12)C(10)N(5)O(6)P(1) 0.0 Post-translational 405 0.0 Phosphoadenosine@T 329.05252 329.2059 H(12)C(10)N(5)O(6)P(1) 0.0 Post-translational 405 0.0 Phosphoadenosine@K 329.05252 329.2059 H(12)C(10)N(5)O(6)P(1) 0.0 Post-translational 405 0.0 Phosphoadenosine@Y 329.05252 329.2059 H(12)C(10)N(5)O(6)P(1) 0.0 Post-translational 405 0.0 Phosphoadenosine@S 329.05252 329.2059 H(12)C(10)N(5)O(6)P(1) 0.0 Post-translational 405 0.0 Glu@E 129.042593 129.114 H(7)C(5)N(1)O(3) 0.0 Post-translational 450 0.0 -Glu@Protein C-term 129.042593 129.114 H(7)C(5)N(1)O(3) 0.0 Chemical derivative 450 0.0 +Glu@Protein_C-term 129.042593 129.114 H(7)C(5)N(1)O(3) 0.0 Chemical derivative 450 0.0 Hydroxycinnamyl@C 146.036779 146.1427 H(6)C(9)O(2) 0.0 Post-translational 407 0.0 Glycosyl@P 148.037173 148.114 H(8)C(5)O(5) 0.0 Other glycosylation 408 0.0 FMNH@H 454.088965 454.3279 H(19)C(17)N(4)O(9)P(1) 0.0 Post-translational 409 0.0 FMNH@C 454.088965 454.3279 H(19)C(17)N(4)O(9)P(1) 0.0 Post-translational 409 0.0 Archaeol@C 634.662782 635.1417 H(86)C(43)O(2) 0.0 Post-translational 410 0.0 -Phenylisocyanate@Any N-term 119.037114 119.1207 H(5)C(7)N(1)O(1) 0.0 Chemical derivative 411 0.0 -Phenylisocyanate:2H(5)@Any N-term 124.068498 124.1515 2H(5)C(7)N(1)O(1) 0.0 Chemical derivative 412 0.0 +Phenylisocyanate@Any_N-term 119.037114 119.1207 H(5)C(7)N(1)O(1) 0.0 Chemical derivative 411 0.0 +Phenylisocyanate:2H(5)@Any_N-term 124.068498 124.1515 2H(5)C(7)N(1)O(1) 0.0 Chemical derivative 412 0.0 Phosphoguanosine@H 345.047435 345.2053 H(12)C(10)N(5)O(7)P(1) 0.0 Post-translational 413 0.0 Phosphoguanosine@K 345.047435 345.2053 H(12)C(10)N(5)O(7)P(1) 0.0 Post-translational 413 0.0 Hydroxymethyl@N 30.010565 30.026 H(2)C(1)O(1) 0.0 Post-translational 414 0.0 @@ -650,13 +650,13 @@ Dipyrrolylmethanemethyl@C 418.137616 418.3973 H(22)C(20)N(2)O(8) 0.0 Post-trans PhosphoUridine@H 306.025302 306.166 H(11)C(9)N(2)O(8)P(1) 0.0 Post-translational 417 0.0 PhosphoUridine@Y 306.025302 306.166 H(11)C(9)N(2)O(8)P(1) 0.0 Post-translational 417 0.0 Glycerophospho@S 154.00311 154.0584 H(7)C(3)O(5)P(1) 0.0 Post-translational 419 0.0 -Carboxy->Thiocarboxy@G^Protein C-term 15.977156 16.0656 O(-1)S(1) 0.0 Post-translational 420 0.0 +Carboxy->Thiocarboxy@G^Protein_C-term 15.977156 16.0656 O(-1)S(1) 0.0 Post-translational 420 0.0 Sulfide@D 31.972071 32.065 S(1) 0.0 Post-translational 421 0.0 Sulfide@C 31.972071 32.065 S(1) 0.0 Post-translational 421 0.0 Sulfide@W 31.972071 32.065 S(1) 0.0 Chemical derivative 421 0.0 PyruvicAcidIminyl@K 70.005479 70.0468 H(2)C(3)O(2) 0.0 Post-translational 422 0.0 -PyruvicAcidIminyl@V^Protein N-term 70.005479 70.0468 H(2)C(3)O(2) 0.0 Post-translational 422 0.0 -PyruvicAcidIminyl@C^Protein N-term 70.005479 70.0468 H(2)C(3)O(2) 0.0 Post-translational 422 0.0 +PyruvicAcidIminyl@V^Protein_N-term 70.005479 70.0468 H(2)C(3)O(2) 0.0 Post-translational 422 0.0 +PyruvicAcidIminyl@C^Protein_N-term 70.005479 70.0468 H(2)C(3)O(2) 0.0 Post-translational 422 0.0 Delta:Se(1)@C 79.91652 78.96 Se(1) 0.0 Post-translational 423 0.0 MolybdopterinGD@D 1572.985775 1572.0146 H(47)C(40)N(20)O(26)P(4)S(4)Mo(1) 0.0 Post-translational 424 0.0 MolybdopterinGD@C 1572.985775 1572.0146 H(47)C(40)N(20)O(26)P(4)S(4)Mo(1) 0.0 Post-translational 424 0.0 @@ -684,12 +684,12 @@ PhosphoHex@S 242.019154 242.1205 H(11)C(6)O(8)P(1) 242.019154 H(11)C(6)O(8)P(1) Palmitoleyl@C 236.214016 236.3929 H(28)C(16)O(1) 0.0 Post-translational 431 0.0 Palmitoleyl@S 236.214016 236.3929 H(28)C(16)O(1) 0.0 Post-translational 431 0.0 Palmitoleyl@T 236.214016 236.3929 H(28)C(16)O(1) 0.0 Pre-translational 431 0.0 -Cholesterol@Protein C-term 368.344302 368.6383 H(44)C(27) 0.0 Post-translational 432 0.0 +Cholesterol@Protein_C-term 368.344302 368.6383 H(44)C(27) 0.0 Post-translational 432 0.0 Didehydroretinylidene@K 264.187801 264.4046 H(24)C(20) 0.0 Post-translational 433 0.0 CHDH@D 294.183109 294.3859 H(26)C(17)O(4) 0.0 Post-translational 434 0.0 Methylpyrroline@K 109.052764 109.1259 H(7)C(6)N(1)O(1) 0.0 Post-translational 435 0.0 Hydroxyheme@E 614.161645 614.4714 H(30)C(34)N(4)O(4)Fe(1) 0.0 Post-translational 436 0.0 -MicrocinC7@Protein C-term 386.110369 386.3003 H(19)C(13)N(6)O(6)P(1) 0.0 Post-translational 437 0.0 +MicrocinC7@Protein_C-term 386.110369 386.3003 H(19)C(13)N(6)O(6)P(1) 0.0 Post-translational 437 0.0 Cyano@C 24.995249 25.0095 H(-1)C(1)N(1) 0.0 Post-translational 438 0.0 Diironsubcluster@C 342.786916 342.876 H(-1)C(5)N(2)O(5)S(2)Fe(2) 0.0 Post-translational 439 0.0 Amidino@C 42.021798 42.04 H(2)C(1)N(2) 0.0 Post-translational 440 0.0 @@ -701,27 +701,27 @@ Hydroxytrimethyl@K 59.04969 59.0871 H(7)C(3)O(1) 0.0 Post-translational 445 0.0 Deoxy@T -15.994915 -15.9994 O(-1) 0.0 Chemical derivative 447 0.0 Deoxy@D -15.994915 -15.9994 O(-1) 0.0 Post-translational 447 0.0 Deoxy@S -15.994915 -15.9994 O(-1) 0.0 Chemical derivative 447 0.0 -Microcin@Protein C-term 831.197041 831.6871 H(37)C(36)N(3)O(20) 0.0 Post-translational 448 0.0 +Microcin@Protein_C-term 831.197041 831.6871 H(37)C(36)N(3)O(20) 0.0 Post-translational 448 0.0 Decanoyl@T 154.135765 154.2493 H(18)C(10)O(1) 0.0 Post-translational 449 0.0 Decanoyl@S 154.135765 154.2493 H(18)C(10)O(1) 0.0 Post-translational 449 0.0 -GluGluGlu@Protein C-term 387.127779 387.3419 H(21)C(15)N(3)O(9) 0.0 Post-translational 452 0.0 +GluGluGlu@Protein_C-term 387.127779 387.3419 H(21)C(15)N(3)O(9) 0.0 Post-translational 452 0.0 GluGluGlu@E 387.127779 387.3419 H(21)C(15)N(3)O(9) 0.0 Post-translational 452 0.0 -GluGluGluGlu@Protein C-term 516.170373 516.4559 H(28)C(20)N(4)O(12) 0.0 Post-translational 453 0.0 +GluGluGluGlu@Protein_C-term 516.170373 516.4559 H(28)C(20)N(4)O(12) 0.0 Post-translational 453 0.0 GluGluGluGlu@E 516.170373 516.4559 H(28)C(20)N(4)O(12) 0.0 Post-translational 453 0.0 HexN@W 161.068808 161.1558 H(11)C(6)N(1)O(4) 0.0 Other glycosylation 454 0.0 HexN@T 161.068808 161.1558 H(11)C(6)N(1)O(4) 161.068808 H(11)C(6)N(1)O(4) O-linked glycosylation 454 0.5 HexN@S 161.068808 161.1558 H(11)C(6)N(1)O(4) 161.068808 H(11)C(6)N(1)O(4) O-linked glycosylation 454 0.5 HexN@N 161.068808 161.1558 H(11)C(6)N(1)O(4) 161.068808 H(11)C(6)N(1)O(4) N-linked glycosylation 454 0.5 HexN@K 161.068808 161.1558 H(11)C(6)N(1)O(4) 0.0 Synth. pep. protect. gp. 454 0.0 -Xlink:DMP[154]@Protein N-term 154.110613 154.2096 H(14)C(8)N(2)O(1) 0.0 Chemical derivative 455 0.0 +Xlink:DMP[154]@Protein_N-term 154.110613 154.2096 H(14)C(8)N(2)O(1) 0.0 Chemical derivative 455 0.0 Xlink:DMP[154]@K 154.110613 154.2096 H(14)C(8)N(2)O(1) 0.0 Chemical derivative 455 0.0 -NDA@Any N-term 175.042199 175.1855 H(5)C(13)N(1) 0.0 Chemical derivative 457 0.0 +NDA@Any_N-term 175.042199 175.1855 H(5)C(13)N(1) 0.0 Chemical derivative 457 0.0 NDA@K 175.042199 175.1855 H(5)C(13)N(1) 0.0 Chemical derivative 457 0.0 -SPITC:13C(6)@Any N-term 220.991213 221.2054 H(5)C(1)13C(6)N(1)O(3)S(2) 0.0 Chemical derivative 464 0.0 +SPITC:13C(6)@Any_N-term 220.991213 221.2054 H(5)C(1)13C(6)N(1)O(3)S(2) 0.0 Chemical derivative 464 0.0 SPITC:13C(6)@K 220.991213 221.2054 H(5)C(1)13C(6)N(1)O(3)S(2) 0.0 Chemical derivative 464 0.0 -TMAB:2H(9)@Any N-term 137.16403 137.2476 H(5)2H(9)C(7)N(1)O(1) 68.12999 2H(9)C(3)N(1) Isotopic label 477 0.5 +TMAB:2H(9)@Any_N-term 137.16403 137.2476 H(5)2H(9)C(7)N(1)O(1) 68.12999 2H(9)C(3)N(1) Isotopic label 477 0.5 TMAB:2H(9)@K 137.16403 137.2476 H(5)2H(9)C(7)N(1)O(1) 68.12999 2H(9)C(3)N(1) Isotopic label 477 0.5 -TMAB@Any N-term 128.107539 128.1922 H(14)C(7)N(1)O(1) 59.073499 H(9)C(3)N(1) Isotopic label 476 0.5 +TMAB@Any_N-term 128.107539 128.1922 H(14)C(7)N(1)O(1) 59.073499 H(9)C(3)N(1) Isotopic label 476 0.5 TMAB@K 128.107539 128.1922 H(14)C(7)N(1)O(1) 59.073499 H(9)C(3)N(1) Isotopic label 476 0.5 FTC@S 421.073241 421.4259 H(15)C(21)N(3)O(5)S(1) 0.0 Chemical derivative 478 0.0 FTC@R 421.073241 421.4259 H(15)C(21)N(3)O(5)S(1) 0.0 Chemical derivative 478 0.0 @@ -749,21 +749,21 @@ BHTOH@C 234.16198 234.334 H(22)C(15)O(2) 0.0 Other 498 0.0 BHTOH@K 234.16198 234.334 H(22)C(15)O(2) 0.0 Other 498 0.0 IGBP:13C(2)@C 298.022748 299.1331 H(13)C(10)13C(2)N(2)O(2)Br(1) 0.0 Isotopic label 499 0.0 Nmethylmaleimide+water@C 129.042593 129.114 H(7)C(5)N(1)O(3) 0.0 Chemical derivative 500 0.0 -PyMIC@Any N-term 134.048013 134.1353 H(6)C(7)N(2)O(1) 0.0 Chemical derivative 501 0.0 -LG-lactam-K@Protein N-term 332.19876 332.4339 H(28)C(20)O(4) 0.0 Post-translational 503 0.0 +PyMIC@Any_N-term 134.048013 134.1353 H(6)C(7)N(2)O(1) 0.0 Chemical derivative 501 0.0 +LG-lactam-K@Protein_N-term 332.19876 332.4339 H(28)C(20)O(4) 0.0 Post-translational 503 0.0 LG-lactam-K@K 332.19876 332.4339 H(28)C(20)O(4) 0.0 Post-translational 503 0.0 BisANS@K 594.091928 594.6569 H(22)C(32)N(2)O(6)S(2) 0.0 Chemical derivative 519 0.0 -Piperidine@Any N-term 68.0626 68.117 H(8)C(5) 0.0 Chemical derivative 520 0.0 +Piperidine@Any_N-term 68.0626 68.117 H(8)C(5) 0.0 Chemical derivative 520 0.0 Piperidine@K 68.0626 68.117 H(8)C(5) 0.0 Chemical derivative 520 0.0 -Diethyl@Any N-term 56.0626 56.1063 H(8)C(4) 0.0 Chemical derivative 518 0.0 +Diethyl@Any_N-term 56.0626 56.1063 H(8)C(4) 0.0 Chemical derivative 518 0.0 Diethyl@K 56.0626 56.1063 H(8)C(4) 0.0 Chemical derivative 518 0.0 -LG-Hlactam-K@Protein N-term 348.193674 348.4333 H(28)C(20)O(5) 0.0 Post-translational 504 0.0 +LG-Hlactam-K@Protein_N-term 348.193674 348.4333 H(28)C(20)O(5) 0.0 Post-translational 504 0.0 LG-Hlactam-K@K 348.193674 348.4333 H(28)C(20)O(5) 0.0 Post-translational 504 0.0 -Dimethyl:2H(4)13C(2)@Protein N-term 34.063117 34.0631 2H(4)13C(2) 0.0 Isotopic label 510 0.0 +Dimethyl:2H(4)13C(2)@Protein_N-term 34.063117 34.0631 2H(4)13C(2) 0.0 Isotopic label 510 0.0 Dimethyl:2H(4)13C(2)@R 34.063117 34.0631 2H(4)13C(2) 0.0 Isotopic label 510 0.0 Dimethyl:2H(4)13C(2)@K 34.063117 34.0631 2H(4)13C(2) 0.0 Isotopic label 510 0.0 -Dimethyl:2H(4)13C(2)@Any N-term 34.063117 34.0631 2H(4)13C(2) 0.0 Isotopic label 510 0.0 -C8-QAT@Any N-term 227.224915 227.3862 H(29)C(14)N(1)O(1) 0.0 Chemical derivative 513 0.0 +Dimethyl:2H(4)13C(2)@Any_N-term 34.063117 34.0631 2H(4)13C(2) 0.0 Isotopic label 510 0.0 +C8-QAT@Any_N-term 227.224915 227.3862 H(29)C(14)N(1)O(1) 0.0 Chemical derivative 513 0.0 C8-QAT@K 227.224915 227.3862 H(29)C(14)N(1)O(1) 0.0 Chemical derivative 513 0.0 Hex(2)@R 