Author

Magnus Palmblad

Leiden University Medical CenterORCID 0000-0002-5865-8994Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 5

Signature Assays, Organisms & Methods

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Assay:proteomics· 5 Research Focus:benchmarking· 4 Approach:benchmark study· 2 Organism:E. coli· 1 Approach:experimental assay· 1 Organism:human· 1 Approach:simulation· 1 Approach:statistical model· 1

Frequent Co-Authors

Julian UszkoreitiD· 2 shared Veit SchwämmleiD· 2 shared Yasset Pérez‐RiveroliD· 2 shared Alireza NameniiD· 1 shared An StaesiD· 1 shared Balázs KunkliiD· 1 shared Baozhen ShaniD· 1 shared Bart Van PuyveldeiD· 1 shared

Activity by Year

2018-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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2 shared papersBioinformatics

Julian UszkoreitORCID

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5 papers

Recent·Most cited

ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

Robbe Devreese, Caroline Jachmann, Bart Van Puyvelde, Holda A. Anagho, Witold Wolski, Henry Emanuel Webel, Matthias Mattanovich, Wout Bittremieux, Karima Chaoui, Cristina Chiva, Tine Claeys, Hector Mauricio Castaneda Cortes, Simon Devos, Maarten Dhaenens, Nadezhda T. Doncheva, , Marie Locard‐Paulet

ProteoBench provides a centralized platform for comparing proteomics data analysis workflows, enabling benchmarking and community collaboration.

bioRxiv · Dec 20, 2025 · PreprintBioinformatics

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows

David Bouyssié, Pınar Altıner, Salvador Capella-Gutiérrez, José M. Fernández, Yanick Paco Hagemeijer, Peter L. Horvatovich, Martin Hubálek, Fredrik Levander, Pierluigi Mauri, Magnus Palmblad, Wolfgang Raffelsberger, Laura Rodríguez‐Navas, Dario Di Silvestre, Balázs Kunkli, Julian Uszkoreit, , Veit Schwämmle

WOMBAT-P benchmarks label-free proteomics workflows by comparing four analysis pipelines using standardized metrics and datasets.

Journal of Proteome Research · Dec 1, 2023Peer-reviewedBioinformatics

Further Theoretical Considerations for Next-Generation Proteomics

Magnus Palmblad

This paper revisits and expands on previous theoretical considerations for next-generation proteomics by clarifying results, exploring alternative metrics, and conducting new simulations.

bioRxiv · Jun 12, 2021 · PreprintBioinformatics

2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Study

Benjamin A. Neely, Paul M. Stemmer, Brian C. Searle, Laura E. Herring, LeRoy B. Martin, Mukul Kumar Midha, Brett S. Phinney, Baozhen Shan, Magnus Palmblad, Yan Wang, Pratik Dilip Jagtap, Joanna M Kirkpatrick

The paper evaluates DIA performance across multiple laboratories using standardized samples and provides benchmark datasets for education and tool development.

bioRxiv · Nov 20, 2020 · PreprintBioinformatics

A protein standard that emulates homology for the characterization of protein inference algorithms

Matthew The, Fredrik Edfors, Yasset Pérez‐Riverol, Samuel Payne, Michael R. Hoopmann, Magnus Palmblad, Björn Forsström, Lukas Käll

The paper introduces a protein standard with shared peptides to benchmark protein inference algorithms, showing that methods excluding shared peptides provide more accurate error estimates.

Journal of Proteome Research · Apr 10, 2018Peer-reviewedBioinformatics