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


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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    ABSTRACT: Ten years ago, the first public proteomics repositories became available online. This anniversary is therefore an excellent occasion to look back on the past decade and evaluate what has changed in this time period. At the same time however, one should also dare to look forward, and therefore prepare for the next 10 years of proteomics data sharing.
    Full-text · Article · Jul 2015 · EuPA Open Proteomics
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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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    ABSTRACT: Compared to other data intensive disciplines such as genomics, public deposition and storage of mass spectrometry (MS)-based proteomics data is still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas and the PRoteomics IDEntifications (PRIDE) database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, MassIVE, Chorus, MaxQB, PASSEL, MOPED and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed for enabling a better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data.This article is protected by copyright. All rights reserved
    Full-text · Article · Aug 2014 · Proteomics
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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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    ABSTRACT: The mzQuantML standard from the HUPO Proteomics Standards Initiative (PSI) has recently been released, capturing quantitative data about peptides and proteins, following analysis of mass spectrometry (MS) data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools ( mzQuantML standard is designed around a multi-level validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool ( for validating mzQuantML files, which is a formal part of the data standard.This article is protected by copyright. All rights reserved
    Full-text · Article · Mar 2014 · Proteomics
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