324.105647 324.2812 H(20)C(12)O(10) 0.0 Other glycosylation 512 0.0 Hex(2)@K 324.105647 324.2812 H(20)C(12)O(10) 0.0 Other glycosylation 512 0.0 @@ -773,30 +773,30 @@ LG-lactam-R@R 290.176961 290.3939 H(26)C(19)N(-2)O(4) 0.0 Post-translational 50 Withaferin@C 470.266839 470.5977 H(38)C(28)O(6) 0.0 Chemical derivative 1036 0.0 Biotin:Thermo-88317@S 443.291294 443.5603 H(42)C(22)N(3)O(4)P(1) 0.0 Chemical derivative 1037 0.0 Biotin:Thermo-88317@Y 443.291294 443.5603 H(42)C(22)N(3)O(4)P(1) 0.0 Chemical derivative 1037 0.0 -CLIP_TRAQ_2@Any N-term 141.098318 141.1756 H(12)C(6)13C(1)N(2)O(1) 0.0 Isotopic label 525 0.0 +CLIP_TRAQ_2@Any_N-term 141.098318 141.1756 H(12)C(6)13C(1)N(2)O(1) 0.0 Isotopic label 525 0.0 CLIP_TRAQ_2@K 141.098318 141.1756 H(12)C(6)13C(1)N(2)O(1) 0.0 Isotopic label 525 0.0 CLIP_TRAQ_2@Y 141.098318 141.1756 H(12)C(6)13C(1)N(2)O(1) 0.0 Isotopic label 525 0.0 LG-Hlactam-R@R 306.171876 306.3933 H(26)C(19)N(-2)O(5) 0.0 Post-translational 506 0.0 Maleimide-PEO2-Biotin@C 525.225719 525.6183 H(35)C(23)N(5)O(7)S(1) 0.0 Chemical derivative 522 0.0 -Sulfo-NHS-LC-LC-Biotin@Any N-term 452.245726 452.6106 H(36)C(22)N(4)O(4)S(1) 0.0 Chemical derivative 523 0.0 +Sulfo-NHS-LC-LC-Biotin@Any_N-term 452.245726 452.6106 H(36)C(22)N(4)O(4)S(1) 0.0 Chemical derivative 523 0.0 Sulfo-NHS-LC-LC-Biotin@K 452.245726 452.6106 H(36)C(22)N(4)O(4)S(1) 0.0 Chemical derivative 523 0.0 FNEM@C 427.069202 427.3625 H(13)C(24)N(1)O(7) 0.0 Chemical derivative 515 0.0 PropylNAGthiazoline@C 232.064354 232.2768 H(14)C(9)N(1)O(4)S(1) 0.0 Chemical derivative 514 0.0 Dethiomethyl@M -48.003371 -48.1075 H(-4)C(-1)S(-1) 0.0 Artefact 526 0.0 iTRAQ4plex114@Y 144.105918 144.168 H(12)C(5)13C(2)N(2)18O(1) 0.0 Isotopic label 532 0.0 -iTRAQ4plex114@Any N-term 144.105918 144.168 H(12)C(5)13C(2)N(2)18O(1) 0.0 Isotopic label 532 0.0 +iTRAQ4plex114@Any_N-term 144.105918 144.168 H(12)C(5)13C(2)N(2)18O(1) 0.0 Isotopic label 532 0.0 iTRAQ4plex114@K 144.105918 144.168 H(12)C(5)13C(2)N(2)18O(1) 0.0 Isotopic label 532 0.0 iTRAQ4plex114@C 144.105918 144.168 H(12)C(5)13C(2)N(2)18O(1) 0.0 Isotopic label 532 0.0 iTRAQ4plex115@Y 144.099599 144.1688 H(12)C(6)13C(1)N(1)15N(1)18O(1) 0.0 Isotopic label 533 0.0 -iTRAQ4plex115@Any N-term 144.099599 144.1688 H(12)C(6)13C(1)N(1)15N(1)18O(1) 0.0 Isotopic label 533 0.0 +iTRAQ4plex115@Any_N-term 144.099599 144.1688 H(12)C(6)13C(1)N(1)15N(1)18O(1) 0.0 Isotopic label 533 0.0 iTRAQ4plex115@K 144.099599 144.1688 H(12)C(6)13C(1)N(1)15N(1)18O(1) 0.0 Isotopic label 533 0.0 iTRAQ4plex115@C 144.099599 144.1688 H(12)C(6)13C(1)N(1)15N(1)18O(1) 0.0 Isotopic label 533 0.0 Dibromo@Y 155.821022 157.7921 H(-2)Br(2) 0.0 Chemical derivative 534 0.0 LRGG@K 383.228103 383.446 H(29)C(16)N(7)O(4) 0.0 Chemical derivative 535 0.0 CLIP_TRAQ_3@Y 271.148736 271.2976 H(20)C(11)13C(1)N(3)O(4) 0.0 Isotopic label 536 0.0 -CLIP_TRAQ_3@Any N-term 271.148736 271.2976 H(20)C(11)13C(1)N(3)O(4) 0.0 Isotopic label 536 0.0 +CLIP_TRAQ_3@Any_N-term 271.148736 271.2976 H(20)C(11)13C(1)N(3)O(4) 0.0 Isotopic label 536 0.0 CLIP_TRAQ_3@K 271.148736 271.2976 H(20)C(11)13C(1)N(3)O(4) 0.0 Isotopic label 536 0.0 -CLIP_TRAQ_4@Any N-term 244.101452 244.2292 H(15)C(9)13C(1)N(2)O(5) 0.0 Isotopic label 537 0.0 +CLIP_TRAQ_4@Any_N-term 244.101452 244.2292 H(15)C(9)13C(1)N(2)O(5) 0.0 Isotopic label 537 0.0 CLIP_TRAQ_4@K 244.101452 244.2292 H(15)C(9)13C(1)N(2)O(5) 0.0 Isotopic label 537 0.0 CLIP_TRAQ_4@Y 244.101452 244.2292 H(15)C(9)13C(1)N(2)O(5) 0.0 Isotopic label 537 0.0 Biotin:Cayman-10141@C 626.386577 626.8927 H(54)C(35)N(4)O(4)S(1) 0.0 Other 538 0.0 @@ -840,12 +840,12 @@ Gly->Val@G 42.04695 42.0797 H(6)C(3)N(0)O(0)S(0) 0.0 AA substitution 575 0.0 Gly->Asp@G 58.005479 58.0361 H(2)C(2)N(0)O(2)S(0) 0.0 AA substitution 576 0.0 Gly->Cys@G 45.987721 46.0916 H(2)C(1)N(0)O(0)S(1) 0.0 AA substitution 577 0.0 Gly->Arg@G 99.079647 99.1344 H(9)C(4)N(3)O(0)S(0) 0.0 AA substitution 578 0.0 -dNIC@Any N-term 109.048119 109.1205 H(1)2H(3)C(6)N(1)O(1) 0.0 Isotopic label 698 0.0 +dNIC@Any_N-term 109.048119 109.1205 H(1)2H(3)C(6)N(1)O(1) 0.0 Isotopic label 698 0.0 dNIC@K 109.048119 109.1205 H(1)2H(3)C(6)N(1)O(1) 0.0 Isotopic label 698 0.0 His->Pro@H -40.006148 -40.0241 H(0)C(-1)N(-2)O(0)S(0) 0.0 AA substitution 580 0.0 His->Tyr@H 26.004417 26.034 H(2)C(3)N(-2)O(1)S(0) 0.0 AA substitution 581 0.0 His->Gln@H -9.000334 -9.0101 H(1)C(-1)N(-1)O(1)S(0) 0.0 AA substitution 582 0.0 -NIC@Any N-term 105.021464 105.0941 H(3)C(6)N(1)O(1) 0.0 Isotopic label 697 0.0 +NIC@Any_N-term 105.021464 105.0941 H(3)C(6)N(1)O(1) 0.0 Isotopic label 697 0.0 NIC@K 105.021464 105.0941 H(3)C(6)N(1)O(1) 0.0 Isotopic label 697 0.0 His->Arg@H 19.042199 19.0464 H(5)C(0)N(1)O(0)S(0) 0.0 AA substitution 584 0.0 His->Xle@H -23.974848 -23.9816 H(4)N(-2) 0.0 AA substitution 585 0.0 @@ -957,23 +957,23 @@ Tyr->Asp@Y -48.036386 -48.0859 H(-4)C(-5)N(0)O(1)S(0) 0.0 AA substitution 682 0 Tyr->Cys@Y -60.054144 -60.0304 H(-4)C(-6)N(0)O(-1)S(1) 0.0 AA substitution 683 0.0 BDMAPP@W 253.010225 254.1231 H(12)C(11)N(1)O(1)Br(1) 0.0 Artefact 684 0.0 BDMAPP@Y 253.010225 254.1231 H(12)C(11)N(1)O(1)Br(1) 0.0 Artefact 684 0.0 -BDMAPP@Protein N-term 253.010225 254.1231 H(12)C(11)N(1)O(1)Br(1) 0.0 Chemical derivative 684 0.0 +BDMAPP@Protein_N-term 253.010225 254.1231 H(12)C(11)N(1)O(1)Br(1) 0.0 Chemical derivative 684 0.0 BDMAPP@K 253.010225 254.1231 H(12)C(11)N(1)O(1)Br(1) 0.0 Chemical derivative 684 0.0 BDMAPP@H 253.010225 254.1231 H(12)C(11)N(1)O(1)Br(1) 0.0 Artefact 684 0.0 NA-LNO2@C 325.225309 325.443 H(31)C(18)N(1)O(4) 0.0 Post-translational 685 0.0 NA-LNO2@H 325.225309 325.443 H(31)C(18)N(1)O(4) 0.0 Post-translational 685 0.0 NA-OA-NO2@C 327.240959 327.4589 H(33)C(18)N(1)O(4) 0.0 Post-translational 686 0.0 NA-OA-NO2@H 327.240959 327.4589 H(33)C(18)N(1)O(4) 0.0 Post-translational 686 0.0 -ICPL:2H(4)@Any N-term 109.046571 109.1188 H(-1)2H(4)C(6)N(1)O(1) 0.0 Isotopic label 687 0.0 -ICPL:2H(4)@Protein N-term 109.046571 109.1188 H(-1)2H(4)C(6)N(1)O(1) 0.0 Isotopic label 687 0.0 +ICPL:2H(4)@Any_N-term 109.046571 109.1188 H(-1)2H(4)C(6)N(1)O(1) 0.0 Isotopic label 687 0.0 +ICPL:2H(4)@Protein_N-term 109.046571 109.1188 H(-1)2H(4)C(6)N(1)O(1) 0.0 Isotopic label 687 0.0 ICPL:2H(4)@K 109.046571 109.1188 H(-1)2H(4)C(6)N(1)O(1) 0.0 Isotopic label 687 0.0 CarboxymethylDTT@C 210.00205 210.2712 H(10)C(6)O(4)S(2) 0.0 Artefact 894 0.0 -iTRAQ8plex@Protein N-term 304.20536 304.3074 H(24)C(7)13C(7)N(3)15N(1)O(3) 0.0 Isotopic label 730 0.0 +iTRAQ8plex@Protein_N-term 304.20536 304.3074 H(24)C(7)13C(7)N(3)15N(1)O(3) 0.0 Isotopic label 730 0.0 iTRAQ8plex@T 304.20536 304.3074 H(24)C(7)13C(7)N(3)15N(1)O(3) 0.0 Isotopic label 730 0.0 iTRAQ8plex@S 304.20536 304.3074 H(24)C(7)13C(7)N(3)15N(1)O(3) 0.0 Isotopic label 730 0.0 iTRAQ8plex@H 304.20536 304.3074 H(24)C(7)13C(7)N(3)15N(1)O(3) 0.0 Isotopic label 730 0.0 iTRAQ8plex@Y 304.20536 304.3074 H(24)C(7)13C(7)N(3)15N(1)O(3) 0.0 Isotopic label 730 0.0 -iTRAQ8plex@Any N-term 304.20536 304.3074 H(24)C(7)13C(7)N(3)15N(1)O(3) 0.0 Isotopic label 730 0.0 +iTRAQ8plex@Any_N-term 304.20536 304.3074 H(24)C(7)13C(7)N(3)15N(1)O(3) 0.0 Isotopic label 730 0.0 iTRAQ8plex@K 304.20536 304.3074 H(24)C(7)13C(7)N(3)15N(1)O(3) 0.0 Isotopic label 730 0.0 iTRAQ8plex@C 304.20536 304.3074 H(24)C(7)13C(7)N(3)15N(1)O(3) 0.0 Isotopic label 730 0.0 Label:13C(6)15N(1)@I 7.017164 6.9493 C(-6)13C(6)N(-1)15N(1) 0.0 Isotopic label 695 0.0 @@ -991,14 +991,14 @@ O-Dimethylphosphate@S 107.997631 108.0331 H(5)C(2)O(3)P(1) 0.0 Chemical derivat O-Methylphosphate@Y 93.981981 94.0065 H(3)C(1)O(3)P(1) 0.0 Chemical derivative 724 0.0 O-Methylphosphate@T 93.981981 94.0065 H(3)C(1)O(3)P(1) 0.0 Chemical derivative 724 0.0 O-Methylphosphate@S 93.981981 94.0065 H(3)C(1)O(3)P(1) 0.0 Chemical derivative 724 0.0 -Diethylphosphate@Any N-term 136.028931 136.0862 H(9)C(4)O(3)P(1) 0.0 Chemical derivative 725 0.0 +Diethylphosphate@Any_N-term 136.028931 136.0862 H(9)C(4)O(3)P(1) 0.0 Chemical derivative 725 0.0 Diethylphosphate@H 136.028931 136.0862 H(9)C(4)O(3)P(1) 0.0 Chemical derivative 725 0.0 Diethylphosphate@C 136.028931 136.0862 H(9)C(4)O(3)P(1) 0.0 Chemical derivative 725 0.0 Diethylphosphate@K 136.028931 136.0862 H(9)C(4)O(3)P(1) 0.0 Chemical derivative 725 0.0 Diethylphosphate@Y 136.028931 136.0862 H(9)C(4)O(3)P(1) 0.0 Chemical derivative 725 0.0 Diethylphosphate@T 136.028931 136.0862 H(9)C(4)O(3)P(1) 0.0 Chemical derivative 725 0.0 Diethylphosphate@S 136.028931 136.0862 H(9)C(4)O(3)P(1) 0.0 Chemical derivative 725 0.0 -Ethylphosphate@Any N-term 107.997631 108.0331 H(5)C(2)O(3)P(1) 0.0 Chemical derivative 726 0.0 +Ethylphosphate@Any_N-term 107.997631 108.0331 H(5)C(2)O(3)P(1) 0.0 Chemical derivative 726 0.0 Ethylphosphate@K 107.997631 108.0331 H(5)C(2)O(3)P(1) 0.0 Chemical derivative 726 0.0 Ethylphosphate@Y 107.997631 108.0331 H(5)C(2)O(3)P(1) 0.0 Chemical derivative 726 0.0 Ethylphosphate@T 107.997631 108.0331 H(5)C(2)O(3)P(1) 0.0 Chemical derivative 726 0.0 @@ -1015,30 +1015,30 @@ O-Isopropylmethylphosphonate@Y 120.034017 120.0868 H(9)C(4)O(2)P(1) 0.0 Chemica O-Isopropylmethylphosphonate@T 120.034017 120.0868 H(9)C(4)O(2)P(1) 0.0 Chemical derivative 729 0.0 O-Isopropylmethylphosphonate@S 120.034017 120.0868 H(9)C(4)O(2)P(1) 0.0 Chemical derivative 729 0.0 iTRAQ8plex:13C(6)15N(2)@Y 304.19904 304.3081 H(24)C(8)13C(6)N(2)15N(2)O(3) 0.0 Isotopic label 731 0.0 -iTRAQ8plex:13C(6)15N(2)@Any N-term 304.19904 304.3081 H(24)C(8)13C(6)N(2)15N(2)O(3) 0.0 Isotopic label 731 0.0 +iTRAQ8plex:13C(6)15N(2)@Any_N-term 304.19904 304.3081 H(24)C(8)13C(6)N(2)15N(2)O(3) 0.0 Isotopic label 731 0.0 iTRAQ8plex:13C(6)15N(2)@K 304.19904 304.3081 H(24)C(8)13C(6)N(2)15N(2)O(3) 0.0 Isotopic label 731 0.0 iTRAQ8plex:13C(6)15N(2)@C 304.19904 304.3081 H(24)C(8)13C(6)N(2)15N(2)O(3) 0.0 Isotopic label 731 0.0 BEMAD_ST@T 136.001656 136.2357 H(8)C(4)O(1)S(2) 0.0 Chemical derivative 735 0.0 BEMAD_ST@S 136.001656 136.2357 H(8)C(4)O(1)S(2) 0.0 Chemical derivative 735 0.0 Ethanolamine@D 43.042199 43.0678 H(5)C(2)N(1) 0.0 Chemical derivative 734 0.0 -Ethanolamine@Any C-term 43.042199 43.0678 H(5)C(2)N(1) 0.0 Chemical derivative 734 0.0 +Ethanolamine@Any_C-term 43.042199 43.0678 H(5)C(2)N(1) 0.0 Chemical derivative 734 0.0 Ethanolamine@E 43.042199 43.0678 H(5)C(2)N(1) 0.0 Chemical derivative 734 