Table 3

Example search results of augmented RAId_DbS

(a) E-value

P-value

Peptide

Mol. Wt.

Protein ID

Novel SAP

Disease


1.184e-01

1.744e-05

RTKLKDC...KIAR

2897.500

(NP_114412;...;Q9H2L5)

disabled

4.084e+00

9.345e-03

KQQELAA...VSSR

2898.520

(NP_072096;...;O75420)

disabled


(b) E-value

P-value

Peptide

Mol. Wt.

Protein ID

Novel SAP

Disease


3.977e-07

1.834e-10

KsVEEYANCHLAR

1448.650

(NP_001054;...;P02787)

disabled

4.779e-01

2.205e-04

KsVqEYANCHLAR

1447.670

(NP_001054;...;P02787)

disabled

7.524e-01

3.470e-04

RℓMNAsMVWAQAAR

1448.720

(NP_000337;...;P48436)

disabled

{(ℓ;2;108;Campomelic dysplasia (CMD1) [MIM:114290])(s;6;...)}


In this example, for the spectrum considered, RAId_DbS performs searches assuming the parent ion to have charge +1, +2, +3. The search results are then pooled together to form a single result ranked by E-values. This is why for the same spectrum RAId_DbS may report peptide hits with very different masses. In part (a) ((b)), searches were done with annotated SAPs and PTMs turned off (on). The lowercase letters in the peptide indicate SAPs. A novel SAP, if present and enabled in the searches, will be specified in the column headed by Novel SAP. Note that in the disease related annotation, there are four fields separated by three semicolons. The first field, a lower case amino acid letter, indicates the SAP; second field, an integer, indexes the SAP position in the peptide; the third field, an integer, indexes the SAP position in the protein; the fourth field shows the annotated disease association.

Alves et al. BMC Genomics 2008 9:505   doi:10.1186/1471-2164-9-505

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