TraML: a standard format for exchange of selected reaction monitoring transition lists
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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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 reservedProteomics 08/2014; 15(5-6). DOI:10.1002/pmic.201400302 · 3.97 Impact Factor
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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 (http://code.google.com/p/jmzquantml/).The 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 (http://code.google.com/p/mzquantml-validator/) for validating mzQuantML files, which is a formal part of the data standard.This article is protected by copyright. All rights reservedProteomics 03/2014; DOI:10.1002/pmic.201300281 · 3.97 Impact Factor
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ABSTRACT: This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the "mapping files" used to ensure correct controlled vocabulary terms are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements.Biochimica et Biophysica Acta 02/2013; 1844(1). DOI:10.1016/j.bbapap.2013.02.017 · 4.66 Impact Factor