A simple workflow to increase MS2 identification rate by subsequent spectral library search |
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| Authors: | Erik Ahrné Alexandre Masselot Pierre‐Alain Binz Markus Müller Frederique Lisacek |
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| Institution: | 1. Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland;2. Geneva Bioinformatics (Genebio) SA, Geneva, Switzerland |
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| Abstract: | Searching a spectral library for the identification of protein MS/MS data has proven to be a fast and accurate method, while yielding a high identification rate. We investigated the potential to increase peptide discovery rate, with little increase in computational time, by constructing a workflow based on a sequence search with Phenyx followed by a library search with SpectraST. Searching a consensus library compiled from the search results of the prior Phenyx search increased the number of confidently matched spectra by up to 156%. Additionally matched spectra by SpectraST included noisy spectra, spectra representing missed cleaved peptides as well as spectra from post‐translationally modified peptides. |
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| Keywords: | False discovery rate Mass spectrometry Protein identification Spectral library search |
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