Evidence map›Paper›PMID 24760958›Full record

ArticleMolecular & cellular proteomics : MCP2014

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

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 and 19 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular & cellular proteomics : MCP, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

14 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Article
  6. Article
  7. A Golden Age for Working with Public Proteomics Data.Trends in biochemical sciences · 2017
    Review
  8. Review
  9. Article
  10. Article
  11. Article
  12. Article
  13. Review
  14. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

29 authors.

Mathias WalzerFrom the ‡Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany;
Lucia Espona Pernas§Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland;
Sara Nasso¶Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland; §Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland;
Wout Bittremieux‖Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; **Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Antwerp, Belgium;
Sven NahnsenFrom the ‡Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany;
Pieter Kelchtermans‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; ¶¶Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol Belgium;
Peter Pichler‖‖Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, A-1030 Vienna, Austria;
Henk W P van den ToornBiomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands;
An Staes‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium;
Jonathan Vandenbussche‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium;
Michael Mazanek‖‖Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, A-1030 Vienna, Austria;
Thomas Taus‖‖Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, A-1030 Vienna, Austria;
Richard A ScheltemaDepartment of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;
Christian D KelstrupNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark;
Laurent GattoCambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom; Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
Bas van BreukelenBiomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands;
Stephan AicheDepartment of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany;
Dirk Valkenborg¶¶Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol Belgium; I-BioStat, Hasselt University, Belgium; CFP-CeProMa, University of Antwerp, Belgium;
Kris Laukens‖Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; **Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Antwerp, Belgium;
Kathryn S LilleyCambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom;
Jesper V OlsenNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark;
Albert J R HeckBiomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands;
Karl Mechtler‖‖Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, A-1030 Vienna, Austria;
Ruedi Aebersold§Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland;
Kris Gevaert‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium;
Juan Antonio VizcaínoEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
Henning HermjakobEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
Oliver KohlbacherFrom the ‡Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany;
Lennart Martens‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; lennart.martens@vib-ugent.be.

Funding

Wellcome TrustWellcome Trust WT085949MA
6 · The paper itself

Abstract

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.

Indexed as

SoftwareDatabases, ProteinMass SpectrometryProgramming LanguagesProteomicsQuality Control

Identifiers

PMID24760958
PMCPMC4125725

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.