qcML: an exchange format for quality control metrics from mass spectrometry experiments

Research output: Contribution to journalJournal articlepeer-review

  • Mathias Walzer
  • Lucia Espona Pernas
  • Sara Nasso
  • Wout Bittremieux
  • Sven Nahnsen
  • Pieter Kelchtermans
  • Peter Pichler
  • Henk W P van den Toorn
  • An Staes
  • Jonathan Vandenbussche
  • Michael Mazanek
  • Thomas Taus
  • Richard A Scheltema
  • Christian D Kelstrup
  • Laurent Gatto
  • Bas van Breukelen
  • Stephan Aiche
  • Dirk Valkenborg
  • Kris Laukens
  • Kathryn S Lilley
  • Albert J R Heck
  • Karl Mechtler
  • Ruedi Aebersold
  • Kris Gevaert
  • Juan Antonio Vizcaino
  • Henning Hermjakob
  • Oliver Kohlbacher
  • Lennart Martens
Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml.
Original languageEnglish
JournalMolecular & Cellular Proteomics
Volume13
Issue number8
Pages (from-to)1905-1913
Number of pages9
ISSN1535-9484
DOIs
Publication statusPublished - 23 Apr 2014

ID: 110600165