#190 add small sample testing data

MannLabs · Aug 6, 2024 · bcff3ad · bcff3ad
1 parent 483878d
commit bcff3ad
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Showing 6 changed files with 2,781 additions and 1,243 deletions.
diff --git a/alphabase/constants/const_files/psm_reader.yaml b/alphabase/constants/const_files/psm_reader.yaml
@@ -174,7 +174,6 @@ spectronaut:
     - 'FullUniModPeptideName'
     - 'ModifiedPeptideSequence'
     - 'LabeledSequence'
-    - 'FullUniModPeptideName'
   column_mapping:
     'raw_name': 'ReferenceRun'
     'sequence': ['StrippedPeptide','PeptideSequence']
@@ -199,11 +198,10 @@ library_reader_base:
     - 'ModifiedSequence'
     - 'FullUniModPeptideName'
     - 'LabeledSequence'
-    - 'FullUniModPeptideName'
   column_mapping:
     'raw_name': 'ReferenceRun'
     'sequence': ['PeptideSequence', 'StrippedPeptide']
-    'modified_sequence': ['ModifiedPeptideSequence','ModifiedPeptide']
+    'modified_sequence': ['ModifiedPeptideSequence','ModifiedPeptide','FullUniModPeptideName','ModifiedSequence']
     'charge': 'PrecursorCharge'
     'rt': ['RT','iRT','Tr_recalibrated','RetentionTime','NormalizedRetentionTime']
     'ccs': 'CCS'

diff --git a/docs/tutorials/data/AlphaBase_figure1-01.png b/docs/tutorials/data/AlphaBase_figure1-01.png
diff --git a/docs/tutorials/data/sample_diann_report.tsv b/docs/tutorials/data/sample_diann_report.tsv
@@ -0,0 +1,21 @@
+File.Name	Protein.Group	Protein.Ids	Protein.Names	Genes	PG.Quantity	PG.Normalised	Genes.Quantity	Genes.Normalised	Genes.MaxLFQ	Genes.MaxLFQ.Unique	Modified.Sequence	Stripped.Sequence	Precursor.Id	Precursor.Charge	Q.Value	Protein.Q.Value	PG.Q.Value	GG.Q.Value	Proteotypic	Precursor.Quantity	Precursor.Normalised	Label.Ratio	RT	RT.Start	RT.Stop	iRT	Predicted.RT	Predicted.iRT	First.Protein.Description	Lib.Q.Value	Ms1.Profile.Corr	Ms1.Area	Evidence	CScore	Decoy.Evidence	Decoy.CScore	Fragment.Quant.Raw	Fragment.Quant.Corrected	Fragment.Correlations
+D:\Raw\PXD010529\KL_Try_001_a.mzML.dia	P0C0T4;Q3E792	P0C0T4;Q3E792	RS25A_YEAST;RS25B_YEAST	RPS25A;RPS25B	128.193	124.069	128.193	124.069	124.069		AAAALAGGK	AAAALAGGK	AAAALAGGK1	1	0.0018018	1	0.00367647	0.00367647	0	128.193	124.069	0	3.47307	3.40655	3.56173	-5.93851	3.49691	-5.48102	40S ribosomal protein S25-B	0	0.979477	1309.47	5.45361	0.962915	1.93559	0.0465092	53.5023;37.4069;34.7302;37.2836;18.0323;5.22494;	53.5023;37.4069;34.7302;37.2836;17.9349;4.82134;	0.984435;0.963165;0.968954;0.968167;0.944554;0.879724;
+D:\Raw\PXD010529\KL_Try_001_b.mzML.dia	P0C0T4;Q3E792	P0C0T4;Q3E792	RS25A_YEAST;RS25B_YEAST	RPS25A;RPS25B	115.42	113.462	115.42	113.462	113.462		AAAALAGGK	AAAALAGGK	AAAALAGGK1	1	0.00524934	1	0.00847458	0.00847458	0	115.42	113.462	0	3.42883	3.36235	3.49533	-5.93851	3.49679	-5.77088	40S ribosomal protein S25-B	0	0.986921	1383.1	5.48846	0.959377	2.0927	0.0608594	50.1353;34.9034;30.7115;31.0511;18.0063;4.84666;	49.4659;34.9034;30.3503;31.0511;18.0063;1.77993;	0.961922;0.965909;0.962709;0.980055;0.940109;0.330862;