0.0 Ethanolamine@C 43.042199 43.0678 H(5)C(2)N(1) 0.0 Chemical derivative 734 0.0 TMT6plex@T 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0 TMT6plex@S 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0 TMT6plex@H 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0 -TMT6plex@Protein N-term 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0 -TMT6plex@Any N-term 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0 +TMT6plex@Protein_N-term 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0 +TMT6plex@Any_N-term 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0 TMT6plex@K 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0 BEMAD_C@C 120.0245 120.1701 H(8)C(4)O(2)S(1) 0.0 Chemical derivative 736 0.0 TMT2plex@H 225.155833 225.2921 H(20)C(11)13C(1)N(2)O(2) 0.0 Isotopic label 738 0.0 TMT2plex@S 225.155833 225.2921 H(20)C(11)13C(1)N(2)O(2) 0.0 Isotopic label 738 0.0 TMT2plex@T 225.155833 225.2921 H(20)C(11)13C(1)N(2)O(2) 0.0 Isotopic label 738 0.0 -TMT2plex@Protein N-term 225.155833 225.2921 H(20)C(11)13C(1)N(2)O(2) 0.0 Isotopic label 738 0.0 -TMT2plex@Any N-term 225.155833 225.2921 H(20)C(11)13C(1)N(2)O(2) 0.0 Isotopic label 738 0.0 +TMT2plex@Protein_N-term 225.155833 225.2921 H(20)C(11)13C(1)N(2)O(2) 0.0 Isotopic label 738 0.0 +TMT2plex@Any_N-term 225.155833 225.2921 H(20)C(11)13C(1)N(2)O(2) 0.0 Isotopic label 738 0.0 TMT2plex@K 225.155833 225.2921 H(20)C(11)13C(1)N(2)O(2) 0.0 Isotopic label 738 0.0 -TMT@Protein N-term 224.152478 224.2994 H(20)C(12)N(2)O(2) 0.0 Chemical derivative 739 0.0 -TMT@Any N-term 224.152478 224.2994 H(20)C(12)N(2)O(2) 0.0 Chemical derivative 739 0.0 +TMT@Protein_N-term 224.152478 224.2994 H(20)C(12)N(2)O(2) 0.0 Chemical derivative 739 0.0 +TMT@Any_N-term 224.152478 224.2994 H(20)C(12)N(2)O(2) 0.0 Chemical derivative 739 0.0 TMT@K 224.152478 224.2994 H(20)C(12)N(2)O(2) 0.0 Chemical derivative 739 0.0 TMT@H 224.152478 224.2994 H(20)C(12)N(2)O(2) 0.0 Isotopic label 739 0.0 TMT@S 224.152478 224.2994 H(20)C(12)N(2)O(2) 0.0 Isotopic label 739 0.0 @@ -1054,9 +1054,9 @@ NO_SMX_SIMD@C 267.031377 267.2612 H(9)C(10)N(3)O(4)S(1) 0.0 Chemical derivative Malonyl@C 86.000394 86.0462 H(2)C(3)O(3) 0.0 Chemical derivative 747 0.0 Malonyl@S 86.000394 86.0462 H(2)C(3)O(3) 0.0 Chemical derivative 747 0.0 Malonyl@K 86.000394 86.0462 H(2)C(3)O(3) 0.0 Post-translational 747 0.0 -3sulfo@Any N-term 183.983029 184.1693 H(4)C(7)O(4)S(1) 0.0 Chemical derivative 748 0.0 +3sulfo@Any_N-term 183.983029 184.1693 H(4)C(7)O(4)S(1) 0.0 Chemical derivative 748 0.0 trifluoro@L 53.971735 53.9714 H(-3)F(3) 0.0 Non-standard residue 750 0.0 -TNBS@Any N-term 210.986535 211.0886 H(1)C(6)N(3)O(6) 0.0 Chemical derivative 751 0.0 +TNBS@Any_N-term 210.986535 211.0886 H(1)C(6)N(3)O(6) 0.0 Chemical derivative 751 0.0 TNBS@K 210.986535 211.0886 H(1)C(6)N(3)O(6) 0.0 Chemical derivative 751 0.0 Biotin-phenacyl@C 626.263502 626.727 H(38)C(29)N(8)O(6)S(1) 0.0 Chemical derivative 774 0.0 Biotin-phenacyl@H 626.263502 626.727 H(38)C(29)N(8)O(6)S(1) 0.0 Chemical derivative 774 0.0 @@ -1069,14 +1069,14 @@ maleimide@C 97.016378 97.0721 H(3)C(4)N(1)O(2) 0.0 Chemical derivative 773 0.0 IDEnT@C 214.990469 216.064 H(7)C(9)N(1)O(1)Cl(2) 0.0 Isotopic label 762 0.0 BEMAD_ST:2H(6)@T 142.039317 142.2727 H(2)2H(6)C(4)O(1)S(2) 0.0 Isotopic label 763 0.0 BEMAD_ST:2H(6)@S 142.039317 142.2727 H(2)2H(6)C(4)O(1)S(2) 0.0 Isotopic label 763 0.0 -Met-loss@M^Protein N-term -131.040485 -131.1961 H(-9)C(-5)N(-1)O(-1)S(-1) 0.0 Co-translational 765 0.0 -Met-loss+Acetyl@M^Protein N-term -89.02992 -89.1594 H(-7)C(-3)N(-1)S(-1) 0.0 Co-translational 766 0.0 +Met-loss@M^Protein_N-term -131.040485 -131.1961 H(-9)C(-5)N(-1)O(-1)S(-1) 0.0 Co-translational 765 0.0 +Met-loss+Acetyl@M^Protein_N-term -89.02992 -89.1594 H(-7)C(-3)N(-1)S(-1) 0.0 Co-translational 766 0.0 Menadione-HQ@K 172.05243 172.18 H(8)C(11)O(2) 0.0 Chemical derivative 767 0.0 Menadione-HQ@C 172.05243 172.18 H(8)C(11)O(2) 0.0 Chemical derivative 767 0.0 Carboxymethyl:13C(2)@C 60.012189 60.0214 H(2)13C(2)O(2) 0.0 Chemical derivative 775 0.0 NEM:2H(5)@C 130.079062 130.1561 H(2)2H(5)C(6)N(1)O(2) 0.0 Chemical derivative 776 0.0 -Gly-loss+Amide@G^Any C-term -58.005479 -58.0361 H(-2)C(-2)O(-2) 0.0 Post-translational 822 0.0 -TMPP-Ac@Any N-term 572.181134 572.5401 H(33)C(29)O(10)P(1) 0.0 Chemical derivative 827 0.0 +Gly-loss+Amide@G^Any_C-term -58.005479 -58.0361 H(-2)C(-2)O(-2) 0.0 Post-translational 822 0.0 +TMPP-Ac@Any_N-term 572.181134 572.5401 H(33)C(29)O(10)P(1) 0.0 Chemical derivative 827 0.0 TMPP-Ac@K 572.181134 572.5401 H(33)C(29)O(10)P(1) 0.0 Artefact 827 0.0 TMPP-Ac@Y 572.181134 572.5401 H(33)C(29)O(10)P(1) 0.0 Artefact 827 0.0 Label:13C(6)+GG@K 120.063056 120.0586 H(6)C(-2)13C(6)N(2)O(2) 0.0 Isotopic label 799 0.0 @@ -1105,7 +1105,7 @@ cGMP@C 343.031785 343.1895 H(10)C(10)N(5)O(7)P(1) 0.0 Post-translational 849 0. cGMP+RMP-loss@C 150.041585 150.1182 H(4)C(5)N(5)O(1) 0.0 Post-translational 851 0.0 cGMP+RMP-loss@S 150.041585 150.1182 H(4)C(5)N(5)O(1) 0.0 Post-translational 851 0.0 mTRAQ@Y 140.094963 140.183 H(12)C(7)N(2)O(1) 0.0 Isotopic label 888 0.0 -mTRAQ@Any N-term 140.094963 140.183 H(12)C(7)N(2)O(1) 0.0 Isotopic label 888 0.0 +mTRAQ@Any_N-term 140.094963 140.183 H(12)C(7)N(2)O(1) 0.0 Isotopic label 888 0.0 mTRAQ@K 140.094963 140.183 H(12)C(7)N(2)O(1) 0.0 Isotopic label 888 0.0 mTRAQ@H 140.094963 140.183 H(12)C(7)N(2)O(1) 0.0 Isotopic label 888 0.0 mTRAQ@S 140.094963 140.183 H(12)C(7)N(2)O(1) 0.0 Isotopic label 888 0.0 @@ -1115,19 +1115,19 @@ Label:2H(4)+GG@K 118.068034 118.1273 H(2)2H(4)C(4)N(2)O(2) 0.0 Post-translation spermine@Q 185.189198 185.3097 H(23)C(10)N(3) 0.0 Chemical derivative 1420 0.0 Label:13C(1)2H(3)@M 4.022185 4.0111 H(-3)2H(3)C(-1)13C(1) 0.0 Isotopic label 862 0.0 ZGB@K 758.380841 758.7261 H(53)C(37)N(6)O(6)F(2)S(1)B(1) 0.0 Other 861 0.0 -ZGB@Any N-term 758.380841 758.7261 H(53)C(37)N(6)O(6)F(2)S(1)B(1) 0.0 Other 861 0.0 +ZGB@Any_N-term 758.380841 758.7261 H(53)C(37)N(6)O(6)F(2)S(1)B(1) 0.0 Other 861 0.0 MG-H1@R 54.010565 54.0474 H(2)C(3)O(1) 0.0 Other 859 0.0 G-H1@R 39.994915 40.0208 C(2)O(1) 0.0 Other 860 0.0 Label:13C(6)15N(2)+GG@K 122.057126 122.0454 H(6)C(-2)13C(6)15N(2)O(2) 0.0 Isotopic label 864 0.0 -ICPL:13C(6)2H(4)@Any N-term 115.0667 115.0747 H(-1)2H(4)13C(6)N(1)O(1) 0.0 Isotopic label 866 0.0 +ICPL:13C(6)2H(4)@Any_N-term 115.0667 115.0747 H(-1)2H(4)13C(6)N(1)O(1) 0.0 Isotopic label 866 0.0 ICPL:13C(6)2H(4)@K 115.0667 115.0747 H(-1)2H(4)13C(6)N(1)O(1) 0.0 Isotopic label 866 0.0 -ICPL:13C(6)2H(4)@Protein N-term 115.0667 115.0747 H(-1)2H(4)13C(6)N(1)O(1) 0.0 Isotopic label 866 0.0 +ICPL:13C(6)2H(4)@Protein_N-term 115.0667 115.0747 H(-1)2H(4)13C(6)N(1)O(1) 0.0 Isotopic label 866 0.0 DyLight-maleimide@C 940.1999 941.0762 H(48)C(39)N(4)O(15)S(4) 0.0 Chemical derivative 890 0.0 mTRAQ:13C(3)15N(1)@S 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 889 0.0 mTRAQ:13C(3)15N(1)@T 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 889 0.0 mTRAQ:13C(3)15N(1)@H 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 889 0.0 mTRAQ:13C(3)15N(1)@Y 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 889 0.0 -mTRAQ:13C(3)15N(1)@Any N-term 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 889 0.0 +mTRAQ:13C(3)15N(1)@Any_N-term 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 889 0.0 mTRAQ:13C(3)15N(1)@K 144.102063 144.1544 H(12)C(4)13C(3)N(1)15N(1)O(1) 0.0 Isotopic label 889 0.0 Methyl-PEO12-Maleimide@C 710.383719 710.8073 H(58)C(32)N(2)O(15) 0.0 Chemical derivative 891 0.0 MDCC@C 383.148121 383.3978 H(21)C(20)N(3)O(5) 0.0 Chemical derivative 887 0.0 @@ -1149,7 +1149,7 @@ Lys->CamCys@K 31.935685 32.0219 H(-4)C(-1)O(1)S(1) 0.0 Pre-translational 903 0. Phe->CamCys@F 12.962234 13.0204 H(-1)C(-4)N(1)O(1)S(1) 0.0 Pre-translational 904 0.0 Leu->MetOx@L 33.951335 34.0378 H(-2)C(-1)O(1)S(1) 0.0 Pre-translational 905 0.0 Lys->MetOx@K 18.940436 19.0232 H(-3)C(-1)N(-1)O(1)S(1) 0.0 Pre-translational 906 0.0 -Galactosyl@Any N-term 178.047738 178.14 H(10)C(6)O(6) 0.0 Other glycosylation 907 0.0 +Galactosyl@Any_N-term 178.047738 178.14 H(10)C(6)O(6) 0.0 Other glycosylation 907 0.0 Galactosyl@K 178.047738 178.14 H(10)C(6)O(6) 0.0 Other glycosylation 907 0.0 Xlink:SMCC[321]@C 321.205242 321.4146 H(27)C(17)N(3)O(3) 0.0 Chemical derivative 908 0.0 Bacillosamine@N 228.111007 228.245 H(16)C(10)N(2)O(4) 228.111007 H(16)C(10)N(2)O(4) N-linked glycosylation 910 0.5 @@ -1184,39 +1184,39 @@ DNPS@W 198.981352 199.164 H(3)C(6)N(2)O(4)S(1) 0.0 Chemical derivative 941 0.0 SulfoGMBS@C 458.162391 458.5306 H(26)C(22)N(4)O(5)S(1) 0.0 Other 942 0.0 DimethylamineGMBS@C 267.158292 267.3241 H(21)C(13)N(3)O(3) 0.0 Chemical derivative 943 0.0 Label:15N(2)2H(9)@K 11.050561 11.0423 H(-9)2H(9)N(-2)15N(2) 0.0 Isotopic label 944 0.0 -LG-anhydrolactam@Any N-term 314.188195 314.4186 H(26)C(20)O(3) 0.0 Post-translational 946 0.0 +LG-anhydrolactam@Any_N-term 314.188195 314.4186 H(26)C(20)O(3) 0.0 Post-translational 946 0.0 LG-anhydrolactam@K 314.188195 314.4186 H(26)C(20)O(3) 0.0 Post-translational 946 0.0 LG-pyrrole@C 316.203845 316.4345 H(28)C(20)O(3) 0.0 Post-translational 947 0.0 -LG-pyrrole@Any N-term 316.203845 316.4345 H(28)C(20)O(3) 0.0 Post-translational 947 0.0 +LG-pyrrole@Any_N-term 316.203845 316.4345 H(28)C(20)O(3) 0.0 Post-translational 947 0.0 LG-pyrrole@K 316.203845 316.4345 H(28)C(20)O(3) 0.0 Post-translational 947 0.0 -LG-anhyropyrrole@Any N-term 298.19328 298.4192 H(26)C(20)O(2) 0.0 Post-translational 948 0.0 +LG-anhyropyrrole@Any_N-term 298.19328 298.4192 H(26)C(20)O(2) 0.0 Post-translational 948 0.0 LG-anhyropyrrole@K 298.19328 298.4192 H(26)C(20)O(2) 0.0 Post-translational 948 0.0 3-deoxyglucosone@R 144.042259 144.1253 H(8)C(6)O(4) 0.0 Multiple 949 0.0 Cation:Li@D 6.008178 5.9331 H(-1)Li(1) 0.0 Artefact 950 0.0 Cation:Li@E 6.008178 5.9331 H(-1)Li(1) 0.0 Artefact 950 0.0 -Cation:Li@Any C-term 6.008178 5.9331 H(-1)Li(1) 0.0 Artefact 950 0.0 -Cation:Ca[II]@Any C-term 37.946941 38.0621 H(-2)Ca(1) 0.0 Artefact 951 0.0 +Cation:Li@Any_C-term 6.008178 5.9331 H(-1)Li(1) 0.0 Artefact 950 0.0 +Cation:Ca[II]@Any_C-term 37.946941 38.0621 H(-2)Ca(1) 0.0 Artefact 951 0.0 Cation:Ca[II]@E 37.946941 38.0621 H(-2)Ca(1) 0.0 Artefact 951 0.0 Cation:Ca[II]@D 37.946941 38.0621 