Evidence map›Paper›PMID 39743223›Full record

ArticleJournal of proteome research2025

A Multiyear Longitudinal Harmonization Study of Quality Controls in Mass Spectrometry Proteomics Core Facilities.

Cristina Chiva, Roger Olivella, An Staes, Teresa Mendes Maia, Christian Panse, Karel Stejskal, Thibaut Douché, Bérangère Lombard, Andrea Schuhmann, Damarys Loew and 9 more

Abstract read
In one paragraph

Article in Journal of proteome research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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

19 authors.

Cristina ChivaCentre for Genomic Regulation, The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.
Roger OlivellaCentre for Genomic Regulation, The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.
An StaesVIB Proteomics Core, VIB, Ghent 9052, Belgium.ORCID 0000-0001-8767-8508
Teresa Mendes MaiaVIB Proteomics Core, VIB, Ghent 9052, Belgium.ORCID 0000-0003-0038-9629
Christian PanseFunctional Genomics Center Zurich, University/ETH Zurich, Zurich 8057, Switzerland.ORCID 0000-0003-1975-3064
Karel StejskalResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria.
Thibaut DouchéInstitut Pasteur, CNRS UAR 2024, Proteomics Platform, Mass Spectrometry for Biology Unit, Université Paris Cité, Paris F-75015, France.ORCID 0000-0001-8627-6726
Bérangère LombardInstitut Curie, Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, PSL Research University, Paris 75248, France.
Andrea SchuhmannMax Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany.
Damarys LoewInstitut Curie, Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, PSL Research University, Paris 75248, France.
Karl MechtlerResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria.ORCID 0000-0002-3392-9946
Mariette MatondoInstitut Pasteur, CNRS UAR 2024, Proteomics Platform, Mass Spectrometry for Biology Unit, Université Paris Cité, Paris F-75015, France.
Mandy RettelProteomics Core Facility, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
Dominic HelmProteomics Core Facility, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
Francis ImpensVIB Proteomics Core, VIB, Ghent 9052, Belgium.ORCID 0000-0003-2886-9616
Simon DevosVIB Proteomics Core, VIB, Ghent 9052, Belgium.ORCID 0000-0002-0623-433X
Anna ShevchenkoMax Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany.
Paolo NanniFunctional Genomics Center Zurich, University/ETH Zurich, Zurich 8057, Switzerland.ORCID 0000-0001-8429-3557
Eduard SabidóCentre for Genomic Regulation, The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.ORCID 0000-0001-6506-7714

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Quality control procedures play a pivotal role in ensuring the reliability and consistency of data generated in mass spectrometry-based proteomics laboratories. However, the lack of standardized quality control practices across laboratories poses challenges for data comparability and reproducibility. In response, we conducted a harmonization study within proteomics laboratories of the Core for Life alliance with the aim of establishing a common quality control framework, which facilitates comprehensive quality assessment and identification of potential sources of performance drift. Through collaborative efforts, we developed a consensus quality control standard for longitudinal assessment and adopted common processing software. We generated a 4-year longitudinal data set from multiple instruments and laboratories, which enabled us to assess intra- and interlaboratory variability, to identify causes of performance drift, and to establish community reference values for several quality control parameters. Our study enhances data comparability and reliability and fosters a culture of collaboration and continuous improvement within the proteomics community to ensure the integrity of proteomics data.

Indexed as

Mass SpectrometryProteomicsHumansLaboratoriesLongitudinal StudiesQuality ControlReproducibility of ResultsSoftwareliquid chromatographylongitudinal studymass spectrometryproteomicsquality control

Identifiers

PMID39743223
PMCPMC11811999

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.