Article

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

Institute for Systems Biology, Seattle, Washington 98109, USA.
Molecular & Cellular Proteomics (Impact Factor: 6.56). 12/2011; 11(4):R111.015040. DOI: 10.1074/mcp.R111.015040
Source: PubMed

ABSTRACT

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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Available from: Lennart Martens, Aug 19, 2015
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    • "The findings also allow us to make some clear recommendations for the next 10 years of proteomics data sharing. One of the most important developments in the past 10 years of public proteomics data sharing is certainly the development of numerous community standards for the various proteomics data types [8] [9] [10] [11], coupled to minimal reporting guidelines that are all linked to the flagship Minimal Information About a Proteomics Experiment (MIAPE) standard [12]. In principle, these combined developments should have created a common minimal level of data formatting, and metadata annotation for public proteomics data. "
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    • "(i) study metadata, such as dataset title, submitter contact information, sample source, sample preparation , and instrument used; (ii) transition lists describing which transitions were measured for each peptide and targeted ions, along with optional supporting information (collision energy, expected retention time, and expected relative intensities). This information is available in a tab-separated file or in the standard TraML format [50]; and (iii) mass spectrometer output files in mzML [45] or mzXML [48] format . If these are not available, the vendor formats .wiff "
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    • "The Proteomics Standards Initiative (PSI) has been working for a number of years to develop data standards to assist data sharing, software development, and database submissions for the different data types produced in these typical workflows. The PSI has released mzML for raw MS data or peak lists [1], mzIdentML for peptide and protein identification, for example exported from a search engine [2], TraML [3] for encoding transition lists and associated metadata, and, recently, mzQuantML for quantitative data [4]. The model is developed as an Extensible Markup Language (XML) Schema Definition file, accompanied by controlled vocabulary (CV) terms and definitions as part of the PSI-MS CV [5], also used in mzML, mzIdentML, and TraML. "
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