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Systematic errors in peptide and protein identification and quantification by modified peptides

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Item Type:Article
Title:Systematic errors in peptide and protein identification and quantification by modified peptides
Creators Name:Bogdanow, B. and Zauber, H. and Selbach, M.
Abstract:The principle of shotgun proteomics is to use peptide mass spectra in order to identify corresponding sequences in a protein database. The quality of peptide and protein identification and quantification critically depends on the sensitivity and specificity of this assignment process. Many peptides in proteomic samples carry biochemical modifications, and a large fraction of unassigned spectra arise from modified peptides. Spectra derived from modified peptides can erroneously be assigned to wrong amino acid sequences. However, the impact of this problem on proteomic data has not yet been investigated systematically. Here we use combinations of different database searches to show that modified peptides can be responsible for 20-50 % of false positive identifications in deep proteomic datasets. These false positive hits are particularly problematic as they have significantly higher scores and higher intensities than other false positive matches. Furthermore, these wrong peptide assignments lead to hundreds of false protein identifications and systematic biases in protein quantification. We devise a "cleaned search" strategy to address this problem and show that this considerably improves the sensitivity and specificity of proteomic data. In summary, we show that modified peptides cause systematic errors in peptide and protein identification and quantification and should therefore be considered to further improve the quality of proteomic data annotation.
Keywords:Algorithms, HEK293 Cells, Peptides, Protein Databases, Proteins, Proteomics, Sensitivity and Specificity, Tandem Mass Spectrometry
Source:Molecular & Cellular Proteomics
ISSN:1535-9476
Publisher:American Society for Biochemistry and Molecular Biology (U.S.A.)
Volume:15
Number:8
Page Range:2791-2801
Date:1 August 2016
Official Publication:https://doi.org/10.1074/mcp.M115.055103
PubMed:View item in PubMed

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