title: 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.
authors.affiliation: Quantitative Biology Center and Department of Computer Science, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
authors.forename: Mathias
authors.initials: M
authors.lastname: Walzer
authors.forename: Da
authors.initials: D
authors.lastname: Qi
authors.forename: Gerhard
authors.initials: G
authors.lastname: Mayer
authors.forename: Julian
authors.initials: J
authors.lastname: Uszkoreit
authors.forename: Martin
authors.initials: M
authors.lastname: Eisenacher
authors.forename: Timo
authors.initials: T
authors.lastname: Sachsenberg
authors.forename: Faviel F
authors.initials: FF
authors.lastname: Gonzalez-Galarza
authors.forename: Jun
authors.initials: J
authors.lastname: Fan
authors.forename: Conrad
authors.initials: C
authors.lastname: Bessant
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: Florian
authors.initials: F
authors.lastname: Reisinger
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
authors.forename: J Alberto
authors.initials: JA
authors.lastname: Medina-Aunon
authors.forename: Juan Pablo
authors.initials: JP
authors.lastname: Albar
authors.forename: Oliver
authors.initials: O
authors.lastname: Kohlbacher
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jones
mesh_terms: D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods / Q000592:standards*; D008962:Models, Theoretical; D040901:Proteomics / Q000379:methods / Q000592:standards*; D012984:Software