Table 2 |
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|
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). |
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|
Brusniak et al. BMC Bioinformatics 2008 9:542 doi:10.1186/1471-2105-9-542 |
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