Table 1

Example output of RAId_DbS containing multiple significant peptide hits. The contents in the "DEFINITION" and "GI-LIST" columns have been shortened to fit the page. The first two hits correspond to the same peptide MYLGYEYVTAIR, while the third to the fifth hits correspond to the same peptide LGEYGFQNALLVR if we follow the mass spectrometry convention not to distinguish Leucine from Isoleucine. After that, the next peptide has an E-value 1.5, indicating a false hit. One thing worth noticing is that there is a clean separation between significant hits and the rest of peptide hits

E-VALUE

PEPTIDE

MASS

DEFINITION

GI-LIST

4.423375e-05

KMYLGYEYVTAIR

1478.720

..|ref|NP 001054.1| transferrin [Homo sapiens]

[4557871,94717618,15021381,31415705,......

4.423375e-05

RMYLGYEYVTAIR

1478.720

..|emb|CAH91543.1| hypothetical protein [Pongo

[55729628]

1.488740e-04

KLGEYGFQNAILVR

1479.780

..|ref|NP 033784.1| albumin 1 [Mus musculus]

[33859506,55391508,191765,19353306, .......

1.488740e-04

KLGEYGFQNALLVR

1479.780

..|emb|CAA59279.1| albumin precursor [Felis

[886485,57977283,633938,30962111, ......

1.488740e-04

KLGEYGFQNALIVR

1479.780

..|gb|AAT98610.1| albumin [Sus scrofa]

[51235682,52353352,15808978,76445989,......

1.526504e+00

KTTLALQFLMEGVR

1478.800

..|ref|YP 466151.1| putative circadian

[86159366]

3.710973e+00

[MFKANMKQLIVR

1478.820

..|dbj|BAD64473.1| cell wall lytic activ

[56909946]

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Alves et al. Biology Direct 2007 2:25   doi:10.1186/1745-6150-2-25