v1.2

Author: sajfb

IDSL.CSA/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: IDSL.CSA
 Type: Package
 Title: Composite Spectra Analysis (CSA) for High-Resolution Mass Spectrometry Analyses
-Version: 1.1
+Version: 1.2
 Authors@R: c(
     person(family = "Fakouri-Baygi", given = "Sadjad", email = "[email protected]",
            role = "aut", comment = c(ORCID = "0000-0002-6864-6911")),
@@ -12,7 +12,7 @@ Imports: IDSL.MXP, IDSL.IPA, IDSL.FSA, readxl
 Author: Sadjad Fakouri-Baygi [aut] (<https://orcid.org/0000-0002-6864-6911>),
     Dinesh Barupal [cre, aut] (<https://orcid.org/0000-0002-9954-8628>)
 Maintainer: Dinesh Barupal <[email protected]>
-Description: A fragmentation spectra detection pipeline for high-throughput LC/HRMS data processing using peaklists generated by the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120>. The 'IDSL.CSA' package can deconvolute fragmentation spectra from Composite Spectra Analysis (CSA), Data Dependent Acquisition (DDA) analysis, and various Data-Independent Acquisition (DIA) methods such as MS^E, All-Ion Fragmentation (AIF) and SWATH-MS analysis. The 'IDSL.CSA' package was introduced in <doi:10.1101/2023.02.09.527886>.
+Description: A fragmentation spectra detection pipeline for high-throughput LC/HRMS data processing using peaklists generated by the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120>. The 'IDSL.CSA' package can deconvolute fragmentation spectra from Composite Spectra Analysis (CSA), Data Dependent Acquisition (DDA) analysis, and various Data-Independent Acquisition (DIA) methods such as MS^E, All-Ion Fragmentation (AIF) and SWATH-MS analysis. The 'IDSL.CSA' package was introduced in <doi:10.1021/acs.analchem.3c00376>.
 License: MIT + file LICENSE
 URL: https://github.com/idslme/idsl.csa
 BugReports: https://github.com/idslme/idsl.csa/issues

IDSL.CSA/inst/CITATION

@@ -1,15 +1,17 @@
 bibentry(bibtype = "Article",
-         author = c(as.person("Sadjad Fakouri Baygi"), as.person("Sanjay K Banerjee"),
-                    as.person("Praloy Chakraborty"), as.person("Yashwant Kumar"),
-                    as.person("Dinesh Kumar Barupal")),
+         author = c(as.person("Sadjad Fakouri Baygi"),
+                    as.person("Yashwant Kumar"), as.person("Dinesh Kumar Barupal")),
          title = "IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets",
-         journal = "bioRxiv",
-         year = "2023",
-         url = "https://doi.org/10.1101/2023.02.09.527886",
+         journal = "Analytical Chemistry",
+         year    = "2023",
+         volume = "95",
+         number  = "25",
+         pages = "9480–9487",
+         url      = "https://doi.org/10.1021/acs.analchem.3c00376",
          textVersion =
          paste0("Fakouri Baygi et. al.,\n",
                "IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets\n",
-               "bioRxiv, doi:10.1101/2023.02.09.527886\n"),
-         header = "To cite IDSL.CSA in publications, please use:",
+               "Analytical Chemistry, 2023, 95(25), 9480–9487, doi:10.1021/acs.analchem.3c00376\n"),
+         header = "To cite IDSL.FSA in publications, please use:",
          footer = "We appreciate citing our manuscript to gain visibility in the scientific community!"
         )

README.md

@@ -88,6 +88,6 @@ IDSL.CSA_workflow("Address of the CSA parameter spreadsheet")
 
 ## Citation
 
-[1] Fakouri Baygi, S., Kumar, Y. Barupal, D.K. [IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets](https://doi.org/10.1101/2023.02.09.527886). *bioRxiv*, **2023**.
+[1] Fakouri Baygi, S., Kumar, Y. Barupal, D.K. [IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets](https://doi.org/10.1021/acs.analchem.3c00376). *Analytical Chemistry*, **2023**, *95(25)*, 9480–9487.
 
 [2] Fakouri Baygi, S., Kumar, Y. Barupal, D.K. [IDSL. IPA characterizes the organic chemical space in untargeted LC/HRMS datasets](https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00120). *Journal of proteome research*, **2022**, *21(6)*, 1485-1494.