Skip to content

Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis

Type Information
Nr 46 (Research article)
Authors Quandt, Andreas; Espona Pernas, Lucia; Balasko, Akos; Weisser, Hendrik; Brusniak, Mi-Youn; Kunszt, Peter; Aebersold, Ruedi; Malmström, Lars
Title Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis
Journal EuPA Open Proteomics (2014) 5 21-31
DOI 10.1016/j.euprot.2014.10.001
Citations 10 citations (journal impact: 0.0)
Abstract Tandem mass spectrometry and sequence database searching are widely used in proteomics to identify peptides in complex mixtures. Here we present a benchmark study in which a pool of 20103 synthetic peptides was measured and the resulting data set was analyzed using around 1800 different software and parameter set combinations. The results indicate a strong relationship between the performance of an analysis workflow and the applied parameter settings. We present and discuss strategies to optimize parameter settings in order to significantly increase the number of correctly assigned fragment ion spectra and to make the analysis method robust.
Synopsis We describe a study where we show that using more than one search engine mitigates sensitivity to suboptimal parameters