Instrument-Software Synergy in Proteomics: Systematic Evaluation Across Mass Spectrometry Platforms, Search Engines, and Rescoring Methods

ChemRxiv

Authors 13

1. Sander Heyndrickx

   Ghent University · VIB-UGent Center for Medical Biotechnology

   Affiliation as printed

   Faculty of Medicine and Health Sciences

   Ghent University

   VIB

   VIB-UGent Center for Medical Biotechnology

2. Robbin Bouwmeester

   Ghent University · VIB-UGent Center for Medical Biotechnology

   Affiliation as printed

   Faculty of Medicine and Health Sciences

   Ghent University

   VIB

   VIB-UGent Center for Medical Biotechnology

3. Arthur Declercq

   Ghent University · VIB-UGent Center for Medical Biotechnology

   Affiliation as printed

   Faculty of Medicine and Health Sciences

   Ghent University

   VIB

   VIB-UGent Center for Medical Biotechnology

4. Robbe Devreese

   Ghent University · VIB-UGent Center for Medical Biotechnology

   Affiliation as printed

   Faculty of Medicine and Health Sciences

   Ghent University

   VIB

   VIB-UGent Center for Medical Biotechnology

5. Magnus Palmblad Aachen

   Leiden University Medical Center

   Affiliation as printed

   Center for Proteomics and Metabolomics

   Leiden University Medical Center

6. Wout Bittremieux

   University of Antwerp

   Affiliation as printed

   Department of Computer Science

   University of Antwerp

7. Tess A. V. Afanasyeva

   The Netherlands Cancer Institute · Sanquin

   Affiliation as printed

   Department of Radiation Oncology

   Netherlands Cancer Institute

   Sanquin Research and Landsteiner Laboratory

8. Joel Lapin

   Technical University of Munich

   Affiliation as printed

   Computational Mass Spectrometry

   Technical University of Munich

9. Arzu Tuğçe Güler

   Boston Children's Hospital · Northeastern University · Harvard University

   Affiliation as printed

   Boston Children's Hospital

   Department of Pathology

   Harvard Medical School

   Institute for Experiential AI

   Northeastern University

10. Pierre-Olivier Schmit

    Bruker (France)

    Affiliation as printed

    Bruker France SAS

11. Christine Carapito

    Centre National de la Recherche Scientifique · Proteomics French Infrastructure Core

    Affiliation as printed

    CNRS

    Infrastructure Nationale de Protéomique ProFI − UAR 2048

12. Lennart Martens

    Centre National de la Recherche Scientifique · Ghent University · VIB-UGent Center for Medical Biotechnology · Proteomics French Infrastructure Core

    Affiliation as printed

    CNRS

    Faculty of Medicine and Health Sciences

    Ghent University

    Infrastructure Nationale de Protéomique ProFI − UAR 2048

    VIB

    VIB-UGent Center for Medical Biotechnology

13. Ralf Gabriels

    Ghent University · VIB-UGent Center for Medical Biotechnology

    Affiliation as printed

    Faculty of Medicine and Health Sciences

    Ghent University

    VIB

    VIB-UGent Center for Medical Biotechnology