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TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists

Targeted proteomics via selected reaction monitoring is a powerful mass spectrometric technique affording higher dynamic range, increased specificity and lower limits of detection than other shotgun mass spectrometry methods when applied to proteome analyses. However, it involves selective measureme...

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Autores principales: Deutsch, Eric W., Chambers, Matthew, Neumann, Steffen, Levander, Fredrik, Binz, Pierre-Alain, Shofstahl, Jim, Campbell, David S., Mendoza, Luis, Ovelleiro, David, Helsens, Kenny, Martens, Lennart, Aebersold, Ruedi, Moritz, Robert L., Brusniak, Mi-Youn
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The American Society for Biochemistry and Molecular Biology 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322582/
https://www.ncbi.nlm.nih.gov/pubmed/22159873
http://dx.doi.org/10.1074/mcp.R111.015040
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author Deutsch, Eric W.
Chambers, Matthew
Neumann, Steffen
Levander, Fredrik
Binz, Pierre-Alain
Shofstahl, Jim
Campbell, David S.
Mendoza, Luis
Ovelleiro, David
Helsens, Kenny
Martens, Lennart
Aebersold, Ruedi
Moritz, Robert L.
Brusniak, Mi-Youn
author_facet Deutsch, Eric W.
Chambers, Matthew
Neumann, Steffen
Levander, Fredrik
Binz, Pierre-Alain
Shofstahl, Jim
Campbell, David S.
Mendoza, Luis
Ovelleiro, David
Helsens, Kenny
Martens, Lennart
Aebersold, Ruedi
Moritz, Robert L.
Brusniak, Mi-Youn
author_sort Deutsch, Eric W.
collection PubMed
description Targeted proteomics via selected reaction monitoring is a powerful mass spectrometric technique affording higher dynamic range, increased specificity and lower limits of detection than other shotgun mass spectrometry methods when applied to proteome analyses. However, it involves selective measurement of predetermined analytes, which requires more preparation in the form of selecting appropriate signatures for the proteins and peptides that are to be targeted. There is a growing number of software programs and resources for selecting optimal transitions and the instrument settings used for the detection and quantification of the targeted peptides, but the exchange of this information is hindered by a lack of a standard format. We have developed a new standardized format, called TraML, for encoding transition lists and associated metadata. In addition to introducing the TraML format, we demonstrate several implementations across the community, and provide semantic validators, extensive documentation, and multiple example instances to demonstrate correctly written documents. Widespread use of TraML will facilitate the exchange of transitions, reduce time spent handling incompatible list formats, increase the reusability of previously optimized transitions, and thus accelerate the widespread adoption of targeted proteomics via selected reaction monitoring.
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spelling pubmed-33225822012-04-12 TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists Deutsch, Eric W. Chambers, Matthew Neumann, Steffen Levander, Fredrik Binz, Pierre-Alain Shofstahl, Jim Campbell, David S. Mendoza, Luis Ovelleiro, David Helsens, Kenny Martens, Lennart Aebersold, Ruedi Moritz, Robert L. Brusniak, Mi-Youn Mol Cell Proteomics Technological Innovation and Resources Targeted proteomics via selected reaction monitoring is a powerful mass spectrometric technique affording higher dynamic range, increased specificity and lower limits of detection than other shotgun mass spectrometry methods when applied to proteome analyses. However, it involves selective measurement of predetermined analytes, which requires more preparation in the form of selecting appropriate signatures for the proteins and peptides that are to be targeted. There is a growing number of software programs and resources for selecting optimal transitions and the instrument settings used for the detection and quantification of the targeted peptides, but the exchange of this information is hindered by a lack of a standard format. We have developed a new standardized format, called TraML, for encoding transition lists and associated metadata. In addition to introducing the TraML format, we demonstrate several implementations across the community, and provide semantic validators, extensive documentation, and multiple example instances to demonstrate correctly written documents. Widespread use of TraML will facilitate the exchange of transitions, reduce time spent handling incompatible list formats, increase the reusability of previously optimized transitions, and thus accelerate the widespread adoption of targeted proteomics via selected reaction monitoring. The American Society for Biochemistry and Molecular Biology 2012-04 2011-12-12 /pmc/articles/PMC3322582/ /pubmed/22159873 http://dx.doi.org/10.1074/mcp.R111.015040 Text en © 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) applies to Author Choice Articles
spellingShingle Technological Innovation and Resources
Deutsch, Eric W.
Chambers, Matthew
Neumann, Steffen
Levander, Fredrik
Binz, Pierre-Alain
Shofstahl, Jim
Campbell, David S.
Mendoza, Luis
Ovelleiro, David
Helsens, Kenny
Martens, Lennart
Aebersold, Ruedi
Moritz, Robert L.
Brusniak, Mi-Youn
TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists
title TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists
title_full TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists
title_fullStr TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists
title_full_unstemmed TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists
title_short TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists
title_sort traml—a standard format for exchange of selected reaction monitoring transition lists
topic Technological Innovation and Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322582/
https://www.ncbi.nlm.nih.gov/pubmed/22159873
http://dx.doi.org/10.1074/mcp.R111.015040
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