H(-2)Ca(1) 0.0 Artefact 951 0.0 Cation:Fe[II]@D 53.919289 53.8291 H(-2)Fe(1) 0.0 Artefact 952 0.0 Cation:Fe[II]@E 53.919289 53.8291 H(-2)Fe(1) 0.0 Artefact 952 0.0 -Cation:Fe[II]@Any C-term 53.919289 53.8291 H(-2)Fe(1) 0.0 Artefact 952 0.0 +Cation:Fe[II]@Any_C-term 53.919289 53.8291 H(-2)Fe(1) 0.0 Artefact 952 0.0 Cation:Ni[II]@D 55.919696 56.6775 H(-2)Ni(1) 0.0 Artefact 953 0.0 Cation:Ni[II]@E 55.919696 56.6775 H(-2)Ni(1) 0.0 Artefact 953 0.0 -Cation:Ni[II]@Any C-term 55.919696 56.6775 H(-2)Ni(1) 0.0 Artefact 953 0.0 -Cation:Zn[II]@Any C-term 61.913495 63.3931 H(-2)Zn(1) 0.0 Artefact 954 0.0 +Cation:Ni[II]@Any_C-term 55.919696 56.6775 H(-2)Ni(1) 0.0 Artefact 953 0.0 +Cation:Zn[II]@Any_C-term 61.913495 63.3931 H(-2)Zn(1) 0.0 Artefact 954 0.0 Cation:Zn[II]@E 61.913495 63.3931 H(-2)Zn(1) 0.0 Artefact 954 0.0 Cation:Zn[II]@D 61.913495 63.3931 H(-2)Zn(1) 0.0 Artefact 954 0.0 Cation:Zn[II]@H 61.913495 63.3931 H(-2)Zn(1) 0.0 Artefact 954 0.0 Cation:Ag@D 105.897267 106.8603 H(-1)Ag(1) 0.0 Artefact 955 0.0 Cation:Ag@E 105.897267 106.8603 H(-1)Ag(1) 0.0 Artefact 955 0.0 -Cation:Ag@Any C-term 105.897267 106.8603 H(-1)Ag(1) 0.0 Artefact 955 0.0 +Cation:Ag@Any_C-term 105.897267 106.8603 H(-1)Ag(1) 0.0 Artefact 955 0.0 Cation:Mg[II]@D 21.969392 22.2891 H(-2)Mg(1) 0.0 Artefact 956 0.0 Cation:Mg[II]@E 21.969392 22.2891 H(-2)Mg(1) 0.0 Artefact 956 0.0 -Cation:Mg[II]@Any C-term 21.969392 22.2891 H(-2)Mg(1) 0.0 Artefact 956 0.0 +Cation:Mg[II]@Any_C-term 21.969392 22.2891 H(-2)Mg(1) 0.0 Artefact 956 0.0 2-succinyl@C 116.010959 116.0722 H(4)C(4)O(4) 0.0 Chemical derivative 957 0.0 Propargylamine@D 37.031634 37.0632 H(3)C(3)N(1)O(-1) 0.0 Chemical derivative 958 0.0 -Propargylamine@Any C-term 37.031634 37.0632 H(3)C(3)N(1)O(-1) 0.0 Chemical derivative 958 0.0 +Propargylamine@Any_C-term 37.031634 37.0632 H(3)C(3)N(1)O(-1) 0.0 Chemical derivative 958 0.0 Propargylamine@E 37.031634 37.0632 H(3)C(3)N(1)O(-1) 0.0 Chemical derivative 958 0.0 Phosphopropargyl@T 116.997965 117.0431 H(4)C(3)N(1)O(2)P(1) 0.0 Multiple 959 0.0 Phosphopropargyl@Y 116.997965 117.0431 H(4)C(3)N(1)O(2)P(1) 0.0 Multiple 959 0.0 @@ -1224,11 +1224,11 @@ Phosphopropargyl@S 116.997965 117.0431 H(4)C(3)N(1)O(2)P(1) 0.0 Multiple 959 0. SUMO2135@K 2135.920496 2137.2343 H(137)C(90)N(21)O(37)S(1) 0.0 Other 960 0.0 SUMO3549@K 3549.536568 3551.6672 H(224)C(150)N(38)O(60)S(1) 0.0 Other 961 0.0 serotonylation@Q 159.068414 159.1846 H(9)C(10)N(1)O(1) 0.0 Post-translational 1992 0.0 -BITC@Any N-term 149.02992 149.2129 H(7)C(8)N(1)S(1) 0.0 Chemical derivative 978 0.0 +BITC@Any_N-term 149.02992 149.2129 H(7)C(8)N(1)S(1) 0.0 Chemical derivative 978 0.0 BITC@K 149.02992 149.2129 H(7)C(8)N(1)S(1) 0.0 Chemical derivative 978 0.0 BITC@C 149.02992 149.2129 H(7)C(8)N(1)S(1) 0.0 Chemical derivative 978 0.0 Carbofuran@S 58.029289 58.0593 H(4)C(2)N(1)O(1) 0.0 Chemical derivative 977 0.0 -PEITC@Any N-term 163.04557 163.2395 H(9)C(9)N(1)S(1) 0.0 Chemical derivative 979 0.0 +PEITC@Any_N-term 163.04557 163.2395 H(9)C(9)N(1)S(1) 0.0 Chemical derivative 979 0.0 PEITC@K 163.04557 163.2395 H(9)C(9)N(1)S(1) 0.0 Chemical derivative 979 0.0 PEITC@C 163.04557 163.2395 H(9)C(9)N(1)S(1) 0.0 Chemical derivative 979 0.0 thioacylPA@K 159.035399 159.2062 H(9)C(6)N(1)O(2)S(1) 0.0 Chemical derivative 967 0.0 @@ -1236,15 +1236,15 @@ maleimide3@K 969.366232 969.8975 H(59)C(37)N(7)O(23) 0.0 Post-translational 971 maleimide3@C 969.366232 969.8975 H(59)C(37)N(7)O(23) 0.0 Post-translational 971 0.0 maleimide5@K 1293.471879 1294.1787 H(79)C(49)N(7)O(33) 0.0 Post-translational 972 0.0 maleimide5@C 1293.471879 1294.1787 H(79)C(49)N(7)O(33) 0.0 Post-translational 972 0.0 -Puromycin@Any C-term 453.212452 453.4943 H(27)C(22)N(7)O(4) 0.0 Co-translational 973 0.0 +Puromycin@Any_C-term 453.212452 453.4943 H(27)C(22)N(7)O(4) 0.0 Co-translational 973 0.0 glucosone@R 160.037173 160.1247 H(8)C(6)O(5) 0.0 Other 981 0.0 Label:13C(6)+Dimethyl@K 34.051429 34.0091 H(4)C(-4)13C(6) 0.0 Isotopic label 986 0.0 cysTMT@C 299.166748 299.4322 H(25)C(14)N(3)O(2)S(1) 0.0 Chemical derivative 984 0.0 cysTMT6plex@C 304.177202 304.3962 H(25)C(10)13C(4)N(2)15N(1)O(2)S(1) 0.0 Isotopic label 985 0.0 -ISD_z+2_ion@Any N-term -15.010899 -15.0146 H(-1)N(-1) 0.0 Artefact 991 0.0 +ISD_z+2_ion@Any_N-term -15.010899 -15.0146 H(-1)N(-1) 0.0 Artefact 991 0.0 Ammonium@E 17.026549 17.0305 H(3)N(1) 0.0 Artefact 989 0.0 Ammonium@D 17.026549 17.0305 H(3)N(1) 0.0 Artefact 989 0.0 -Ammonium@Any C-term 17.026549 17.0305 H(3)N(1) 0.0 Artefact 989 0.0 +Ammonium@Any_C-term 17.026549 17.0305 H(3)N(1) 0.0 Artefact 989 0.0 Biotin:Sigma-B1267@C 449.17329 449.5239 H(27)C(20)N(5)O(5)S(1) 0.0 Chemical derivative 993 0.0 Label:15N(1)@M 0.997035 0.9934 N(-1)15N(1) 0.0 Isotopic label 994 0.0 Label:15N(1)@E 0.997035 0.9934 N(-1)15N(1) 0.0 Isotopic label 994 0.0 @@ -1280,34 +1280,34 @@ Thiazolidine@Y 12.0 12.0107 C(1) 0.0 Chemical derivative 1009 0.0 Thiazolidine@H 12.0 12.0107 C(1) 0.0 Chemical derivative 1009 0.0 Thiazolidine@R 12.0 12.0107 C(1) 0.0 Chemical derivative 1009 0.0 Thiazolidine@K 12.0 12.0107 C(1) 0.0 Chemical derivative 1009 0.0 -Thiazolidine@Protein N-term 12.0 12.0107 C(1) 0.0 Chemical derivative 1009 0.0 +Thiazolidine@Protein_N-term 12.0 12.0107 C(1) 0.0 Chemical derivative 1009 0.0 Thiazolidine@C 12.0 12.0107 C(1) 0.0 Chemical derivative 1009 0.0 Thiazolidine@F 12.0 12.0107 C(1) 0.0 Chemical derivative 1009 0.0 DEDGFLYMVYASQETFG@K 1970.824411 1972.088 H(122)C(89)N(18)O(31)S(1) 18.010565 H(2)O(1) Post-translational 1010 0.5 Biotin:Invitrogen-M1602@C 523.210069 523.6024 H(33)C(23)N(5)O(7)S(1) 0.0 Chemical derivative 1012 0.0 Xlink:DSS[156]@K 156.078644 156.1791 H(12)C(8)O(3) 0.0 Chemical derivative 1020 0.0 -Xlink:DSS[156]@Protein N-term 156.078644 156.1791 H(12)C(8)O(3) 0.0 Chemical derivative 1020 0.0 +Xlink:DSS[156]@Protein_N-term 156.078644 156.1791 H(12)C(8)O(3) 0.0 Chemical derivative 1020 0.0 DMPO@H 111.068414 111.1418 H(9)C(6)N(1)O(1) 0.0 Post-translational 1017 0.0 DMPO@Y 111.068414 111.1418 H(9)C(6)N(1)O(1) 0.0 Post-translational 1017 0.0 DMPO@C 111.068414 111.1418 H(9)C(6)N(1)O(1) 0.0 Post-translational 1017 0.0 glycidamide@K 87.032028 87.0773 H(5)C(3)N(1)O(2) 0.0 Chemical derivative 1014 0.0 -glycidamide@Any N-term 87.032028 87.0773 H(5)C(3)N(1)O(2) 0.0 Chemical derivative 1014 0.0 -Ahx2+Hsl@Any C-term 309.205242 309.4039 H(27)C(16)N(3)O(3) 0.0 Non-standard residue 1015 0.0 +glycidamide@Any_N-term 87.032028 87.0773 H(5)C(3)N(1)O(2) 0.0 Chemical derivative 1014 0.0 +Ahx2+Hsl@Any_C-term 309.205242 309.4039 H(27)C(16)N(3)O(3) 0.0 Non-standard residue 1015 0.0 ICDID@C 138.06808 138.1638 H(10)C(8)O(2) 0.0 Isotopic label 1018 0.0 ICDID:2H(6)@C 144.10574 144.2008 H(4)2H(6)C(8)O(2) 0.0 Isotopic label 1019 0.0 -Xlink:EGS[244]@Protein N-term 244.058303 244.1981 H(12)C(10)O(7) 0.0 Chemical derivative 1021 0.0 +Xlink:EGS[244]@Protein_N-term 244.058303 244.1981 H(12)C(10)O(7) 0.0 Chemical derivative 1021 0.0 Xlink:EGS[244]@K 244.058303 244.1981 H(12)C(10)O(7) 0.0 Chemical derivative 1021 0.0 -Xlink:DST[132]@Protein N-term 132.005873 132.0716 H(4)C(4)O(5) 0.0 Chemical derivative 1022 0.0 +Xlink:DST[132]@Protein_N-term 132.005873 132.0716 H(4)C(4)O(5) 0.0 Chemical derivative 1022 0.0 Xlink:DST[132]@K 132.005873 132.0716 H(4)C(4)O(5) 0.0 Chemical derivative 1022 0.0 -Xlink:DTSSP[192]@Protein N-term 191.991486 192.2559 H(8)C(6)O(3)S(2) 0.0 Chemical derivative 1023 0.0 +Xlink:DTSSP[192]@Protein_N-term 191.991486 192.2559 H(8)C(6)O(3)S(2) 0.0 Chemical derivative 1023 0.0 Xlink:DTSSP[192]@K 191.991486 192.2559 H(8)C(6)O(3)S(2) 0.0 Chemical derivative 1023 0.0 Xlink:SMCC[237]@C 237.100108 237.2518 H(15)C(12)N(1)O(4) 0.0 Chemical derivative 1024 0.0 Xlink:SMCC[237]@K 237.100108 237.2518 H(15)C(12)N(1)O(4) 0.0 Chemical derivative 1024 0.0 -Xlink:SMCC[237]@Protein N-term 237.100108 237.2518 H(15)C(12)N(1)O(4) 0.0 Chemical derivative 1024 0.0 +Xlink:SMCC[237]@Protein_N-term 237.100108 237.2518 H(15)C(12)N(1)O(4) 0.0 Chemical derivative 1024 0.0 2-nitrobenzyl@Y 135.032028 135.1201 H(5)C(7)N(1)O(2) 0.0 Chemical derivative 1032 0.0 -Xlink:DMP[140]@Protein N-term 140.094963 140.183 H(12)C(7)N(2)O(1) 0.0 Chemical derivative 1027 0.0 +Xlink:DMP[140]@Protein_N-term 140.094963 140.183 H(12)C(7)N(2)O(1) 0.0 Chemical derivative 1027 0.0 Xlink:DMP[140]@K 140.094963 140.183 H(12)C(7)N(2)O(1) 0.0 Chemical derivative 1027 0.0 -Xlink:EGS[115]@Protein N-term 115.026943 115.0874 H(5)C(4)N(1)O(3) 0.0 Chemical derivative 1028 0.0 +Xlink:EGS[115]@Protein_N-term 115.026943 115.0874 H(5)C(4)N(1)O(3) 0.0 Chemical derivative 1028 0.0 Xlink:EGS[115]@K 115.026943 115.0874 H(5)C(4)N(1)O(3) 0.0 Chemical derivative 1028 0.0 Cys->SecNEM@C 172.992127 172.0203 H(7)C(6)N(1)O(2)S(-1)Se(1) 0.0 Non-standard residue 1033 0.0 Cys->SecNEM:2H(5)@C 178.023511 177.0511 H(2)2H(5)C(6)N(1)O(2)S(-1)Se(1) 0.0 Chemical derivative 1034 0.0 @@ -1571,17 +1571,17 @@ BMP-piperidinol@C 263.131014 263.3337 H(17)C(18)N(1)O(1) 0.0 Chemical derivativ BMP-piperidinol@M 263.131014 263.3337 H(17)C(18)N(1)O(1) 0.0 Chemical derivative 1281 0.0 UgiJoullieProGlyProGly@D 308.148455 308.333 H(20)C(14)N(4)O(4) 0.0 Chemical derivative 1283 0.0 UgiJoullieProGlyProGly@E 308.148455 308.333 H(20)C(14)N(4)O(4) 0.0 Chemical derivative 1283 0.0 -Arg-loss@R^Any C-term -156.101111 -156.1857 H(-12)C(-6)N(-4)O(-1) 0.0 Other 1287 0.0 -Arg@Any N-term 156.101111 156.1857 H(12)C(6)N(4)O(1) 0.0 Other 1288 0.0 +Arg-loss@R^Any_C-term -156.101111 -156.1857 H(-12)C(-6)N(-4)O(-1) 0.0 Other 1287 0.0 +Arg@Any_N-term 156.101111 156.1857 H(12)C(6)N(4)O(1) 0.0 Other 1288 0.0 IMEHex(2)NeuAc(1)@K 688.199683 688.6527 H(40)C(25)N(2)O(18)S(1) 0.0 Other glycosylation 1286 0.0 Butyryl@K 70.041865 70.0898 H(6)C(4)O(1) 0.0 Post-translational 1289 0.0 Dicarbamidomethyl@K 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Artefact 1290 0.0 Dicarbamidomethyl@H 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Artefact 1290 0.0 Dicarbamidomethyl@C 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Artefact 1290 0.0 Dicarbamidomethyl@R 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Artefact 1290 0.0 -Dicarbamidomethyl@Any N-term 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Artefact 1290 0.0 +Dicarbamidomethyl@Any_N-term 