ProbID: A probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data

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Abstract
With the recent quick expansion of DNA and protein sequence databases, intensive efforts are underway to interpret the linear genetic information of DNA in terms of function, structure, and control of biological processes. The systematic identification and quantification of expressed proteins has proven particularly powerful in this regard. Large‐scale protein identification is usually achieved by automated liquid chromatography‐tandem mass spectrometry of complex peptide mixtures and sequence database searching of the resulting spectra [Aebersold and Goodlett, Chem. Rev. 2001, 101, 269–295]. As generating large numbers of sequence‐specific mass spectra (collision‐induced dissociation/CID) spectra has become a routine operation, research has shifted from the generation of sequence database search results to their validation. Here we describe in detail a novel probabilistic model and score function that ranks the quality of the match between tandem mass spectral data and a peptide sequence in a database. We document the performance of the algorithm on a reference data set and in comparison with another sequence database search tool. The software is publicly available for use and evaluation at http://www.systemsbiology.org/research/software/proteomics/ProbID.