RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration

BMC Genomics

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.

ISSN: 1471-2164