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Artefact 1290 0.0 Dimethyl:2H(6)@K 34.068961 34.0901 H(-2)2H(6)C(2) 0.0 Isotopic label 1291 0.0 -Dimethyl:2H(6)@Any N-term 34.068961 34.0901 H(-2)2H(6)C(2) 0.0 Isotopic label 1291 0.0 +Dimethyl:2H(6)@Any_N-term 34.068961 34.0901 H(-2)2H(6)C(2) 0.0 Isotopic label 1291 0.0 Dimethyl:2H(6)@R 34.068961 34.0901 H(-2)2H(6)C(2) 0.0 Isotopic label 1291 0.0 GGQ@K 242.101505 242.2319 H(14)C(9)N(4)O(4) 0.0 Other 1292 0.0 QTGG@K 343.149184 343.3357 H(21)C(13)N(5)O(6) 0.0 Other 1293 0.0 @@ -1591,9 +1591,9 @@ Label:13C(3)@A 3.010064 2.978 C(-3)13C(3) 0.0 Isotopic label 1296 0.0 Label:13C(4)15N(1)@D 5.010454 4.964 C(-4)13C(4)N(-1)15N(1) 0.0 Isotopic label 1298 0.0 Label:2H(10)@L 10.062767 10.0616 H(-10)2H(10) 0.0 Isotopic label 1299 0.0 Label:2H(4)13C(1)@R 5.028462 5.0173 H(-4)2H(4)C(-1)13C(1) 0.0 Isotopic label 1300 0.0 -Lys@Any N-term 128.094963 128.1723 H(12)C(6)N(2)O(1) 0.0 Other 1301 0.0 +Lys@Any_N-term 128.094963 128.1723 H(12)C(6)N(2)O(1) 0.0 Other 1301 0.0 mTRAQ:13C(6)15N(2)@K 148.109162 148.1257 H(12)C(1)13C(6)15N(2)O(1) 0.0 Isotopic label 1302 0.0 -mTRAQ:13C(6)15N(2)@Any N-term 148.109162 148.1257 H(12)C(1)13C(6)15N(2)O(1) 0.0 Isotopic label 1302 0.0 +mTRAQ:13C(6)15N(2)@Any_N-term 148.109162 148.1257 H(12)C(1)13C(6)15N(2)O(1) 0.0 Isotopic label 1302 0.0 mTRAQ:13C(6)15N(2)@Y 148.109162 148.1257 H(12)C(1)13C(6)15N(2)O(1) 0.0 Isotopic label 1302 0.0 mTRAQ:13C(6)15N(2)@H 148.109162 148.1257 H(12)C(1)13C(6)15N(2)O(1) 0.0 Isotopic label 1302 0.0 mTRAQ:13C(6)15N(2)@S 148.109162 148.1257 H(12)C(1)13C(6)15N(2)O(1) 0.0 Isotopic label 1302 0.0 @@ -1606,11 +1606,11 @@ NeuGc@S 307.090331 307.254 H(17)C(11)N(1)O(9) 307.090331 H(17)C(11)N(1)O(9) O-li NeuGc@N 307.090331 307.254 H(17)C(11)N(1)O(9) 307.090331 H(17)C(11)N(1)O(9) N-linked glycosylation 1304 0.5 Propyl@D 42.04695 42.0797 H(6)C(3) 0.0 Chemical derivative 1305 0.0 Propyl@K 42.04695 42.0797 H(6)C(3) 0.0 Isotopic label 1305 0.0 -Propyl@Any N-term 42.04695 42.0797 H(6)C(3) 0.0 Isotopic label 1305 0.0 +Propyl@Any_N-term 42.04695 42.0797 H(6)C(3) 0.0 Isotopic label 1305 0.0 Propyl@E 42.04695 42.0797 H(6)C(3) 0.0 Chemical derivative 1305 0.0 -Propyl@Any C-term 42.04695 42.0797 H(6)C(3) 0.0 Chemical derivative 1305 0.0 -Propyl@Protein C-term 42.04695 42.0797 H(6)C(3) 0.0 Chemical derivative 1305 0.0 -Propyl:2H(6)@Any N-term 48.084611 48.1167 2H(6)C(3) 0.0 Isotopic label 1306 0.0 +Propyl@Any_C-term 42.04695 42.0797 H(6)C(3) 0.0 Chemical derivative 1305 0.0 +Propyl@Protein_C-term 42.04695 42.0797 H(6)C(3) 0.0 Chemical derivative 1305 0.0 +Propyl:2H(6)@Any_N-term 48.084611 48.1167 2H(6)C(3) 0.0 Isotopic label 1306 0.0 Propyl:2H(6)@K 48.084611 48.1167 2H(6)C(3) 0.0 Isotopic label 1306 0.0 Propiophenone@C 132.057515 132.1592 H(8)C(9)O(1) 0.0 Chemical derivative 1310 0.0 Propiophenone@W 132.057515 132.1592 H(8)C(9)O(1) 0.0 Chemical derivative 1310 0.0 @@ -1623,36 +1623,36 @@ PS_Hapten@H 120.021129 120.1055 H(4)C(7)O(2) 0.0 Chemical derivative 1345 0.0 PS_Hapten@C 120.021129 120.1055 H(4)C(7)O(2) 0.0 Chemical derivative 1345 0.0 PS_Hapten@K 120.021129 120.1055 H(4)C(7)O(2) 0.0 Chemical derivative 1345 0.0 Cy3-maleimide@C 753.262796 753.9046 H(45)C(37)N(4)O(9)S(2) 0.0 Chemical derivative 1348 0.0 -Delta:H(6)C(3)O(1)@Protein N-term 58.041865 58.0791 H(6)C(3)O(1) 0.0 Chemical derivative 1312 0.0 +Delta:H(6)C(3)O(1)@Protein_N-term 58.041865 58.0791 H(6)C(3)O(1) 0.0 Chemical derivative 1312 0.0 Delta:H(6)C(3)O(1)@K 58.041865 58.0791 H(6)C(3)O(1) 0.0 Chemical derivative 1312 0.0 Delta:H(6)C(3)O(1)@H 58.041865 58.0791 H(6)C(3)O(1) 0.0 Chemical derivative 1312 0.0 Delta:H(6)C(3)O(1)@C 58.041865 58.0791 H(6)C(3)O(1) 0.0 Chemical derivative 1312 0.0 -Delta:H(8)C(6)O(1)@Protein N-term 96.057515 96.1271 H(8)C(6)O(1) 0.0 Chemical derivative 1313 0.0 +Delta:H(8)C(6)O(1)@Protein_N-term 96.057515 96.1271 H(8)C(6)O(1) 0.0 Chemical derivative 1313 0.0 Delta:H(8)C(6)O(1)@K 96.057515 96.1271 H(8)C(6)O(1) 0.0 Chemical derivative 1313 0.0 biotinAcrolein298@H 298.146347 298.4044 H(22)C(13)N(4)O(2)S(1) 0.0 Chemical derivative 1314 0.0 biotinAcrolein298@K 298.146347 298.4044 H(22)C(13)N(4)O(2)S(1) 0.0 Chemical derivative 1314 0.0 -biotinAcrolein298@Protein N-term 298.146347 298.4044 H(22)C(13)N(4)O(2)S(1) 0.0 Chemical derivative 1314 0.0 +biotinAcrolein298@Protein_N-term 298.146347 298.4044 H(22)C(13)N(4)O(2)S(1) 0.0 Chemical derivative 1314 0.0 biotinAcrolein298@C 298.146347 298.4044 H(22)C(13)N(4)O(2)S(1) 0.0 Chemical derivative 1314 0.0 MM-diphenylpentanone@C 265.146664 265.3496 H(19)C(18)N(1)O(1) 0.0 Chemical derivative 1315 0.0 EHD-diphenylpentanone@M 266.13068 266.3343 H(18)C(18)O(2) 0.0 Chemical derivative 1317 0.0 EHD-diphenylpentanone@C 266.13068 266.3343 H(18)C(18)O(2) 0.0 Chemical derivative 1317 0.0 benzylguanidine@K 132.068748 132.1625 H(8)C(8)N(2) 0.0 Chemical derivative 1349 0.0 -CarboxymethylDMAP@Any N-term 162.079313 162.1885 H(10)C(9)N(2)O(1) 0.0 Chemical derivative 1350 0.0 +CarboxymethylDMAP@Any_N-term 162.079313 162.1885 H(10)C(9)N(2)O(1) 0.0 Chemical derivative 1350 0.0 Biotin:Thermo-21901+2H2O@C 561.246849 561.6489 H(39)C(23)N(5)O(9)S(1) 0.0 Chemical derivative 1320 0.0 DiLeu4plex115@K 145.12 145.1966 H(15)C(7)13C(1)15N(1)18O(1) 0.0 Isotopic label 1321 0.0 -DiLeu4plex115@Any N-term 145.12 145.1966 H(15)C(7)13C(1)15N(1)18O(1) 0.0 Isotopic label 1321 0.0 +DiLeu4plex115@Any_N-term 145.12 145.1966 H(15)C(7)13C(1)15N(1)18O(1) 0.0 Isotopic label 1321 0.0 DiLeu4plex115@Y 145.12 145.1966 H(15)C(7)13C(1)15N(1)18O(1) 0.0 Isotopic label 1321 0.0 -DiLeu4plex@Any N-term 145.132163 145.2229 H(13)2H(2)C(8)N(1)18O(1) 0.0 Isotopic label 1322 0.0 +DiLeu4plex@Any_N-term 145.132163 145.2229 H(13)2H(2)C(8)N(1)18O(1) 0.0 Isotopic label 1322 0.0 DiLeu4plex@K 145.132163 145.2229 H(13)2H(2)C(8)N(1)18O(1) 0.0 Isotopic label 1322 0.0 DiLeu4plex@Y 145.132163 145.2229 H(13)2H(2)C(8)N(1)18O(1) 0.0 Isotopic label 1322 0.0 DiLeu4plex117@K 145.128307 145.2092 H(13)2H(2)C(7)13C(1)15N(1)O(1) 0.0 Isotopic label 1323 0.0 -DiLeu4plex117@Any N-term 145.128307 145.2092 H(13)2H(2)C(7)13C(1)15N(1)O(1) 0.0 Isotopic label 1323 0.0 +DiLeu4plex117@Any_N-term 145.128307 145.2092 H(13)2H(2)C(7)13C(1)15N(1)O(1) 0.0 Isotopic label 1323 0.0 DiLeu4plex117@Y 145.128307 145.2092 H(13)2H(2)C(7)13C(1)15N(1)O(1) 0.0 Isotopic label 1323 0.0 DiLeu4plex118@K 145.140471 145.2354 H(11)2H(4)C(8)N(1)O(1) 0.0 Isotopic label 1324 0.0 -DiLeu4plex118@Any N-term 145.140471 145.2354 H(11)2H(4)C(8)N(1)O(1) 0.0 Isotopic label 1324 0.0 +DiLeu4plex118@Any_N-term 145.140471 145.2354 H(11)2H(4)C(8)N(1)O(1) 0.0 Isotopic label 1324 0.0 DiLeu4plex118@Y 145.140471 145.2354 H(11)2H(4)C(8)N(1)O(1) 0.0 Isotopic label 1324 0.0 Xlink:BuUrBu[213]@K 213.111341 213.2337 H(15)C(9)N(3)O(3) 0.0 Chemical derivative 1887 0.0 -Xlink:BuUrBu[213]@Protein N-term 213.111341 213.2337 H(15)C(9)N(3)O(3) 0.0 Chemical derivative 1887 0.0 +Xlink:BuUrBu[213]@Protein_N-term 213.111341 213.2337 H(15)C(9)N(3)O(3) 0.0 Chemical derivative 1887 0.0 bisANS-sulfonates@S 437.201774 437.5543 H(25)C(32)N(2) 0.0 Chemical derivative 1330 0.0 bisANS-sulfonates@T 437.201774 437.5543 H(25)C(32)N(2) 0.0 Chemical derivative 1330 0.0 bisANS-sulfonates@K 437.201774 437.5543 H(25)C(32)N(2) 0.0 Chemical derivative 1330 0.0 @@ -1691,7 +1691,7 @@ iodoTMT6plex@E 329.226595 329.3825 H(28)C(12)13C(4)N(3)15N(1)O(3) 0.0 Chemical iodoTMT6plex@D 329.226595 329.3825 H(28)C(12)13C(4)N(3)15N(1)O(3) 0.0 Chemical derivative 1342 0.0 iodoTMT6plex@C 329.226595 329.3825 H(28)C(12)13C(4)N(3)15N(1)O(3) 0.0 Chemical derivative 1342 0.0 Label:13C(2)15N(2)@K 4.00078 3.9721 C(-2)13C(2)N(-2)15N(2) 0.0 Isotopic label 1787 0.0 -Phosphogluconoylation@Any N-term 258.014069 258.1199 H(11)C(6)O(9)P(1) 0.0 Post-translational 1344 0.0 +Phosphogluconoylation@Any_N-term 258.014069 258.1199 H(11)C(6)O(9)P(1) 0.0 Post-translational 1344 0.0 Phosphogluconoylation@K 258.014069 258.1199 H(11)C(6)O(9)P(1) 0.0 Post-translational 1344 0.0 Methyl:2H(3)+Acetyl:2H(3)@K 62.063875 62.1002 H(-2)2H(6)C(3)O(1) 0.0 Isotopic label 1368 0.0 dHex(1)Hex(1)@T 308.110732 308.2818 H(20)C(12)O(9) 308.110732 H(20)C(12)O(9) O-linked glycosylation 1367 0.5 @@ -1703,7 +1703,7 @@ Label:2H(3)+Oxidation@M 19.013745 19.0179 H(-3)2H(3)O(1) 0.0 Isotopic label 137 Trimethyl:2H(9)@R 51.103441 51.1352 H(-3)2H(9)C(3) 0.0 Isotopic label 1371 0.0 Trimethyl:2H(9)@K 51.103441 51.1352 H(-3)2H(9)C(3) 0.0 Isotopic label 1371 0.0 Acetyl:13C(2)@K 44.017274 44.022 H(2)13C(2)O(1) 0.0 Isotopic label 1372 0.0 -Acetyl:13C(2)@Protein N-term 44.017274 44.022 H(2)13C(2)O(1) 0.0 Isotopic label 1372 0.0 +Acetyl:13C(2)@Protein_N-term 44.017274 44.022 H(2)13C(2)O(1) 0.0 Isotopic label 1372 0.0 dHex(1)Hex(2)@T 470.163556 470.4224 H(30)C(18)O(14) 470.163556 H(30)C(18)O(14) O-linked glycosylation 1375 0.5 dHex(1)Hex(2)@S 470.163556 470.4224 H(30)C(18)O(14) 470.163556 H(30)C(18)O(14) O-linked glycosylation 1375 0.5 dHex(1)Hex(3)@T 632.216379 632.563 H(40)C(24)O(19) 632.216379 H(40)C(24)O(19) O-linked glycosylation 1376 0.5 @@ -1725,31 +1725,31 @@ Hydroxamic_acid@D 15.010899 15.0146 H(1)N(1) 0.0 Artefact 1385 0.0 Oxidation+NEM@C 141.042593 141.1247 H(7)C(6)N(1)O(3) 0.0 Chemical derivative 1390 0.0 NHS-fluorescein@K 471.131802 471.4581 H(21)C(27)N(1)O(7) 0.0 Chemical derivative 1391 0.0 DiART6plex@Y 217.162932 217.2527 H(20)C(7)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 1392 0.0 -DiART6plex@Protein N-term 217.162932 217.2527 H(20)C(7)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 1392 0.0 -DiART6plex@Any N-term 217.162932 217.2527 H(20)C(7)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 1392 0.0 +DiART6plex@Protein_N-term 217.162932 217.2527 H(20)C(7)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 1392 0.0 +DiART6plex@Any_N-term 217.162932 217.2527 H(20)C(7)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 1392 0.0 DiART6plex@K 217.162932 217.2527 H(20)C(7)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 1392 0.0 DiART6plex115@K 217.156612 217.2535 H(20)C(8)13C(3)15N(2)O(2) 0.0 Isotopic label 1393 0.0 -DiART6plex115@Any N-term 217.156612 217.2535 H(20)C(8)13C(3)15N(2)O(2) 0.0 Isotopic label 1393 0.0 -DiART6plex115@Protein N-term 217.156612 217.2535 H(20)C(8)13C(3)15N(2)O(2) 0.0 Isotopic label 1393 0.0 +DiART6plex115@Any_N-term 217.156612 217.2535 H(20)C(8)13C(3)15N(2)O(2) 0.0 Isotopic label 1393 0.0 +DiART6plex115@Protein_N-term 217.156612 217.2535 H(20)C(8)13C(3)15N(2)O(2) 0.0 Isotopic label 1393 0.0 DiART6plex115@Y 217.156612 217.2535 H(20)C(8)13C(3)15N(2)O(2) 0.0 Isotopic label 1393 0.0 DiART6plex116/119@Y 217.168776 217.2797 H(18)2H(2)C(9)13C(2)N(1)15N(1)O(2) 0.0 Isotopic label 1394 0.0 -DiART6plex116/119@Protein N-term 217.168776 217.2797 H(18)2H(2)C(9)13C(2)N(1)15N(1)O(2) 0.0 Isotopic label 1394 0.0 +DiART6plex116/119@Protein_N-term 217.168776 217.2797 H(18)2H(2)C(9)13C(2)N(1)15N(1)O(2) 0.0 Isotopic label 1394 0.0 DiART6plex116/119@K 217.168776 217.2797 H(18)2H(2)C(9)13C(2)N(1)15N(1)O(2) 0.0 Isotopic label 1394 0.0 -DiART6plex116/119@Any N-term 217.168776 217.2797 H(18)2H(2)C(9)13C(2)N(1)15N(1)O(2) 0.0 Isotopic label 1394 0.0 +DiART6plex116/119@Any_N-term 217.168776 217.2797 H(18)2H(2)C(9)13C(2)N(1)15N(1)O(2) 0.0 Isotopic label 1394 0.0 DiART6plex117@K 217.162456 217.2805 H(18)2H(2)C(10)13C(1)15N(2)O(2) 0.0 Isotopic label 1395 0.0 -DiART6plex117@Any N-term 217.162456 217.2805 H(18)2H(2)C(10)13C(1)15N(2)O(2) 0.0 Isotopic label 1395 0.0 -DiART6plex117@Protein N-term 217.162456 217.2805 H(18)2H(2)C(10)13C(1)15N(2)O(2) 0.0 Isotopic label 1395 0.0 +DiART6plex117@Any_N-term 217.162456 217.2805 H(18)2H(2)C(10)13C(1)15N(2)O(2) 0.0 Isotopic label 1395 0.0 +DiART6plex117@Protein_N-term 217.162456 217.2805 H(18)2H(2)C(10)13C(1)15N(2)O(2) 0.0 Isotopic label 1395 0.0 DiART6plex117@Y 217.162456 217.2805 H(18)2H(2)C(10)13C(1)15N(2)O(2) 0.0 Isotopic label 1395 0.0 DiART6plex118@K 217.175096 217.279 H(18)2H(2)C(8)13C(3)N(2)O(2) 0.0 Isotopic label 1396 0.0 -DiART6plex118@Any N-term 217.175096 217.279 H(18)2H(2)C(8)13C(3)N(2)O(2) 0.0 Isotopic label 1396 0.0 -DiART6plex118@Protein N-term 217.175096 217.279 H(18)2H(2)C(8)13C(3)N(2)O(2) 0.0 Isotopic label 1396 0.0 +DiART6plex118@Any_N-term 217.175096 217.279 H(18)2H(2)C(8)13C(3)N(2)O(2) 0.0 Isotopic label 1396 0.0 +DiART6plex118@Protein_N-term 217.175096 217.279 H(18)2H(2)C(8)13C(3)N(2)O(2) 0.0 Isotopic label 1396 0.0 DiART6plex118@Y 217.175096 217.279 H(18)2H(2)C(8)13C(3)N(2)O(2) 0.0 Isotopic label 1396 0.0 Iodoacetanilide@K 133.052764 133.1473 H(7)C(8)N(1)O(1) 0.0 Artefact 1397 0.0 Iodoacetanilide@C 133.052764 133.1473 H(7)C(8)N(1)O(1) 0.0 Chemical derivative 1397 0.0 -Iodoacetanilide@Any N-term 133.052764 133.1473 H(7)C(8)N(1)O(1) 0.0 Artefact 1397 0.0 +Iodoacetanilide@Any_N-term 133.052764 133.1473 H(7)C(8)N(1)O(1) 0.0 Artefact 1397 0.0 Iodoacetanilide:13C(6)@K 139.072893 139.1032 H(7)C(2)13C(6)N(1)O(1) 0.0 Artefact 1398 0.0 Iodoacetanilide:13C(6)@C 139.072893 139.1032 H(7)C(2)13C(6)N(1)O(1) 0.0 Chemical derivative 1398 0.0 -Iodoacetanilide:13C(6)@Any N-term 139.072893 139.1032 H(7)C(2)13C(6)N(1)O(1) 0.0 Artefact 1398 0.0 +Iodoacetanilide:13C(6)@Any_N-term 139.072893 139.1032 H(7)C(2)13C(6)N(1)O(1) 0.0 Artefact 1398 0.0 Dap-DSP@K 364.076278 364.4377 H(20)C(13)N(2)O(6)S(2) 0.0 Chemical derivative 1399 0.0 Dap-DSP@E 364.076278 364.4377 H(20)C(13)N(2)O(6)S(2) 0.0 Non-standard residue 1399 0.0 Dap-DSP@A 364.076278 364.4377 H(20)C(13)N(2)O(6)S(2) 0.0 Non-standard residue 1399 0.0 @@ -1769,11 +1769,11 @@ PhosphoHex(2)@T 404.071978 404.2611 H(21)C(12)O(13)P(1) 404.071978 H(21)C(12)O(1 PhosphoHex(2)@S 404.071978 404.2611 H(21)C(12)O(13)P(1) 404.071978 H(21)C(12)O(13)P(1) O-linked glycosylation 1413 0.5 Trimethyl:13C(3)2H(9)@K 54.113505 54.1132 H(-3)2H(9)13C(3) 0.0 Isotopic label 1414 0.0 Trimethyl:13C(3)2H(9)@R 54.113505 54.1132 H(-3)2H(9)13C(3) 0.0 Isotopic label 1414 0.0 -15N-oxobutanoic@S^Protein N-term -18.023584 -18.0239 H(-3)15N(-1) 0.0 Post-translational 1419 0.0 -15N-oxobutanoic@C^Any N-term -18.023584 -18.0239 H(-3)15N(-1) 0.0 Artefact 1419 0.0 -15N-oxobutanoic@T^Protein N-term -18.023584 -18.0239 H(-3)15N(-1) 0.0 Post-translational 1419 0.0 +15N-oxobutanoic@S^Protein_N-term -18.023584 -18.0239 H(-3)15N(-1) 0.0 Post-translational 1419 0.0 +15N-oxobutanoic@C^Any_N-term -18.023584 -18.0239 H(-3)15N(-1) 0.0 Artefact 1419 0.0 +15N-oxobutanoic@T^Protein_N-term -18.023584 -18.0239 H(-3)15N(-1) 0.0 Post-translational 1419 0.0 spermidine@Q 128.131349 128.2153 H(16)C(7)N(2) 0.0 Chemical derivative 1421 0.0 -Biotin:Thermo-21330@Any N-term 473.219571 473.5835 H(35)C(21)N(3)O(7)S(1) 0.0 Chemical derivative 1423 0.0 +Biotin:Thermo-21330@Any_N-term 473.219571 473.5835 H(35)C(21)N(3)O(7)S(1) 0.0 Chemical derivative 1423 0.0 Biotin:Thermo-21330@K 473.219571 473.5835 H(35)C(21)N(3)O(7)S(1) 0.0 Chemical derivative 1423 0.0 Hex(1)Pent(2)@T 426.137341 426.3698 H(26)C(16)O(13) 426.137341 H(26)C(16)O(13) O-linked glycosylation 1428 0.5 Hex(1)Pent(2)@S 426.137341 426.3698 H(26)C(16)O(13) 426.137341 H(26)C(16)O(13) O-linked glycosylation 1428 0.5 @@ -1803,7 +1803,7 @@ Hex(1)HexNAc(1)dHex(1)Me(1)@T 525.205755 525.5009 H(35)C(21)N(1)O(14) 525.205755 Hex(1)HexNAc(1)dHex(1)Me(1)@S 525.205755 525.5009 H(35)C(21)N(1)O(14) 525.205755 H(35)C(21)N(1)O(14) O-linked glycosylation 1436 0.5 Hex(1)HexNAc(1)dHex(1)Me(2)@T 539.221405 539.5275 H(37)C(22)N(1)O(14) 539.221405 H(37)C(22)N(1)O(14) O-linked glycosylation 1437 0.5 Hex(1)HexNAc(1)dHex(1)Me(2)@S 539.221405 539.5275 H(37)C(22)N(1)O(14) 539.221405 H(37)C(22)N(1)O(14) O-linked glycosylation 1437 0.5 -Xlink:DSS[155]@Protein N-term 155.094629 155.1943 H(13)C(8)N(1)O(2) 0.0 Chemical derivative 1789 0.0 +Xlink:DSS[155]@Protein_N-term 155.094629 155.1943 H(13)C(8)N(1)O(2) 0.0 Chemical derivative 1789 0.0 Xlink:DSS[155]@K 155.094629 155.1943 H(13)C(8)N(1)O(2) 0.0 Chemical derivative 1789 0.0 Hex(2)HexNAc(1)@N 527.18502 527.4737 H(33)C(20)N(1)O(15) 527.18502 H(33)C(20)N(1)O(15) N-linked glycosylation 1438 0.5 Hex(2)HexNAc(1)@T 527.18502 527.4737 H(33)C(20)N(1)O(15) 527.18502 H(33)C(20)N(1)O(15) O-linked glycosylation 1438 0.5 @@ -2407,25 +2407,25 @@ Fluorescein-tyramine@Y 493.116152 493.4637 H(19)C(29)N(1)O(7) 0.0 Chemical deri dHex(1)Hex(7)HexNAc(4)@N 2092.745164 2093.8955 H(132)C(80)N(4)O(59) 0.0 N-linked glycosylation 1840 0.0 betaFNA@C 454.210387 454.5155 H(30)C(25)N(2)O(6) 0.0 Chemical derivative 1839 0.0 betaFNA@K 454.210387 454.5155 H(30)C(25)N(2)O(6) 0.0 Chemical derivative 1839 0.0 -Brij58@Any N-term 224.250401 224.4253 H(32)C(16) 0.0 Other 1838 0.0 -Brij35@Any N-term 168.187801 168.319 H(24)C(12) 0.0 Other 1837 0.0 -Triton@Any N-term 188.156501 188.3086 H(20)C(14) 0.0 Other 1836 0.0 -Triton@Any C-term 188.156501 188.3086 H(20)C(14) 0.0 Other 1836 0.0 -Tween80@Any C-term 263.237491 263.4381 H(31)C(18)O(1) 0.0 Other 1835 0.0 -Tween20@Any N-term 165.164326 165.2951 H(21)C(12) 0.0 Other 1834 0.0 +Brij58@Any_N-term 224.250401 224.4253 H(32)C(16) 0.0 Other 1838 0.0 +Brij35@Any_N-term 168.187801 168.319 H(24)C(12) 0.0 Other 1837 0.0 +Triton@Any_N-term 188.156501 188.3086 H(20)C(14) 0.0 Other 1836 0.0 +Triton@Any_C-term 188.156501 188.3086 H(20)C(14) 0.0 Other 1836 0.0 +Tween80@Any_C-term 263.237491 263.4381 H(31)C(18)O(1) 0.0 Other 1835 0.0 +Tween20@Any_N-term 165.164326 165.2951 H(21)C(12) 0.0 Other 1834 0.0 Tris@N 104.071154 104.1277 H(10)C(4)N(1)O(2) 0.0 Artefact 1831 0.0 Biotin-tyramide@Y 361.146012 361.4585 H(23)C(18)N(3)O(3)S(1) 0.0 Chemical derivative 1830 0.0 LRGG+dimethyl@K 411.259403 411.4991 H(33)C(18)N(7)O(4) 0.0 Post-translational 1829 0.0 -RNPXL@R^Any N-term 324.035867 324.1813 H(13)C(9)N(2)O(9)P(1) 324.035867 H(13)C(9)N(2)O(9)P(1) Other 1825 0.5 -RNPXL@K^Any N-term 324.035867 324.1813 H(13)C(9)N(2)O(9)P(1) 324.035867 H(13)C(9)N(2)O(9)P(1) Other 1825 0.5 +RNPXL@R^Any_N-term 324.035867 324.1813 H(13)C(9)N(2)O(9)P(1) 324.035867 H(13)C(9)N(2)O(9)P(1) Other 1825 0.5 +RNPXL@K^Any_N-term 324.035867 324.1813 H(13)C(9)N(2)O(9)P(1) 324.035867 H(13)C(9)N(2)O(9)P(1) Other 1825 0.5 GEE@Q 86.036779 86.0892 H(6)C(4)O(2) 0.0 Chemical derivative 1824 0.0 -Glu->pyro-Glu+Methyl@E^Any N-term -3.994915 -3.9887 C(1)O(-1) 0.0 Artefact 1826 0.0 -Glu->pyro-Glu+Methyl:2H(2)13C(1)@E^Any N-term -0.979006 -0.9837 H(-2)2H(2)13C(1)O(-1) 0.0 Artefact 1827 0.0 +Glu->pyro-Glu+Methyl@E^Any_N-term -3.994915 -3.9887 C(1)O(-1) 0.0 Artefact 1826 0.0 +Glu->pyro-Glu+Methyl:2H(2)13C(1)@E^Any_N-term -0.979006 -0.9837 H(-2)2H(2)13C(1)O(-1) 0.0 Artefact 1827 0.0 LRGG+methyl@K 397.243753 397.4725 H(31)C(17)N(7)O(4) 0.0 Post-translational 1828 0.0 -NP40@Any N-term 220.182715 220.3505 H(24)C(15)O(1) 0.0 Other 1833 0.0 +NP40@Any_N-term 220.182715 220.3505 H(24)C(15)O(1) 0.0 Other 1833 0.0 IASD@C 452.034807 452.4582 H(16)C(18)N(2)O(8)S(2) 0.0 Chemical derivative 1832 0.0 Biotin:Thermo-21328@K 389.090154 389.5564 H(23)C(15)N(3)O(3)S(3) 0.0 Chemical derivative 1841 0.0 -Biotin:Thermo-21328@Any N-term 389.090154 389.5564 H(23)C(15)N(3)O(3)S(3) 0.0 Chemical derivative 1841 0.0 +Biotin:Thermo-21328@Any_N-term 389.090154 389.5564 H(23)C(15)N(3)O(3)S(3) 0.0 Chemical derivative 1841 0.0 PhosphoCytidine@Y 305.041287 305.1812 H(12)C(9)N(3)O(7)P(1) 0.0 Post-translational 1843 0.0 PhosphoCytidine@T 305.041287 305.1812 H(12)C(9)N(3)O(7)P(1) 0.0 Post-translational 1843 0.0 PhosphoCytidine@S 305.041287 305.1812 H(12)C(9)N(3)O(7)P(1) 0.0 Post-translational 1843 0.0 @@ -2436,65 +2436,65 @@ hydroxyisobutyryl@K 86.036779 86.0892 H(6)C(4)O(2) 0.0 Post-translational 1849 MeMePhosphorothioate@S 107.979873 108.0993 H(5)C(2)O(1)P(1)S(1) 0.0 Chemical derivative 1868 0.0 Cation:Fe[III]@D 52.911464 52.8212 H(-3)Fe(1) 0.0 Artefact 1870 0.0 Cation:Fe[III]@E 52.911464 52.8212 H(-3)Fe(1) 0.0 Artefact 1870 0.0 -Cation:Fe[III]@Any C-term 52.911464 52.8212 H(-3)Fe(1) 0.0 Artefact 1870 0.0 +Cation:Fe[III]@Any_C-term 52.911464 52.8212 H(-3)Fe(1) 0.0 Artefact 1870 0.0 DTT@C 151.996571 152.2351 H(8)C(4)O(2)S(2) 0.0 Artefact 1871 0.0 DYn-2@C 161.09664 161.2203 H(13)C(11)O(1) 0.0 Other 1872 0.0 Xlink:DSSO[176]@K 176.01433 176.1903 H(8)C(6)O(4)S(1) 0.0 Chemical derivative 1878 0.0 -Xlink:DSSO[176]@Protein N-term 176.01433 176.1903 H(8)C(6)O(4)S(1) 0.0 Chemical derivative 1878 0.0 +Xlink:DSSO[176]@Protein_N-term 176.01433 176.1903 H(8)C(6)O(4)S(1) 0.0 Chemical derivative 1878 0.0 MesitylOxide@K 98.073165 98.143 H(10)C(6)O(1) 0.0 Chemical derivative 1873 0.0 MesitylOxide@H 98.073165 98.143 H(10)C(6)O(1) 0.0 Chemical derivative 1873 0.0 -MesitylOxide@Protein N-term 98.073165 98.143 H(10)C(6)O(1) 0.0 Chemical