The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience

Abstract

The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online.

Cited by papers we hold 13

• The PRIDE database at 20 years: 2025 update · 2024
  No notice
• PaxDb 5.0: Curated Protein Quantification Data Suggests Adaptive Proteome Changes in Yeasts · 2023
  No notice
• The ProteomeXchange consortium at 10 years: 2023 update · 2022
  No notice
• A knowledge graph to interpret clinical proteomics data · 2022
  No notice
• The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences · 2021
  No notice
• A proteomics sample metadata representation for multiomics integration and big data analysis · 2021
  No notice
• MaxDIA enables library-based and library-free data-independent acquisition proteomics · 2021
  No notice
• The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics · 2019
  No notice
• The PRIDE database and related tools and resources in 2019: improving support for quantification data · 2018
  No notice
• The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition · 2016
  No notice
• PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets · 2016
  No notice
• 2016 update of the PRIDE database and its related tools · 2015
  No notice
• Making proteomics data accessible and reusable: Current state of proteomics databases and repositories · 2015
  No notice

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.