Table II. The number of identified MS/MS and unique sequences comparing four different spectral libraries using different scoring metrics. The Sigma UPS1 dataset was searched against each library using RDP, RSIM, SHP, and MHP scores. Thresholds correspond to 3% FDR, where FDR is calculated as the proportion of accepted assignments that fail to match known proteins in the UPS1 sample. Mascot was searched using peptide databases equivalent to each library, using the ions score for FDR threshold determination.
| Library | Correct MS/MS and unique sequence assignments at 3% FDRa |
||||
|---|---|---|---|---|---|
| RSIM | RDP | SHP | MHP | Mascot | |
| NISTb | 5434 (651) | 5457 (651) | 5363 (647) | 5451 (657) | 4055 (617) |
| TargetSSc | 3859 (678) | 3867 (675) | 4223 (715) | 4557 (732) | 3661 (656) |
| NIST+DecoySSd | 4494 (611) | 4628 (618) | 4415 (614) | 4626 (623) | 3111 (545) |
| SSNIST+DecoySSe | 2970 (534) | 3033 (538) | 3306 (561) | 3425 (552) | 3111 (545) |
| Hybridf | 5281 (743) | 5387 (744) | 5247 (753) | 5583 (769) | 3661 (656) |
a The number of accepted MS/MS assignments in a search of the Sigma UPS1 standard, using a score threshold corresponding to 3% FDR. The number of unique sequences identified is indicated in parentheses.
b Filtered NIST human LTQ reference library, build Feb 4, 2009 (see Table I).
c TargetSS library (see Table I).
d Filtered NIST reference library concatenated with DecoySS library (see Table I).
e Spectra were simulated for peptides in NIST reference library (SSNIST) and concatenated with DecoySS library.
f The Hybrid library is the union of the NIST reference library and the TargetSS library, where simulated spectra in TargetSS library are replaced with NIST reference spectra only for peptide ions represented in both libraries. Library size is equal to that of TargetSS library.