derivative 1873 0.0 +MesitylOxide@Protein_N-term 98.073165 98.143 H(10)C(6)O(1) 0.0 Chemical derivative 1873 0.0 Xlink:DSS[259]@K 259.141973 259.2988 H(21)C(12)N(1)O(5) 0.0 Chemical derivative 1877 0.0 -Xlink:DSS[259]@Protein N-term 259.141973 259.2988 H(21)C(12)N(1)O(5) 0.0 Chemical derivative 1877 0.0 +Xlink:DSS[259]@Protein_N-term 259.141973 259.2988 H(21)C(12)N(1)O(5) 0.0 Chemical derivative 1877 0.0 methylol@Y 30.010565 30.026 H(2)C(1)O(1) 0.0 Chemical derivative 1875 0.0 methylol@W 30.010565 30.026 H(2)C(1)O(1) 0.0 Chemical derivative 1875 0.0 methylol@K 30.010565 30.026 H(2)C(1)O(1) 0.0 Chemical derivative 1875 0.0 Xlink:DSSO[175]@K 175.030314 175.2056 H(9)C(6)N(1)O(3)S(1) 0.0 Chemical derivative 1879 0.0 -Xlink:DSSO[175]@Protein N-term 175.030314 175.2056 H(9)C(6)N(1)O(3)S(1) 0.0 Chemical derivative 1879 0.0 +Xlink:DSSO[175]@Protein_N-term 175.030314 175.2056 H(9)C(6)N(1)O(3)S(1) 0.0 Chemical derivative 1879 0.0 Xlink:DSSO[279]@K 279.077658 279.3101 H(17)C(10)N(1)O(6)S(1) 0.0 Chemical derivative 1880 0.0 -Xlink:DSSO[279]@Protein N-term 279.077658 279.3101 H(17)C(10)N(1)O(6)S(1) 0.0 Chemical derivative 1880 0.0 -Xlink:DSSO[54]@Protein N-term 54.010565 54.0474 H(2)C(3)O(1) 0.0 Chemical derivative 1881 0.0 +Xlink:DSSO[279]@Protein_N-term 279.077658 279.3101 H(17)C(10)N(1)O(6)S(1) 0.0 Chemical derivative 1880 0.0 +Xlink:DSSO[54]@Protein_N-term 54.010565 54.0474 H(2)C(3)O(1) 0.0 Chemical derivative 1881 0.0 Xlink:DSSO[54]@K 54.010565 54.0474 H(2)C(3)O(1) 0.0 Chemical derivative 1881 0.0 Xlink:DSSO[86]@K 85.982635 86.1124 H(2)C(3)O(1)S(1) 0.0 Chemical derivative 1882 0.0 -Xlink:DSSO[86]@Protein N-term 85.982635 86.1124 H(2)C(3)O(1)S(1) 0.0 Chemical derivative 1882 0.0 +Xlink:DSSO[86]@Protein_N-term 85.982635 86.1124 H(2)C(3)O(1)S(1) 0.0 Chemical derivative 1882 0.0 Xlink:DSSO[104]@K 103.9932 104.1277 H(4)C(3)O(2)S(1) 0.0 Chemical derivative 1883 0.0 -Xlink:DSSO[104]@Protein N-term 103.9932 104.1277 H(4)C(3)O(2)S(1) 0.0 Chemical derivative 1883 0.0 +Xlink:DSSO[104]@Protein_N-term 103.9932 104.1277 H(4)C(3)O(2)S(1) 0.0 Chemical derivative 1883 0.0 Xlink:BuUrBu[111]@K 111.032028 111.0987 H(5)C(5)N(1)O(2) 0.0 Chemical derivative 1885 0.0 -Xlink:BuUrBu[111]@Protein N-term 111.032028 111.0987 H(5)C(5)N(1)O(2) 0.0 Chemical derivative 1885 0.0 +Xlink:BuUrBu[111]@Protein_N-term 111.032028 111.0987 H(5)C(5)N(1)O(2) 0.0 Chemical derivative 1885 0.0 Xlink:BuUrBu[85]@K 85.052764 85.1045 H(7)C(4)N(1)O(1) 0.0 Chemical derivative 1886 0.0 -Xlink:BuUrBu[85]@Protein N-term 85.052764 85.1045 H(7)C(4)N(1)O(1) 0.0 Chemical derivative 1886 0.0 -Xlink:BuUrBu[214]@Protein N-term 214.095357 214.2185 H(14)C(9)N(2)O(4) 0.0 Chemical derivative 1888 0.0 +Xlink:BuUrBu[85]@Protein_N-term 85.052764 85.1045 H(7)C(4)N(1)O(1) 0.0 Chemical derivative 1886 0.0 +Xlink:BuUrBu[214]@Protein_N-term 214.095357 214.2185 H(14)C(9)N(2)O(4) 0.0 Chemical derivative 1888 0.0 Xlink:BuUrBu[214]@K 214.095357 214.2185 H(14)C(9)N(2)O(4) 0.0 Chemical derivative 1888 0.0 -Xlink:BuUrBu[317]@Protein N-term 317.158686 317.3382 H(23)C(13)N(3)O(6) 0.0 Chemical derivative 1889 0.0 +Xlink:BuUrBu[317]@Protein_N-term 317.158686 317.3382 H(23)C(13)N(3)O(6) 0.0 Chemical derivative 1889 0.0 Xlink:BuUrBu[317]@K 317.158686 317.3382 H(23)C(13)N(3)O(6) 0.0 Chemical derivative 1889 0.0 Xlink:DSSO[158]@K 158.003765 158.175 H(6)C(6)O(3)S(1) 0.0 Chemical derivative 1896 0.0 -Xlink:DSSO[158]@Protein N-term 158.003765 158.175 H(6)C(6)O(3)S(1) 0.0 Chemical derivative 1896 0.0 +Xlink:DSSO[158]@Protein_N-term 158.003765 158.175 H(6)C(6)O(3)S(1) 0.0 Chemical derivative 1896 0.0 Xlink:DSS[138]@K 138.06808 138.1638 H(10)C(8)O(2) 0.0 Chemical derivative 1898 0.0 -Xlink:DSS[138]@Protein N-term 138.06808 138.1638 H(10)C(8)O(2) 0.0 Chemical derivative 1898 0.0 -Xlink:BuUrBu[196]@Protein N-term 196.084792 196.2032 H(12)C(9)N(2)O(3) 0.0 Chemical derivative 1899 0.0 +Xlink:DSS[138]@Protein_N-term 138.06808 138.1638 H(10)C(8)O(2) 0.0 Chemical derivative 1898 0.0 +Xlink:BuUrBu[196]@Protein_N-term 196.084792 196.2032 H(12)C(9)N(2)O(3) 0.0 Chemical derivative 1899 0.0 Xlink:BuUrBu[196]@K 196.084792 196.2032 H(12)C(9)N(2)O(3) 0.0 Chemical derivative 1899 0.0 Xlink:DTBP[172]@K 172.01289 172.2711 H(8)C(6)N(2)S(2) 0.0 Chemical derivative 1900 0.0 -Xlink:DTBP[172]@Protein N-term 172.01289 172.2711 H(8)C(6)N(2)S(2) 0.0 Chemical derivative 1900 0.0 +Xlink:DTBP[172]@Protein_N-term 172.01289 172.2711 H(8)C(6)N(2)S(2) 0.0 Chemical derivative 1900 0.0 Xlink:DST[114]@K 113.995309 114.0563 H(2)C(4)O(4) 0.0 Chemical derivative 1901 0.0 -Xlink:DST[114]@Protein N-term 113.995309 114.0563 H(2)C(4)O(4) 0.0 Chemical derivative 1901 0.0 +Xlink:DST[114]@Protein_N-term 113.995309 114.0563 H(2)C(4)O(4) 0.0 Chemical derivative 1901 0.0 Xlink:DTSSP[174]@K 173.980921 174.2406 H(6)C(6)O(2)S(2) 0.0 Chemical derivative 1902 0.0 -Xlink:DTSSP[174]@Protein N-term 173.980921 174.2406 H(6)C(6)O(2)S(2) 0.0 Chemical derivative 1902 0.0 +Xlink:DTSSP[174]@Protein_N-term 173.980921 174.2406 H(6)C(6)O(2)S(2) 0.0 Chemical derivative 1902 0.0 Xlink:SMCC[219]@C 219.089543 219.2365 H(13)C(12)N(1)O(3) 0.0 Chemical derivative 1903 0.0 Xlink:SMCC[219]@K 219.089543 219.2365 H(13)C(12)N(1)O(3) 0.0 Chemical derivative 1903 0.0 -Xlink:SMCC[219]@Protein N-term 219.089543 219.2365 H(13)C(12)N(1)O(3) 0.0 Chemical derivative 1903 0.0 +Xlink:SMCC[219]@Protein_N-term 219.089543 219.2365 H(13)C(12)N(1)O(3) 0.0 Chemical derivative 1903 0.0 Cation:Al[III]@D 23.958063 23.9577 H(-3)Al(1) 0.0 Artefact 1910 0.0 Cation:Al[III]@E 23.958063 23.9577 H(-3)Al(1) 0.0 Artefact 1910 0.0 -Cation:Al[III]@Any C-term 23.958063 23.9577 H(-3)Al(1) 0.0 Artefact 1910 0.0 -Xlink:BS2G[113]@Protein N-term 113.047679 113.1146 H(7)C(5)N(1)O(2) 0.0 Chemical derivative 1906 0.0 +Cation:Al[III]@Any_C-term 23.958063 23.9577 H(-3)Al(1) 0.0 Artefact 1910 0.0 +Xlink:BS2G[113]@Protein_N-term 113.047679 113.1146 H(7)C(5)N(1)O(2) 0.0 Chemical derivative 1906 0.0 Xlink:BS2G[113]@K 113.047679 113.1146 H(7)C(5)N(1)O(2) 0.0 Chemical derivative 1906 0.0 -Xlink:BS2G[114]@Protein N-term 114.031694 114.0993 H(6)C(5)O(3) 0.0 Chemical derivative 1907 0.0 +Xlink:BS2G[114]@Protein_N-term 114.031694 114.0993 H(6)C(5)O(3) 0.0 Chemical derivative 1907 0.0 Xlink:BS2G[114]@K 114.031694 114.0993 H(6)C(5)O(3) 0.0 Chemical derivative 1907 0.0 -Xlink:BS2G[217]@Protein N-term 217.095023 217.2191 H(15)C(9)N(1)O(5) 0.0 Chemical derivative 1908 0.0 +Xlink:BS2G[217]@Protein_N-term 217.095023 217.2191 H(15)C(9)N(1)O(5) 0.0 Chemical derivative 1908 0.0 Xlink:BS2G[217]@K 217.095023 217.2191 H(15)C(9)N(1)O(5) 0.0 Chemical derivative 1908 0.0 Xlink:DMP[139]@K 139.110947 139.1982 H(13)C(7)N(3) 0.0 Chemical derivative 1911 0.0 -Xlink:DMP[139]@Protein N-term 139.110947 139.1982 H(13)C(7)N(3) 0.0 Chemical derivative 1911 0.0 +Xlink:DMP[139]@Protein_N-term 139.110947 139.1982 H(13)C(7)N(3) 0.0 Chemical derivative 1911 0.0 Xlink:DMP[122]@K 122.084398 122.1677 H(10)C(7)N(2) 0.0 Chemical derivative 1912 0.0 -Xlink:DMP[122]@Protein N-term 122.084398 122.1677 H(10)C(7)N(2) 0.0 Chemical derivative 1912 0.0 +Xlink:DMP[122]@Protein_N-term 122.084398 122.1677 H(10)C(7)N(2) 0.0 Chemical derivative 1912 0.0 glyoxalAGE@R 21.98435 22.0055 H(-2)C(2) 0.0 Post-translational 1913 0.0 Met->AspSA@M -32.008456 -32.1081 H(-4)C(-1)O(1)S(-1) 0.0 Chemical derivative 1914 0.0 Decarboxylation@D -30.010565 -30.026 H(-2)C(-1)O(-1) 0.0 Chemical derivative 1915 0.0 @@ -2589,44 +2589,44 @@ Hex(5)HexNAc(4)NeuAc(1)Ac(1)@N 1955.687589 1956.7643 H(121)C(75)N(5)O(54) 1955.6 Hex(3)HexNAc(3)NeuAc(3)@S 1968.682838 1969.7631 H(120)C(75)N(6)O(54) 1968.682838 H(120)C(75)N(6)O(54) O-linked glycosylation 1968 0.5 Hex(3)HexNAc(3)NeuAc(3)@T 1968.682838 1969.7631 H(120)C(75)N(6)O(54) 1968.682838 H(120)C(75)N(6)O(54) O-linked glycosylation 1968 0.5 Hex(5)HexNAc(4)NeuAc(1)Ac(2)@N 1997.698154 1998.801 H(123)C(77)N(5)O(55) 1997.698154 H(123)C(77)N(5)O(55) N-linked glycosylation 1969 0.5 -Unknown:162@Any C-term 162.125595 162.2267 H(18)C(8)O(3) 0.0 Artefact 1970 0.0 +Unknown:162@Any_C-term 162.125595 162.2267 H(18)C(8)O(3) 0.0 Artefact 1970 0.0 Unknown:162@E 162.125595 162.2267 H(18)C(8)O(3) 0.0 Artefact 1970 0.0 Unknown:162@D 162.125595 162.2267 H(18)C(8)O(3) 0.0 Artefact 1970 0.0 -Unknown:162@Any N-term 162.125595 162.2267 H(18)C(8)O(3) 0.0 Artefact 1970 0.0 +Unknown:162@Any_N-term 162.125595 162.2267 H(18)C(8)O(3) 0.0 Artefact 1970 0.0 Unknown:177@D 176.744957 176.4788 H(-7)O(1)Fe(3) 0.0 Artefact 1971 0.0 Unknown:177@E 176.744957 176.4788 H(-7)O(1)Fe(3) 0.0 Artefact 1971 0.0 -Unknown:177@Any C-term 176.744957 176.4788 H(-7)O(1)Fe(3) 0.0 Artefact 1971 0.0 -Unknown:177@Any N-term 176.744957 176.4788 H(-7)O(1)Fe(3) 0.0 Artefact 1971 0.0 +Unknown:177@Any_C-term 176.744957 176.4788 H(-7)O(1)Fe(3) 0.0 Artefact 1971 0.0 +Unknown:177@Any_N-term 176.744957 176.4788 H(-7)O(1)Fe(3) 0.0 Artefact 1971 0.0 Unknown:210@D 210.16198 210.3126 H(22)C(13)O(2) 0.0 Artefact 1972 0.0 Unknown:210@E 210.16198 210.3126 H(22)C(13)O(2) 0.0 Artefact 1972 0.0 -Unknown:210@Any C-term 210.16198 210.3126 H(22)C(13)O(2) 0.0 Artefact 1972 0.0 -Unknown:210@Any N-term 210.16198 210.3126 H(22)C(13)O(2) 0.0 Artefact 1972 0.0 +Unknown:210@Any_C-term 210.16198 210.3126 H(22)C(13)O(2) 0.0 Artefact 1972 0.0 +Unknown:210@Any_N-term 210.16198 210.3126 H(22)C(13)O(2) 0.0 Artefact 1972 0.0 Unknown:216@D 216.099774 216.231 H(16)C(10)O(5) 0.0 Artefact 1973 0.0 Unknown:216@E 216.099774 216.231 H(16)C(10)O(5) 0.0 Artefact 1973 0.0 -Unknown:216@Any C-term 216.099774 216.231 H(16)C(10)O(5) 0.0 Artefact 1973 0.0 -Unknown:216@Any N-term 216.099774 216.231 H(16)C(10)O(5) 0.0 Artefact 1973 0.0 +Unknown:216@Any_C-term 216.099774 216.231 H(16)C(10)O(5) 0.0 Artefact 1973 0.0 +Unknown:216@Any_N-term 216.099774 216.231 H(16)C(10)O(5) 0.0 Artefact 1973 0.0 Unknown:234@D 234.073953 234.2033 H(14)C(9)O(7) 0.0 Artefact 1974 0.0 Unknown:234@E 234.073953 234.2033 H(14)C(9)O(7) 0.0 Artefact 1974 0.0 -Unknown:234@Any C-term 234.073953 234.2033 H(14)C(9)O(7) 0.0 Artefact 1974 0.0 -Unknown:234@Any N-term 234.073953 234.2033 H(14)C(9)O(7) 0.0 Artefact 1974 0.0 +Unknown:234@Any_C-term 234.073953 234.2033 H(14)C(9)O(7) 0.0 Artefact 1974 0.0 +Unknown:234@Any_N-term 234.073953 234.2033 H(14)C(9)O(7) 0.0 Artefact 1974 0.0 Unknown:248@D 