+D:\Raw\PXD010529\KL_Try_001_c.mzML.dia	P0C0T4;Q3E792	P0C0T4;Q3E792	RS25A_YEAST;RS25B_YEAST	RPS25A;RPS25B	106.064	112.884	106.064	112.884	112.884		AAAALAGGK	AAAALAGGK	AAAALAGGK1	1	0.00233645	1	0.00446429	0.00446429	0	106.064	112.884	0	3.47295	3.40648	3.53945	-5.93851	3.52259	-5.10413	40S ribosomal protein S25-B	0	0.992176	1216.13	5.51099	0.958271	2.37261	0.042487	45.1315;34.9482;29.0278;27.9588;14.9464;2.37267;	43.875;34.2306;28.9171;27.9588;14.9118;2.19111;	0.980755;0.974401;0.96806;0.973072;0.926134;0.802259;
+D:\Raw\PXD010529\KL_Try_001_a.mzML.dia	P09938	P09938	RIR2_YEAST	RNR2	771.44	711.027	771.44	711.027	711.027	711.027	AAADALSDLEIK	AAADALSDLEIK	AAADALSDLEIK2	2	0.0018018	0.00444444	0.00367647	0.00367647	1	771.44	711.027	0	19.5573	19.4465	19.8454	87.3647	19.116	89.0581	Ribonucleoside-diphosphate reductase small chain 1	0	0.973548	1572.07	5.25393	0.962886	1.63131	0.273278	348.905;260.317;195.701;398.941;185.665;102.401;	340.384;245.392;189.196;322.219;185.665;84.2377;	0.956445;0.940838;0.958822;0.746483;0.979243;0.85293;
+D:\Raw\PXD010529\KL_Try_001_b.mzML.dia	P09938	P09938	RIR2_YEAST	RNR2	601.648	589.141	601.648	589.141	589.141	589.141	AAADALSDLEIK	AAADALSDLEIK	AAADALSDLEIK2	2	0.0035461	0.00671141	0.00706714	0.00706714	1	601.648	589.141	0	19.6901	19.5794	19.9118	87.3647	19.2922	90.4101	Ribonucleoside-diphosphate reductase small chain 1	0	0.959851	1269.51	5.26058	0.960601	2.74161	0.359838	276.575;219.15;162.237;330.749;139.61;64.8123;	259.346;202.692;154.024;260.071;139.61;56.507;	0.954445;0.9126;0.939449;0.788262;0.986421;0.800586;
+D:\Raw\PXD010529\KL_Try_001_c.mzML.dia	P09938	P09938	RIR2_YEAST	RNR2	576.849	644.057	576.849	644.057	644.057	644.057	AAADALSDLEIK	AAADALSDLEIK	AAADALSDLEIK2	2	0.00233645	0.00552486	0.00446429	0.00446429	1	576.849	644.057	0	19.7565	19.5571	20.0003	87.3647	19.2206	89.5895	Ribonucleoside-diphosphate reductase small chain 1	0	0.936235	1391.38	5.35032	0.958348	2.78618	0.145591	239.095;208.723;138.07;325.904;133.56;72.8043;	235.233;208.723;133.467;310.796;132.893;62.4847;	0.95409;0.9832;0.907138;0.944164;0.938714;0.86405;
+D:\Raw\PXD010529\KL_Try_001_a.mzML.dia	P32263	P32263	P5CR_YEAST	PRO3	161.094	154.834	161.094	154.834	154.834	154.834	AADETAAAFYPSK	AADETAAAFYPSK	AADETAAAFYPSK2	2	0.00322581	0.00649351	0.00651466	0.00651466	1	161.094	154.834	0	6.08523	5.8193	6.2847	46.1616	5.91506	48.0049	Pyrroline-5-carboxylate reductase	0	0.389702	354.611	5.28349	0.962639	1.8309	0.0704945	62.2654;51.0341;55.4372;43.6856;46.785;64.6734;	59.7661;34.675;55.4372;43.2536;45.8912;35.7748;	0.875395;0.789351;0.97835;0.802494;0.862977;0.705339;
+D:\Raw\PXD010529\KL_Try_001_b.mzML.dia	P32263	P32263	P5CR_YEAST	PRO3	111.732	109.714	111.732	109.714	109.714	109.714	AADETAAAFYPSK	AADETAAAFYPSK	AADETAAAFYPSK2	2	0.00322581	0.00588235	0.00497512	0.00497512	1	111.732	109.714	0	6.10755	5.84162	6.307	46.1616	5.98491	48.4809	Pyrroline-5-carboxylate reductase	0	0.307048	292.382	5.10065	0.960846	2.59125	0.0412323	64.881;61.7448;43.8795;60.9907;43.2852;80.1167;	39.7012;19.5175;28.7454;60.4019;43.2852;43.9172;	0.792464;0.665902;0.627921;0.819597;0.862502;0.660094;
