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TraML: a standard format for exchange of selected reaction monitoring transition lists

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Abstract
Targeted proteomics via selected reaction monitoring (SRM) 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 SRM.
Keywords
SOFTWARE, PROTEOMICS DATA, QUANTITATIVE-ANALYSIS, MASS-SPECTROMETRY, PROTEIOS, CAPTURE, MIAPE, PSI

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MLA
Deutsch, Eric W, Matthew Chambers, Steffen Neumann, et al. “TraML: a Standard Format for Exchange of Selected Reaction Monitoring Transition Lists.” MOLECULAR & CELLULAR PROTEOMICS 11.4 (2012): n. pag. Print.
APA
Deutsch, E. W., Chambers, M., Neumann, S., Levander, F., Binz, P.-A., Shofstahl, J., Campbell, D. S., et al. (2012). TraML: a standard format for exchange of selected reaction monitoring transition lists. MOLECULAR & CELLULAR PROTEOMICS, 11(4).
Chicago author-date
Deutsch, Eric W, Matthew Chambers, Steffen Neumann, Fredrik Levander, Pierre-Alain Binz, Jim Shofstahl, David S Campbell, et al. 2012. “TraML: a Standard Format for Exchange of Selected Reaction Monitoring Transition Lists.” Molecular & Cellular Proteomics 11 (4).
Chicago author-date (all authors)
Deutsch, Eric W, Matthew Chambers, Steffen Neumann, Fredrik Levander, Pierre-Alain Binz, Jim Shofstahl, David S Campbell, Luis Mendoza, David Ovelleiro, Kenny Helsens, Lennart Martens, Ruedi Aebersold, Robert L Moritz, and Mi-Youn Brusniak. 2012. “TraML: a Standard Format for Exchange of Selected Reaction Monitoring Transition Lists.” Molecular & Cellular Proteomics 11 (4).
Vancouver
1.
Deutsch EW, Chambers M, Neumann S, Levander F, Binz P-A, Shofstahl J, et al. TraML: a standard format for exchange of selected reaction monitoring transition lists. MOLECULAR & CELLULAR PROTEOMICS. 2012;11(4).
IEEE
[1]
E. W. Deutsch et al., “TraML: a standard format for exchange of selected reaction monitoring transition lists,” MOLECULAR & CELLULAR PROTEOMICS, vol. 11, no. 4, 2012.
@article{2031104,
  abstract     = {{Targeted proteomics via selected reaction monitoring (SRM) 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 SRM.}},
  author       = {{Deutsch, Eric W and Chambers, Matthew and Neumann, Steffen and Levander, Fredrik and Binz, Pierre-Alain and Shofstahl, Jim and Campbell, David S and Mendoza, Luis and Ovelleiro, David and Helsens, Kenny and Martens, Lennart and Aebersold, Ruedi and Moritz, Robert L and Brusniak, Mi-Youn}},
  issn         = {{1535-9476}},
  journal      = {{MOLECULAR & CELLULAR PROTEOMICS}},
  keywords     = {{SOFTWARE,PROTEOMICS DATA,QUANTITATIVE-ANALYSIS,MASS-SPECTROMETRY,PROTEIOS,CAPTURE,MIAPE,PSI}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{6}},
  title        = {{TraML: a standard format for exchange of selected reaction monitoring transition lists}},
  url          = {{http://dx.doi.org/10.1074/mcp.R111.015040}},
  volume       = {{11}},
  year         = {{2012}},
}

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