248.19876 248.359 H(28)C(13)O(4) 0.0 Artefact 1975 0.0 Unknown:248@E 248.19876 248.359 H(28)C(13)O(4) 0.0 Artefact 1975 0.0 -Unknown:248@Any C-term 248.19876 248.359 H(28)C(13)O(4) 0.0 Artefact 1975 0.0 -Unknown:248@Any N-term 248.19876 248.359 H(28)C(13)O(4) 0.0 Artefact 1975 0.0 +Unknown:248@Any_C-term 248.19876 248.359 H(28)C(13)O(4) 0.0 Artefact 1975 0.0 +Unknown:248@Any_N-term 248.19876 248.359 H(28)C(13)O(4) 0.0 Artefact 1975 0.0 Unknown:250@D 249.981018 250.2075 H(4)C(10)N(1)O(5)S(1) 0.0 Artefact 1976 0.0 Unknown:250@E 249.981018 250.2075 H(4)C(10)N(1)O(5)S(1) 0.0 Artefact 1976 0.0 -Unknown:250@Any C-term 249.981018 250.2075 H(4)C(10)N(1)O(5)S(1) 0.0 Artefact 1976 0.0 -Unknown:250@Any N-term 249.981018 250.2075 H(4)C(10)N(1)O(5)S(1) 0.0 Artefact 1976 0.0 +Unknown:250@Any_C-term 249.981018 250.2075 H(4)C(10)N(1)O(5)S(1) 0.0 Artefact 1976 0.0 +Unknown:250@Any_N-term 249.981018 250.2075 H(4)C(10)N(1)O(5)S(1) 0.0 Artefact 1976 0.0 Unknown:302@D 301.986514 302.2656 H(8)C(4)N(5)O(7)S(2) 0.0 Artefact 1977 0.0 Unknown:302@E 301.986514 302.2656 H(8)C(4)N(5)O(7)S(2) 0.0 Artefact 1977 0.0 -Unknown:302@Any C-term 301.986514 302.2656 H(8)C(4)N(5)O(7)S(2) 0.0 Artefact 1977 0.0 -Unknown:302@Any N-term 301.986514 302.2656 H(8)C(4)N(5)O(7)S(2) 0.0 Artefact 1977 0.0 +Unknown:302@Any_C-term 301.986514 302.2656 H(8)C(4)N(5)O(7)S(2) 0.0 Artefact 1977 0.0 +Unknown:302@Any_N-term 301.986514 302.2656 H(8)C(4)N(5)O(7)S(2) 0.0 Artefact 1977 0.0 Unknown:306@D 306.095082 306.2659 H(18)C(12)O(9) 0.0 Artefact 1978 0.0 Unknown:306@E 306.095082 306.2659 H(18)C(12)O(9) 0.0 Artefact 1978 0.0 -Unknown:306@Any C-term 306.095082 306.2659 H(18)C(12)O(9) 0.0 Artefact 1978 0.0 -Unknown:306@Any N-term 306.095082 306.2659 H(18)C(12)O(9) 0.0 Artefact 1978 0.0 -Unknown:420@Any N-term 420.051719 420.5888 H(24)C(12)N(2)O(6)S(4) 420.051719 H(24)C(12)N(2)O(6)S(4) Artefact 1979 0.5 -Unknown:420@Any C-term 420.051719 420.5888 H(24)C(12)N(2)O(6)S(4) 420.051719 H(24)C(12)N(2)O(6)S(4) Artefact 1979 0.5 +Unknown:306@Any_C-term 306.095082 306.2659 H(18)C(12)O(9) 0.0 Artefact 1978 0.0 +Unknown:306@Any_N-term 306.095082 306.2659 H(18)C(12)O(9) 0.0 Artefact 1978 0.0 +Unknown:420@Any_N-term 420.051719 420.5888 H(24)C(12)N(2)O(6)S(4) 420.051719 H(24)C(12)N(2)O(6)S(4) Artefact 1979 0.5 +Unknown:420@Any_C-term 420.051719 420.5888 H(24)C(12)N(2)O(6)S(4) 420.051719 H(24)C(12)N(2)O(6)S(4) Artefact 1979 0.5 Diethylphosphothione@Y 152.006087 152.1518 H(9)C(4)O(2)P(1)S(1) 0.0 Chemical derivative 1986 0.0 Diethylphosphothione@T 152.006087 152.1518 H(9)C(4)O(2)P(1)S(1) 0.0 Chemical derivative 1986 0.0 Diethylphosphothione@S 152.006087 152.1518 H(9)C(4)O(2)P(1)S(1) 0.0 Chemical derivative 1986 0.0 @@ -2649,9 +2649,9 @@ monomethylphosphothione@T 109.959137 110.0721 H(3)C(1)O(2)P(1)S(1) 0.0 Chemical monomethylphosphothione@Y 109.959137 110.0721 H(3)C(1)O(2)P(1)S(1) 0.0 Chemical derivative 1989 0.0 TMPP-Ac:13C(9)@Y 581.211328 581.474 H(33)C(20)13C(9)O(10)P(1) 0.0 Artefact 1993 0.0 TMPP-Ac:13C(9)@K 581.211328 581.474 H(33)C(20)13C(9)O(10)P(1) 0.0 Artefact 1993 0.0 -TMPP-Ac:13C(9)@Any N-term 581.211328 581.474 H(33)C(20)13C(9)O(10)P(1) 0.0 Chemical derivative 1993 0.0 +TMPP-Ac:13C(9)@Any_N-term 581.211328 581.474 H(33)C(20)13C(9)O(10)P(1) 0.0 Chemical derivative 1993 0.0 ZQG@K 320.100836 320.2973 H(16)C(15)N(2)O(6) 134.036779 H(6)C(8)O(2) Chemical derivative 2001 0.5 -Xlink:DST[56]@Protein N-term 55.989829 56.0202 C(2)O(2) 0.0 Chemical derivative 1999 0.0 +Xlink:DST[56]@Protein_N-term 55.989829 56.0202 C(2)O(2) 0.0 Chemical derivative 1999 0.0 Xlink:DST[56]@K 55.989829 56.0202 C(2)O(2) 0.0 Chemical derivative 1999 0.0 Haloxon@Y 203.950987 204.9763 H(7)C(4)O(3)P(1)Cl(2) 0.0 Chemical derivative 2006 0.0 Haloxon@T 203.950987 204.9763 H(7)C(4)O(3)P(1)Cl(2) 0.0 Chemical derivative 2006 0.0 @@ -2666,19 +2666,19 @@ Methamidophos-O@K 92.997965 93.0217 H(4)C(1)N(1)O(2)P(1) 0.0 Chemical derivativ Methamidophos-O@H 92.997965 93.0217 H(4)C(1)N(1)O(2)P(1) 0.0 Chemical derivative 2008 0.0 Methamidophos-O@C 92.997965 93.0217 H(4)C(1)N(1)O(2)P(1) 0.0 Chemical derivative 2008 0.0 Nitrene@Y 12.995249 12.9988 H(-1)N(1) 0.0 Artefact 2014 0.0 -shTMT@Any N-term 235.176741 235.2201 H(20)C(3)13C(9)15N(2)O(2) 0.0 Chemical derivative 2015 0.0 -shTMT@Protein N-term 235.176741 235.2201 H(20)C(3)13C(9)15N(2)O(2) 0.0 Chemical derivative 2015 0.0 +shTMT@Any_N-term 235.176741 235.2201 H(20)C(3)13C(9)15N(2)O(2) 0.0 Chemical derivative 2015 0.0 +shTMT@Protein_N-term 235.176741 235.2201 H(20)C(3)13C(9)15N(2)O(2) 0.0 Chemical derivative 2015 0.0 shTMT@K 235.176741 235.2201 H(20)C(3)13C(9)15N(2)O(2) 0.0 Chemical derivative 2015 0.0 TMTpro@S 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0 TMTpro@H 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0 -TMTpro@Protein N-term 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0 -TMTpro@Any N-term 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0 +TMTpro@Protein_N-term 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0 +TMTpro@Any_N-term 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0 TMTpro@K 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0 TMTpro@T 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0 TMTpro_zero@S 295.189592 295.3773 H(25)C(15)N(3)O(3) 0.0 Chemical derivative 2017 0.0 TMTpro_zero@H 295.189592 295.3773 H(25)C(15)N(3)O(3) 0.0 Chemical derivative 2017 0.0 -TMTpro_zero@Protein N-term 295.189592 295.3773 H(25)C(15)N(3)O(3) 0.0 Chemical derivative 2017 0.0 -TMTpro_zero@Any N-term 295.189592 295.3773 H(25)C(15)N(3)O(3) 0.0 Chemical derivative 2017 0.0 +TMTpro_zero@Protein_N-term 295.189592 295.3773 H(25)C(15)N(3)O(3) 0.0 Chemical derivative 2017 0.0 +TMTpro_zero@Any_N-term 295.189592 295.3773 H(25)C(15)N(3)O(3) 0.0 Chemical derivative 2017 0.0 TMTpro_zero@K 295.189592 295.3773 H(25)C(15)N(3)O(3) 0.0 Chemical derivative 2017 0.0 TMTpro_zero@T 295.189592 295.3773 H(25)C(15)N(3)O(3) 0.0 Chemical derivative 2017 0.0 Andro-H2O@C 332.19876 332.4339 H(28)C(20)O(4) 0.0 Chemical derivative 2025 0.0 diff --git a/scripts/unimod_to_tsv.ipynb b/scripts/unimod_to_tsv.ipynb index d07f983a..fe640ada 100644 --- a/scripts/unimod_to_tsv.ipynb +++ b/scripts/unimod_to_tsv.ipynb @@ -1,28 +1,45 @@ { "cells": [ { - "cell_type": "code", - "execution_count": 1, "metadata": {}, + "cell_type": "code", "outputs": [], + "execution_count": null, "source": [ "import xml.etree.ElementTree as ET\n", "import yaml\n", - "import pandas as pd\n", - "\n", + "import pandas as pd" + ] + }, + { + "metadata": {}, + "cell_type": "code", + "outputs": [], + "execution_count": null, + "source": [ "def save_yaml(filename, unimod):\n", " with open(filename, \"w\") as file:\n", " yaml.dump(unimod, file)\n", "\n", - "xml = ET.parse('unimod.xml')\n", - "root = xml.getroot()\n", - "\n", "\n", "def get_composition(node):\n", " composition = \"\"\n", " for elem in node.findall(f'{xmlns}element'):\n", " composition += elem.attrib['symbol']+'('+elem.attrib['number']+')'\n", - " return composition\n", + " return composition" + ] + }, + { + "cell_type": "code", + "metadata": { + "ExecuteTime": { + "end_time": "2024-06-25T11:39:09.284411Z", + "start_time": "2024-06-25T11:39:08.507205Z" + } + }, + "source": [ + "xml = ET.parse('unimod.xml')\n", + "root = xml.getroot()\n", "\n", "xmlns = '{http://www.unimod.org/xmlns/schema/unimod_2}'\n", "unimod = {}\n", @@ -72,15 +89,78 @@ " unimod[mod_site]['modloss_composition'] = ptm_nl_composition\n", " unimod[mod_site]['classification'] = _class\n", " unimod[mod_site]['unimod_id'] = int(id)" - ] + ], + "outputs": [], + "execution_count": 1 }, { "cell_type": "code", - "execution_count": 2, - "metadata": {}, + "metadata": { + "ExecuteTime": { + "end_time": "2024-06-25T11:56:30.184321Z", + "start_time": "2024-06-25T11:56:30.165972Z" + } + }, + "source": [ + "df = pd.DataFrame().from_dict(unimod, orient='index')\n", + "df.index = df.index.str.replace(\" \", \"_\", regex=False)\n", + "df['modloss_importance'] = 0.0\n", + "df.loc[df.modloss_composition != '','modloss_importance'] = 0.5\n", + "df.loc['Phospho@S','modloss_importance'] = 1e8\n", + "df.loc['Phospho@T','modloss_importance'] = 1e7\n", + "df.loc['GG@K','modloss_importance'] = 1e6\n", + "df.loc['GlyGly@K',:] = df.loc['GG@K']\n", + "df.loc['GlyGly@K','classification'] = 'Multiple'\n", + "df['mod_name'] = df.index.values\n", + "df = df[['mod_name']+[col for col in df.columns if col != 'mod_name']]\n", + "df['unimod_id'] = df.unimod_id.astype(int)\n", + "df" + ], "outputs": [ { "data": { + "text/plain": [ + " mod_name unimod_mass unimod_avge_mass \\\n", + "Acetyl@T Acetyl@T 42.010565 42.0367 \n", + "Acetyl@Protein_N-term Acetyl@Protein_N-term 42.010565 42.0367 \n", + "Acetyl@S Acetyl@S 42.010565 42.0367 \n", + "Acetyl@C Acetyl@C 42.010565 42.0367 \n", + "Acetyl@Any_N-term Acetyl@Any_N-term 42.010565 42.0367 \n", + "... ... ... ... \n", + "TMTpro_zero@K TMTpro_zero@K 295.189592 295.3773 \n", + "TMTpro_zero@T TMTpro_zero@T 295.189592 295.3773 \n", + "Andro-H2O@C Andro-H2O@C 332.198760 332.4339 \n", + "His+O(2)@H His+O(2)@H 169.048741 169.1381 \n", + "GlyGly@K GlyGly@K 114.042927 114.1026 \n", + "\n", + " composition unimod_modloss modloss_composition \\\n", + "Acetyl@T H(2)C(2)O(1) 0.0 \n", + "Acetyl@Protein_N-term H(2)C(2)O(1) 0.0 \n", + "Acetyl@S H(2)C(2)O(1) 0.0 \n", + "Acetyl@C H(2)C(2)O(1) 0.0 \n", + "Acetyl@Any_N-term H(2)C(2)O(1) 0.0 \n", + "... ... ... ... \n", + "TMTpro_zero@K H(25)C(15)N(3)O(3) 0.0 \n", + "TMTpro_zero@T H(25)C(15)N(3)O(3) 0.0 \n", + "Andro-H2O@C H(28)C(20)O(4) 0.0 \n", + "His+O(2)@H H(7)C(6)N(3)O(3) 0.0 \n", + "GlyGly@K H(6)C(4)N(2)O(2) 0.0 \n", + "\n", + " classification unimod_id modloss_importance \n", + "Acetyl@T Post-translational 1 0.0 \n", + "Acetyl@Protein_N-term Post-translational 1 0.0 \n", + "Acetyl@S Post-translational 1 0.0 \n", + "Acetyl@C Post-translational 1 0.0 \n", + "Acetyl@Any_N-term Multiple 1 0.0 \n", + "... ... ... ... \n", + "TMTpro_zero@K Chemical derivative 2017 0.0 \n", + "TMTpro_zero@T Chemical derivative 2017 0.0 \n", + "Andro-H2O@C Chemical derivative 2025 0.0 \n", + "His+O(2)@H Post-translational 2027 0.0 \n", + "GlyGly@K Multiple 121 1000000.0 \n", + "\n", + "[2685 rows x 9 columns]" + ], "text/html": [ "