Table 1

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

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


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.

Brusniak et al. BMC Bioinformatics 2008 9:542   doi:10.1186/1471-2105-9-542

Open Data