mzQuantML

mzQuantML is an XML-based data standard developed by the Proteomics Standards Initiative (PSI) for representing quantitative mass spectrometry data in proteomics experiments. It is designed to encode the full quantitative workflow, from experimental design and sample metadata to peptide and protein level quantifications, along with associated statistics and data provenance. The aim is to enable interoperable data exchange among laboratories and software tools, facilitate reanalysis, and support long-term data preservation.

The standard covers a range of quantification strategies, including label-free quantification, isotopic labeling methods (such as SILAC and ICAT), and isobaric labeling approaches (such as iTRAQ and TMT). It captures quantitative values such as peak areas or intensities, calculated ratios, normalization factors, and statistical measures, together with detailed metadata and measurement units. By organizing quantitative results at multiple levels—peptide, peptide-spectrum match, and protein—it supports both comprehensive reporting and flexible data integration.

Structure and interoperability: mzQuantML defines a formal schema to represent studies, experiments, analytes, quantification methods, and results. It is designed to interoperate with other PSI standards, notably mzML for raw mass spectrometry data and mzIdentML for identifications. Quantification data can reference data from these formats, and the standard employs controlled vocabulary terms to ensure consistent annotation of methods, units, and concepts across platforms.

History and status: mzQuantML was developed as part of the PSI’s family of proteomics data standards to promote data sharing and reproducibility. It has influenced subsequent data representations and is supported by tools within the proteomics community, though adoption varies by workflow and software ecosystem.