In-depth analysis of tandem mass spectrometry data from disparate instrument types.

ABSTRACT: Mass spectrometric analyses of protein digests produce large numbers of fragmentation spectra that are not identified by routine database searching strategies. Some of these spectra could be identified by development of improved search engines. However, many of these spectra represent fragmentation of peptide components bearing modifications that are not routinely considered in database searches. Here we present new software within Protein Prospector that allows comprehensive analysis of data sets by analyzing the data at increasing levels of depth. Analysis of published data sets is presented to illustrate that the software is not biased to any instrument types. The results show that these data sets contain many modified peptides. As well as searching for known modification types, Protein

SUBMITTER: Chalkley RJ 

PROVIDER: S-EPMC2596346 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature