Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis
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 20,103 synthetic peptides was measured and the resulting data set was analyzed using around 1800 different software an...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2014-12-01
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| Series: | EuPA Open Proteomics |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S221296851400066X |
| _version_ | 1818228912918888448 |
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| author | Andreas Quandt Lucia Espona Akos Balasko Hendrik Weisser Mi-Youn Brusniak Peter Kunszt Ruedi Aebersold Lars Malmström |
| author_facet | Andreas Quandt Lucia Espona Akos Balasko Hendrik Weisser Mi-Youn Brusniak Peter Kunszt Ruedi Aebersold Lars Malmström |
| author_sort | Andreas Quandt |
| collection | DOAJ |
| description | 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 20,103 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. |
| first_indexed | 2024-12-12T10:10:15Z |
| format | Article |
| id | doaj.art-62e5854b56534d75b758102c65373d4d |
| institution | Directory Open Access Journal |
| issn | 2212-9685 |
| language | English |
| last_indexed | 2024-12-12T10:10:15Z |
| publishDate | 2014-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | EuPA Open Proteomics |
| spelling | doaj.art-62e5854b56534d75b758102c65373d4d2022-12-22T00:27:49ZengElsevierEuPA Open Proteomics2212-96852014-12-015C213110.1016/j.euprot.2014.10.001Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysisAndreas Quandt0Lucia Espona1Akos Balasko2Hendrik Weisser3Mi-Youn Brusniak4Peter Kunszt5Ruedi Aebersold6Lars Malmström7Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, SwitzerlandDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, SwitzerlandMTA SZTAKI, Laboratory of Parallel and Distributed Systems, Budapest, HungaryDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, SwitzerlandInstitute for Systems Biology, Seattle, USASyBIT, SystemsX.ch, SwitzerlandDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, SwitzerlandDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, SwitzerlandTandem 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 20,103 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.http://www.sciencedirect.com/science/article/pii/S221296851400066XMass spectrometryData analysisClassical database searchSynthetic peptidesSearch engine |
| spellingShingle | Andreas Quandt Lucia Espona Akos Balasko Hendrik Weisser Mi-Youn Brusniak Peter Kunszt Ruedi Aebersold Lars Malmström Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis EuPA Open Proteomics Mass spectrometry Data analysis Classical database search Synthetic peptides Search engine |
| title | Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis |
| title_full | Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis |
| title_fullStr | Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis |
| title_full_unstemmed | Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis |
| title_short | Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis |
| title_sort | using synthetic peptides to benchmark peptide identification software and search parameters for ms ms data analysis |
| topic | Mass spectrometry Data analysis Classical database search Synthetic peptides Search engine |
| url | http://www.sciencedirect.com/science/article/pii/S221296851400066X |
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