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Table 1 Top 20 most discriminatory peptides for diabetes identified by follow-up targeted MS/MS analysis.

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 MS1 Peptide Sequence IPI Accession Number
17.02 0.99 529.27 3 529.27 3 R.THLAPYSDELRQR.L IPI00021841
16.68 0.99 522.77 2 522.77 2 R.LDVDQALN#R.S IPI00023019
10.99 1.00 697.81 2 697.82 2 K.AADDTWEPFASGK.T IPI00022432,IPI00646384
10.76 0.93 1181.57 3 1181.58 3 K.SLGNVN#FTVSAEALESQELCGTEVPSVPEHGRK.D IPI00478003
9.75 1.00 820.90 2 820.91 2 K.AGLQAFFQVQECN#K.S IPI00017601,IPI00794184
8.63 0.95 730.85 2 730.85 2 K.NLFLN#HSEN#ATAK.D IPI00431645,IPI00477597,IPI00478493, IPI00607707,IPI00641737
8.48 0.98 637.86 2 637.87 2 R.LLVVYPWTQR.F IPI00217471,IPI00220706,IPI00473011, IPI00554676,IPI00654755,IPI00657660, IPI00657911,IPI00744503,IPI00749035, IPI00784636,IPI00791558,IPI00796636
8.43 0.99 1340.69 2 1340.69 2 K.MVSHHN#LTTGATLINEQWLLTTAK.N IPI00431645,IPI00477597,IPI00478493, IPI00607707,IPI00641737
8.00 0.99 579.76 2 579.76 2 R.EEQFN#STFR.V IPI00168728,IPI00399007,IPI00426051, IPI00470657,IPI00472345,IPI00784807, IPI00784942
6.96 1.00 1082.58 2 1082.58 2 K.VSN#QTLSLFFTVLQDVPVR.D IPI00478003
5.79 1.00 599.34 3 599.34 3 K.VVLHPN#YSQVDIGLIK.L IPI00431645,IPI00478493,IPI00641737
5.49 1.00 553.30 2 553.30 2 R.GLN#VTLSSTGR.N IPI00032258,IPI00418163,IPI00643525, IPI00654875
5.29 0.95 1274.91 3 1274.92 3 R.GNEANYYSN#ATTDEHGLVQFSIN#TTNVMGTSLTVR.V IPI00478003
5.09 1.00 1178.53 2 1178.55 2 R.GLTFQQN#ASSMCVPDQDTAIR.V IPI00479708,IPI00549291,IPI00748158, IPI00784931
3.95 0.91 758.05 3 758.05 3 K.TVLTPATNHMGN#VTFTIPANR.E IPI00164623,IPI00783987
3.58 0.99 952.44 2 952.45 2 R.FSDGLESN#SSTQFEVKK.Y IPI00032258,IPI00418163,IPI00643525, IPI00654875
3.24 0.94 598.77 2 598.78 2 R.DIENFN#STQK.F IPI00019943
2.82 1.00 799.43 2 799.43 2 V.LHPN#YSQVDIGLIK.L IPI00431645,IPI00478493,IPI00641737
2.69 1.00 1183.55 2 1183.56 2 K.STGKPTLYN#VSLVMSDTAGTCY.- IPI00385264,IPI00549291,IPI00748158, IPI00784931,IPI00788597
2.50 1.00 634.29 2 634.29 2 K.LGN#WSAMPSCK.A IPI00298828
  1. B (log Odds) indicates Odds of the peptide/proteins are differentially expressed between NGT and DB groups. PeptideProphet [29] probability (Prob.) indicates the probability of correctly assigning MS/MS spectra to the given peptide. To be listed here, a peptide first had to score log Odds of ≥ 2.5 for differential abundance, and then ≥ 0.9 by PeptideProphet for subsequent MS/MS peptide sequence assignment. 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, N# is used to indicate the predicted position of the modified asparagine residues, resulting from their conversion to aspartic acid during the deglycosylation step used during sample preparation. The consensus sequence for N- glycosylation is -N-X-S/T- where X is any amino acid except proline, and S/T is serine or threonine. The IPI database entries that were matched to the given sequences are also listed. 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, where we used a log Odds cut-off of ≥ 2.5, the probability that a feature at this value really is differentially abundant is: exp(2.5)/(1+exp(2.5)) = 0.924, (i.e. 92.4% likely that the observed differential abundance was non-random). Thus a log Odds value of 0 corresponds to a 50–50 chance that the feature is genuinely differentially abundant.