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.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

“…3). OpenMS provides implementations for over 30 file formats, including the current and upcoming open standards defined by the Proteomics Standards Initiative of the Human Proteome Organization (HUPO-PSI) such as mzML, TraML, mzIdentML, mzQuantML, mzTab and qcML [2,3,4,5,17,18] (see Supplementary Note 1). In addition, OpenMS includes standard algorithms related to biomolecular properties (such as mass calculation, isotopic composition, protein digestion etc.)…”

“…Past efforts to mitigate these issues have led to the development of standardized data exchange formats [2,3,4,5] , which have recently been adopted by several software projects [6,7,8,9,10] . These standard formats enable the integration of tools from different sources, simplify the analysis of MS data from multiple vendors, and render published results more readily accessible.…”

Exploring the potential of public proteomics data

“…This ongoing endeavor, led by the HUPO‐PSI (Human Proteome Organization−Proteomics Standards Initiative−http://www.psidev.info), has resulted in key data standards for the field, including mzML (for MS data), mzIdentML (for peptide/protein identification data), mzTab (for peptide/protein identification and quantification data), mzQuantML (for peptide/protein quantification data), and TraML (for transition lists in targeted proteomics approaches) 18, 19, 20, 21, 22. Importantly, support for these standards is provided through software libraries or tools such as ProteoWizard 23, PRIDE Converter 24, 25, mzidLibrary 26, and PRIDE Inspector 27.…”

The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard

“…First, the PSI has written minimum reporting guidelines describing what information should be included in a materials and methods section of an article or accompanying a data set, described in a “parent” document 1 and a set of modules describing individual techniques used in proteomics 2, 3, 4, 5, 6, 7, 8. Second, the PSI has developed standard data formats, including mzML for raw or processed MS data 9, mzIdentML for peptide or protein identification data 10 and two formats with different levels of support for quantitative data – mzQuantML 11 and mzTab 12 (further described below). Third, the different data formats require a common terminology set, which is captured in a controlled vocabulary (CV) – called the PSI‐MS CV 13.…”

“…There is a close association between mzQuantML and the recently released mzTab format 12. mzTab similarly captures quantitative values about peptides and proteins, measured across individual samples or grouped replicates ( Assays and StudyVariables ), but in a simplified tab‐separated format designed to be loaded straightforwardly into spreadsheet or statistical processing software.…”