+D:\Raw\PXD010529\KL_Try_001_c.mzML.dia	P32263	P32263	P5CR_YEAST	PRO3	112.233	120.051	112.233	120.051	120.051	120.051	AADETAAAFYPSK	AADETAAAFYPSK	AADETAAAFYPSK2	2	0.00331126	0.00687285	0.00704225	0.00704225	1	112.233	120.051	0	6.2626	6.04097	6.48422	46.1616	6.17098	47.2595	Pyrroline-5-carboxylate reductase	0	0.538956	315.843	4.44177	0.958215	1.76498	0.0569845	61.7778;49.6488;43.9515;56.8732;43.645;51.1233;	41.477;30.5974;43.9515;26.278;26.8041;32.0761;	0.544185;0.355265;0.944637;0.29052;0.693085;0.487641;
+D:\Raw\PXD010529\KL_Try_001_a.mzML.dia	Q12363	Q12363	WTM1_YEAST	WTM1	1438.71	1353.03	1438.71	1353.03	1307.82	1307.82	AAEAATTDLTYR	AAEAATTDLTYR	AAEAATTDLTYR2	2	0.0018018	0.00444444	0.00367647	0.00367647	1	625.784	605.654	0	4.53332	4.44468	4.66628	32.4202	4.80597	29.0905	Transcriptional modulator WTM1	0	0.983188	650.279	5.93208	0.962821	2.3506	0.0540581	297.387;267.029;178.516;149.881;91.4665;77.1344;	297.387;267.029;178.516;149.881;91.4665;77.1344;	0.997303;0.994629;0.991394;0.988814;0.983996;0.986495;
+D:\Raw\PXD010529\KL_Try_001_b.mzML.dia	Q12363	Q12363	WTM1_YEAST	WTM1	1216.35	1193.61	1216.35	1193.61	1197.09	1197.09	AAEAATTDLTYR	AAEAATTDLTYR	AAEAATTDLTYR2	2	0.00322581	0.00588235	0.00497512	0.00497512	1	553.908	544.51	0	4.53338	4.44475	4.66633	32.4202	4.79542	28.6054	Transcriptional modulator WTM1	0	0.981809	607.265	5.90191	0.960704	1.85977	0.0407824	268.754;236.407;148.837;136.701;80.2494;71.1019;	268.754;236.407;148.837;136.317;78.9152;70.9042;	0.993294;0.997304;0.980163;0.992845;0.959951;0.985351;
+D:\Raw\PXD010529\KL_Try_001_c.mzML.dia	Q12363	Q12363	WTM1_YEAST	WTM1	1077.3	1185.16	1077.3	1185.16	1222.56	1222.56	AAEAATTDLTYR	AAEAATTDLTYR	AAEAATTDLTYR2	2	0.00233645	0.00552486	0.00446429	0.00446429	1	541.614	576.437	0	4.57762	4.46682	4.7106	32.4202	4.88394	27.7314	Transcriptional modulator WTM1	0	0.988483	592.15	5.85402	0.958327	2.0423	0.0483367	257.504;206.761;153.952;130.908;73.2146;62.4957;	256.963;205.45;153.952;130.699;73.2146;62.4957;	0.992992;0.973439;0.995579;0.992178;0.989177;0.978518;
+D:\Raw\PXD010529\KL_Try_001_a.mzML.dia	P19097	P19097	FAS2_YEAST	FAS2	6338.83	5858.8	6338.83	5858.8	5982.38	5982.38	AAEEAGVTDVK	AAEEAGVTDVK	AAEEAGVTDVK2	2	0.0018018	0.00444444	0.00367647	0.00367647	1	111.715	108.121	0	3.55405	3.48755	3.70915	5.29179	3.75928	-3.32938	Fatty acid synthase subunit alpha	0	0.811498	289.769	5.4807	0.962748	2.75939	0.0802736	42.3852;45.6852;44.3233;25.0065;21.6507;9.88623;	42.3852;44.5463;44.3233;25.0065;20.5835;9.58631;	0.981284;0.899703;0.965871;0.972235;0.90283;0.92031;
+D:\Raw\PXD010529\KL_Try_001_b.mzML.dia	P19097	P19097	FAS2_YEAST	FAS2	6275.78	6138.18	6275.78	6138.18	5985.59	5985.59	AAEEAGVTDVK	AAEEAGVTDVK	AAEEAGVTDVK2	2	0.0035461	0.00588235	0.00497512	0.00497512	1	110.663	108.786	0	3.5098	3.42117	3.59847	5.29179	3.72461	-2.50913	Fatty acid synthase subunit alpha	0	0.425342	200.608	5.4726	0.960638	2.01975	0.0525826	43.5898;41.3329;40.2533;27.501;22.9715;6.3735;	42.909;36.4286;40.2533;27.501;20.3304;6.0459;	0.995904;0.881634;0.96788;0.988575;0.911633;0.932928;
