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Prediction of Hopeless Peptides Unlikely to be Selected for Targeted Proteome Analysis
In targeted proteomics using liquid chromatography-tandem triple quadrupole mass spectrometry (LC/MS/MS) in the selected reaction monitoring (SRM) mode, selecting the best observable or visible peptides is a key step in the development of SRM assay methods of target proteins. A direct comparison of...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Mass Spectrometry Society of Japan
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451515/ https://www.ncbi.nlm.nih.gov/pubmed/28580222 http://dx.doi.org/10.5702/massspectrometry.A0056 |
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author | Matsuda, Fumio Tomita, Atsumi Shimizu, Hiroshi |
author_facet | Matsuda, Fumio Tomita, Atsumi Shimizu, Hiroshi |
author_sort | Matsuda, Fumio |
collection | PubMed |
description | In targeted proteomics using liquid chromatography-tandem triple quadrupole mass spectrometry (LC/MS/MS) in the selected reaction monitoring (SRM) mode, selecting the best observable or visible peptides is a key step in the development of SRM assay methods of target proteins. A direct comparison of signal intensities among all candidate peptides by brute-force LC/MS/MS analysis is a concrete approach for peptide selection. However, the analysis requires an SRM method with hundreds of transitions. This study reports on the development of a method for predicting and identifying hopeless peptides to reduce the number of candidate peptides needed for brute-force experiments. Hopeless peptides are proteotypic peptides that are unlikely to be selected for targets in SRM analysis owing to their poor ionization characteristics. Targeted proteomics data from Escherichia coli demonstrated that the relative ionization efficiency between two peptides could be predicted from sequences of two peptides, when a multivariate regression model is used. Validation of the method showed that >20% of the candidate peptides could be successfully eliminated as hopeless peptides with a false positive rate of less than 2%. |
format | Online Article Text |
id | pubmed-5451515 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | The Mass Spectrometry Society of Japan |
record_format | MEDLINE/PubMed |
spelling | pubmed-54515152017-06-02 Prediction of Hopeless Peptides Unlikely to be Selected for Targeted Proteome Analysis Matsuda, Fumio Tomita, Atsumi Shimizu, Hiroshi Mass Spectrom (Tokyo) Original Article In targeted proteomics using liquid chromatography-tandem triple quadrupole mass spectrometry (LC/MS/MS) in the selected reaction monitoring (SRM) mode, selecting the best observable or visible peptides is a key step in the development of SRM assay methods of target proteins. A direct comparison of signal intensities among all candidate peptides by brute-force LC/MS/MS analysis is a concrete approach for peptide selection. However, the analysis requires an SRM method with hundreds of transitions. This study reports on the development of a method for predicting and identifying hopeless peptides to reduce the number of candidate peptides needed for brute-force experiments. Hopeless peptides are proteotypic peptides that are unlikely to be selected for targets in SRM analysis owing to their poor ionization characteristics. Targeted proteomics data from Escherichia coli demonstrated that the relative ionization efficiency between two peptides could be predicted from sequences of two peptides, when a multivariate regression model is used. Validation of the method showed that >20% of the candidate peptides could be successfully eliminated as hopeless peptides with a false positive rate of less than 2%. The Mass Spectrometry Society of Japan 2017 2017-06-02 /pmc/articles/PMC5451515/ /pubmed/28580222 http://dx.doi.org/10.5702/massspectrometry.A0056 Text en Copyright © 2017 Fumio Matsuda, Atsumi Tomita, and Hiroshi Shimizu. http://creativecommons.org/licenses/by-nc/3.0/ This is an open access article distributed under the terms of Creative Commons Attribution License, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. For permission to reuse copyrighted content from this publication, please go to www.copyright.com (http://www.copyright.com) , or contact Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923 |
spellingShingle | Original Article Matsuda, Fumio Tomita, Atsumi Shimizu, Hiroshi Prediction of Hopeless Peptides Unlikely to be Selected for Targeted Proteome Analysis |
title | Prediction of Hopeless Peptides Unlikely to be Selected for Targeted Proteome Analysis |
title_full | Prediction of Hopeless Peptides Unlikely to be Selected for Targeted Proteome Analysis |
title_fullStr | Prediction of Hopeless Peptides Unlikely to be Selected for Targeted Proteome Analysis |
title_full_unstemmed | Prediction of Hopeless Peptides Unlikely to be Selected for Targeted Proteome Analysis |
title_short | Prediction of Hopeless Peptides Unlikely to be Selected for Targeted Proteome Analysis |
title_sort | prediction of hopeless peptides unlikely to be selected for targeted proteome analysis |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451515/ https://www.ncbi.nlm.nih.gov/pubmed/28580222 http://dx.doi.org/10.5702/massspectrometry.A0056 |
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