Advanced

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

Deutsch, Eric W.; Chambers, Matthew; Neumann, Steffen; Levander, Fredrik LU ; Binz, Pierre-Alain; Shofstahl, Jim; Campbell, David S.; Mendoza, Luis; Ovelleiro, David and Helsens, Kenny, et al. (2012) In Molecular & Cellular Proteomics 11(4). p.111-015040
Abstract (Swedish)
Abstract in Undetermined

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... (More)
Abstract in Undetermined

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. (Less)
Please use this url to cite or link to this publication:
author
, et al. (More)
(Less)
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Molecular & Cellular Proteomics
volume
11
issue
4
pages
111 - 015040
publisher
American Society for Biochemistry and Molecular Biology
external identifiers
  • wos:000302786500026
  • scopus:84859843750
ISSN
1535-9484
DOI
10.1074/mcp.R111.015040
language
English
LU publication?
yes
id
56a84c71-3224-4e58-942c-1219fe51aa4d (old id 2225759)
date added to LUP
2011-12-19 09:46:14
date last changed
2017-09-24 03:24:54
@article{56a84c71-3224-4e58-942c-1219fe51aa4d,
  abstract     = {<b>Abstract in Undetermined</b><br/><br>
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         = {1535-9484},
  language     = {eng},
  number       = {4},
  pages        = {111--015040},
  publisher    = {American Society for Biochemistry and Molecular Biology},
  series       = {Molecular & Cellular Proteomics},
  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},
}