+D:\Raw\PXD010529\KL_Try_001_c.mzML.dia	P19097	P19097	FAS2_YEAST	FAS2	5416.58	6041.72	5416.58	6041.72	6067.77	6067.77	AAEEAGVTDVK	AAEEAGVTDVK	AAEEAGVTDVK2	2	0.00331126	0.00552486	0.00446429	0.00446429	1	112.846	120.101	0	3.55395	3.46528	3.68688	5.29179	3.77086	-2.20753	Fatty acid synthase subunit alpha	0	0.643903	268.81	5.11072	0.958014	3.08218	0.249725	49.1639;42.4479;40.4389;24.9152;22.9608;7.28928;	49.1639;38.7159;39.7982;23.8836;20.2161;5.46;	0.990309;0.90133;0.9217;0.906221;0.869036;0.795397;
+D:\Raw\PXD010529\KL_Try_001_a.mzML.dia	P38431	P38431	IF5_YEAST	TIF5	880.259	818.055	880.259	818.055	830.305	830.305	AAELDVLNDPK	AAELDVLNDPK	AAELDVLNDPK2	2	0.0018018	0.00444444	0.00367647	0.00367647	1	790.534	744.293	0	10.4262	10.2489	10.8251	64.079	13.1583	61.4867	Eukaryotic translation initiation factor 5	0	0.913543	1128.96	5.63304	0.963015	1.58141	0.0449807	371.614;226.764;193.531;105.554;123.551;80.2432;	371.614;226.764;192.157;105.554;123.551;80.1105;	0.987408;0.944806;0.964722;0.917752;0.884036;0.893708;
+D:\Raw\PXD010529\KL_Try_001_b.mzML.dia	P38431	P38431	IF5_YEAST	TIF5	780.119	763.632	780.119	763.632	780.854	780.854	AAELDVLNDPK	AAELDVLNDPK	AAELDVLNDPK2	2	0.00322581	0.00588235	0.00497512	0.00497512	1	718.465	705.191	0	10.6256	10.4483	11.0023	64.079	13.8907	60.671	Eukaryotic translation initiation factor 5	0	0.966342	1061.89	5.67401	0.960787	1.9026	0.0761464	328.151;213.327;181.569;118.283;108.873;86.4835;	326.332;212.91;179.224;118.283;108.222;82.8155;	0.963128;0.927321;0.936841;0.983551;0.909934;0.856805;
+D:\Raw\PXD010529\KL_Try_001_c.mzML.dia	P38431	P38431	IF5_YEAST	TIF5	675.837	750.877	675.837	750.877	723.483	723.483	AAELDVLNDPK	AAELDVLNDPK	AAELDVLNDPK2	2	0.00233645	0.00552486	0.00446429	0.00446429	1	560.367	615.654	0	11.0687	10.8471	11.3124	64.079	14.278	61.6374	Eukaryotic translation initiation factor 5	0	0.937675	989.408	5.59483	0.958292	2.6506	0.0935499	258.308;169.981;143.992;94.8828;84.7077;65.3075;	248.971;169.981;141.415;94.2585;84.2997;63.9518;	0.925562;0.974505;0.894225;0.89343;0.860062;0.953912;
+D:\Raw\PXD010529\KL_Try_001_a.mzML.dia	P0CX39;P0CX40	P0CX39;P0CX40	RS8A_YEAST;RS8B_YEAST	RPS8A;RPS8B	3128.28	2886.55	3128.28	2886.55	2785.27		AAIVQIDATPFR	AAIVQIDATPFR	AAIVQIDATPFR2	2	0.0018018	1	0.00367647	0.00367647	0	3128.28	2886.55	0	21.1101	20.822	21.509	96.4696	20.9493	97.6359	40S ribosomal protein S8-A	0	0.551688	3646.8	5.80266	0.962879	2.1628	0.0972782	1340.72;950.237;837.323;1054.38;497.575;329.375;	1340.72;950.237;837.323;1012.96;497.575;329.375;	0.97769;0.973325;0.989487;0.84009;0.957244;0.962877;
+D:\Raw\PXD010529\KL_Try_001_b.mzML.dia	P0CX39;P0CX40	P0CX39;P0CX40	RS8A_YEAST;RS8B_YEAST	RPS8A;RPS8B	2445.22	2394.39	2445.22	2394.39	2460.4		AAIVQIDATPFR	AAIVQIDATPFR	AAIVQIDATPFR2	2	0.00322581	1	0.00497512	0.00497512	0	2445.22	2394.39	0	21.2206	20.999	21.6195	96.4696	21.0897	97.7731	40S ribosomal protein S8-A	0	0.86564	2542.72	5.75859	0.96072	1.68399	0.0442737	1056.5;757.705;632.313;713.379;341.249;262.934;	1056.5;756.404;632.313;701.683;341.249;262.934;	0.939122;0.962911;0.992289;0.847707;0.890037;0.942195;