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).

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

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