Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

BMC Bioinformatics

Table 2 Top 12 most discriminatory yeast phosphopeptides identified by follow-up targeted MS/MS.

B (log Odds)	Prob.	MS1 *m/z*	z MS1	MS2 *m/z*	z MS2	Peptide Sequence	SGD ID	Protein
6.45	1.00	874.74	3	875.25	3	EQAEASIDNLKNEAT*PEAEQVKK	S000005469	YOL109W
6.45	0.91	874.74	3	875.22	3	RYSNTT*INNANGGTSAGSTTGAALSR	S000001397	YIL135C
6.20	0.88	546.27	3	546.61	3	KMS*FSGYSPKPISK	S000005701	YOR175C
6.19	0.73	994.82	3	995.40	3	LGSLPASAGSTTLINTPSEASSS*TPDLLSK	S000000133	YBL037W
6.09	1.00	459.91	3	460.18	3	RPS*VIGFLSGHK	S000000197	YBL101C
6.04	0.93	1152.90	3	1153.57	3	SNGAPTNAS*PAPPPVILQPTLQPNDQGNPLNTR	S000000316	YBR112C
5.97	0.99	411.54	3	445.15	3	RHS*LGLNEAKK	S000002701	YDR293C
5.94	0.99	637.00	3	637.37	3	RPVS*IAAAQHVPTAPASR	S000004715	YMR109W
5.48	0.99	938.44	3	938.98	3	S*INDFFSKPNNNVNSNINNTLPNR	S000003843	YJR083C
5.45	0.94	840.91	2	841.37	2	TTS*LVNNILNGNNAR	S000004748	YMR140W
5.26	0.91	1068.77	3	1069.39	3	QQHRPVPATSAGEPTDETEPES*DTEVETS	S000005609	YOR083W
4.33	0.94	754.66	3	663.72	3	RSS*GPMDFQNTIHNMQYR	S000001913	YFR017C

B (log Odds) indicates Odds of the peptide/proteins are differentially expressed between wild type yeast and deletion strain group. PeptideProphet [29] probability (Prob.) indicates the probability of correctly assigning MS/MS spectra to the given peptide. We also give the m/z value and charge state (z) for both the feature initially detected by MS1, as well for the peptide subsequently identified by MS/MS (MS2). For peptide sequence identifications, S* and T* indicate the predicted position of the modified (phosphorylated) serine or threonine residues reported by SEQUEST search and manual/visual inspection of the MS/MS spectra. The yeast SDG database accession numbers matched to the sequences are also listed, along with their corresponding SGD systematic protein names. The log Odds B value is a statistical measure of the likelihood that a given feature is genuinely differentially expressed/abundant, where higher log Odds values represent increased probability of such. Log Odds can be converted to a probability. In this case, a log Odds of 4 corresponds exp(4)/(1+exp(4)) = 0.982 (i.e. 98.2% likely that the observed differential abundance was non-random).

ISSN: 1471-2105