jmzTab-M: A Reference Parser, Writer and Validator for the Proteomics Standards Initiative mzTab 2.0 Metabolomics Standard

Nils Hoffmann, Jürgen Hartler, Robert Ahrends

Research output: Contribution to journalArticleResearchpeer-review

Abstract

mzTab 2.0 for metabolomics (mzTab-M) is the most recent standard format developed in collaboration by the Proteomics and Metabolomics Standards Initiatives including contributions by the recently founded Lipidomics Standards Initiative. mzTab-M is a redesign of the original mzTab format which was geared towards reporting of proteomics results, and as such provided only limited support for metabolites. As a tab-delimited, spread-sheet like format, mzTab-M captures experimental metadata, summary information on small molecules across assays, MS features as a basis for quantitation, and evidence to support reporting of individual or feature group identifications. Here, we present the Java reference implementation for reading, writing and validating mzTab-M files. Furthermore, we provide a web-application for conveniently validating mzTab-M files by a graphical user interface, and a command line validator that accompanies the library. The jmzTab-M library, version 1.0.41 is available at https://github.com/lifs-tools/jmzTab-m and from Maven Central at https://search.maven.org/search?q=jmztabm under the terms of the open source Apache License 2.0. The web-application, as well as the Python and R implementations are available at https://github.com/lifs-tools. The respective websites link to additional API documentation, as well as to usage examples.

Original languageEnglish
Number of pages4
JournalAnalytical Chemistry
DOIs
Publication statusE-pub ahead of print - 17 Sep 2019

Keywords

  • Mass spectrometry
  • Metabolomics
  • data format
  • experimental results
  • controlled vocabulary
  • semantic validation

ASJC Scopus subject areas

  • Computer Science Applications

Fields of Expertise

  • Human- & Biotechnology

Treatment code (Nähere Zuordnung)

  • Application

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