AMASS: software for automatically validating the quality of MS/MS spectrum from SEQUEST results.

Time-consuming and experience-dependent manual validations of tandem mass spectra are usually applied to SEQUEST results. This inefficient method has become a significant bottleneck for MS/MS data processing. Here we introduce a program AMASS (advanced mass spectrum screener), which can filter the tandem mass spectra of SEQUEST results by measuring the match percentage of high-abundant ions and the continuity of matched fragment ions in b, y series. Compared with Xcorr and DeltaCn filter, AMASS can increase the number of positives and reduce the number of negatives in 22 datasets generated from 18 known protein mixtures. It effectively removed most noisy spectra, false interpretations, and about half of poor fragmentation spectra, and AMASS can work synergistically with Rscore filter. We believe the use of AMASS and Rscore can result in a more accurate identification of peptide MS/MS spectra and reduce the time and energy for manual validation.