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

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

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
  1. 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).