Table III.

Searches of the ABRF data set using Mascot with and without consensus with Sequest or X!Hunter

Search methoda	Identifications		Protein identifications
	No mass filter	Mass filter appliedb
Mascotc
ABRF	873 (459 unique)d	765 (433 unique)d	49
Non-ABRF	1,761	22
Decoy	2,391	63
FDR (%) normal/decoy	67/91e	2.8/8.0e
Sequest
ABRF	893 (466 unique)d	763 (435 unique)d	48
Non-ABRF	1,758	39
Decoy	2,421	63
FDR (%) normal/decoy	66/91e	4.9/7.9e
SM consensus
ABRF	823 (440 unique)d	729 (419 unique)d	48
Non-ABRF	161	3
Decoy	278	13
FDR (%) normal/decoy	16/28e	0.4/1.8e
XM consensus
ABRF	771 (433 unique)d	688 (412 unique)d	48
Non-ABRF	65	1
Decoy	93	4
FDR (%) normal/decoy	66/91e	4.9/7.9e

^aIn each case, the results of the normal search are broken out into correct versus incorrect assignments, and total decoy hits for both are shown. No score thresholds were used in accepting the assignments. Results are filtered to remove unlikely missed cleavage products, peptides with fewer than 9 amino acids, and ions with charge >3+.

^bResults are postfiltered by parent ion mass accuracy within −2 to +7 ppm.

^cCriteria applied to Mascot-only result allow spectra with charge up to 3 and sequences with at least 9 amino acids that pass the missed cleavage rules (14). The difference in total number for the decoy search (2,391) versus the normal search (2,634) is due to the fact that the cases assigned as an unlikely missed cleavage product have a higher probability of occurring in the decoy search.

^dNumber of MS/MS identified; number of unique peptide sequences in parentheses.

^eFDR values are shown for the ABRF protein assignments and for the estimated FDR from the decoy search. A high FDR is obtained for the Mascot- and Sequest-only searches because assignments for all MS/MS are considered correct to show the effect of consensus before the mass accuracy filter is applied.