mzTab-M: a data standard for sharing quantitative results in mass spectrometry metabolomics

Nils Hoffmann, Joel Rein, Timo Tobias Sachsenberg, Jürgen Hartler, Kenneth Haug, Gerhard Mayer, Oliver Alka, Saravanan Dayalan, Jake Thomas Midwinter Pearce, Philippe Rocca-Serra, Da Qi, Martin Eisenacher, Yasset Perez-Riverol, Juan Antonio Vizcaíno, Reza M Salek, Steffen Neumann, Andrew R Jones

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Mass spectrometry (MS) is one of the primary techniques used for large scale analysis of small molecules in metabolomics studies. To date, there has been little data format standardization in this field, as different software packages export results in different formats represented in XML or plain text, making data sharing, database deposition and re-analysis highly challenging. Working within the consortia of the Metabolomics Standards Initiative, Proteomics Standards Initiative and the Metabolomics Society, we have created mzTab-M to act as common output format from analytical approaches using MS on small molecules. The format has been developed over several years, with input from a wide range of stakeholders. mzTab-M is a simple tab-separated text format, but, importantly, the structure is highly standardized through the design of a detailed specification document, tightly coupled to validation software, and a mandatory controlled vocabulary of terms to populate it. The format is able to represent final quantification values from analyses, as well as the evidence trail in terms of features measured directly from MS (e.g. LC-MS, GC-MS, DIMS, etc), as well as different types of approaches used to identify molecules. mzTab-M allows for ambiguity in the identification of molecules to be communicated clearly to readers of the files (both people and software). There are several implementations of the format available, and we anticipate widespread adoption in the field.

LanguageEnglish
Pages3302-3310
Number of pages9
JournalAnalytical Chemistry
Volume91
Issue number5
DOIs
StatusPublished - 28 Jan 2019

Fingerprint

Mass spectrometry
Molecules
Thesauri
XML
Software packages
Standardization
Metabolomics
Specifications

Keywords

  • file format
  • standardization
  • Metabolomics
  • data standard
  • Quantification
  • Lipidomics

ASJC Scopus subject areas

  • Computer Science (miscellaneous)

Fields of Expertise

  • Human- & Biotechnology
  • Information, Communication & Computing

Treatment code (Nähere Zuordnung)

  • Application

Cooperations

  • BioTechMed-Graz

Cite this

Hoffmann, N., Rein, J., Sachsenberg, T. T., Hartler, J., Haug, K., Mayer, G., ... Jones, A. R. (2019). mzTab-M: a data standard for sharing quantitative results in mass spectrometry metabolomics. Analytical Chemistry, 91(5), 3302-3310. https://doi.org/10.1021/acs.analchem.8b04310

mzTab-M: a data standard for sharing quantitative results in mass spectrometry metabolomics. / Hoffmann, Nils; Rein, Joel; Sachsenberg, Timo Tobias; Hartler, Jürgen; Haug, Kenneth; Mayer, Gerhard; Alka, Oliver; Dayalan, Saravanan; Pearce, Jake Thomas Midwinter; Rocca-Serra, Philippe; Qi, Da; Eisenacher, Martin; Perez-Riverol, Yasset; Vizcaíno, Juan Antonio; Salek, Reza M; Neumann, Steffen; Jones, Andrew R.

In: Analytical Chemistry, Vol. 91, No. 5, 28.01.2019, p. 3302-3310.

Research output: Contribution to journalArticleResearchpeer-review

Hoffmann, N, Rein, J, Sachsenberg, TT, Hartler, J, Haug, K, Mayer, G, Alka, O, Dayalan, S, Pearce, JTM, Rocca-Serra, P, Qi, D, Eisenacher, M, Perez-Riverol, Y, Vizcaíno, JA, Salek, RM, Neumann, S & Jones, AR 2019, 'mzTab-M: a data standard for sharing quantitative results in mass spectrometry metabolomics', Analytical Chemistry, vol. 91, no. 5, pp. 3302-3310. https://doi.org/10.1021/acs.analchem.8b04310
Hoffmann, Nils ; Rein, Joel ; Sachsenberg, Timo Tobias ; Hartler, Jürgen ; Haug, Kenneth ; Mayer, Gerhard ; Alka, Oliver ; Dayalan, Saravanan ; Pearce, Jake Thomas Midwinter ; Rocca-Serra, Philippe ; Qi, Da ; Eisenacher, Martin ; Perez-Riverol, Yasset ; Vizcaíno, Juan Antonio ; Salek, Reza M ; Neumann, Steffen ; Jones, Andrew R. / mzTab-M: a data standard for sharing quantitative results in mass spectrometry metabolomics. In: Analytical Chemistry. 2019 ; Vol. 91, No. 5. pp. 3302-3310.
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