ReSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

ABSTRACT: Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a

SUBMITTER: Shteynberg D 

PROVIDER: S-EPMC4750398 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature