The mzQuantML Data Standard for Mass Spectrometry–based Quantitative Studies in Proteomics

Abstract

The range of heterogeneous approaches available for quantifying protein abundance via mass spectrometry (MS)1 leads to considerable challenges in modeling, archiving, exchanging, or submitting experimental data sets as supplemental material to journals. To date, there has been no widely accepted format for capturing the evidence trail of how quantitative analysis has been performed by software, for transferring data between software packages, or for submitting to public databases. In the context of the Proteomics Standards Initiative, we have developed the mzQuantML data standard. The standard can represent quantitative data about regions in two-dimensional retention time versus mass/charge space (called features), peptides, and proteins and protein groups (where there is ambiguity regarding peptide-to-protein inference), and it offers limited support for small molecule (metabolomic) data. The format has structures for representing replicate MS runs, grouping of replicates (for example, as study variables), and capturing the parameters used by software packages to arrive at these values. The format has the capability to reference other standards such as mzML and mzIdentML, and thus the evidence trail for the MS workflow as a whole can now be described. Several software implementations are available, and we encourage other bioinformatics groups to use mzQuantML as an input, internal, or output format for quantitative software and for structuring local repositories. All project resources are available in the public domain from the HUPO Proteomics Standards Initiative http://www.psidev.info/mzquantml.

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

“…The routine is designed to take as input mzQuantML files that have Feature elements containing coordinates ( m/z and RT) and peptide lists containing aligned (but as yet unidentified) PeptideConsensus elements (see 11 for a full description of elements and structures in mzQuantML). The routine requires n mzIdentML files as input – one per FeatureList (e.g.…”

“…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.…”

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.…”