Author

Dennis Trede

Bruker (United States)

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2 Biochemistry· 1

Signature Assays, Organisms & Methods

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Assay:proteomics· 3 Research Focus:benchmarking· 2 Approach:deep learning· 2 Approach:experimental assay· 1 Organism:human· 1 Research Focus:software / tool· 1 Approach:statistical model· 1 Research Focus:variant calling· 1

Frequent Co-Authors

Jonathan R. KriegeriD· 2 shared Tharan SrikumariD· 2 shared Alain J. van GooliD· 1 shared Annica PreikschatiD· 1 shared Arthur DeclercqiD· 1 shared Aurélie HirschleriD· 1 shared Bettina Streckenbach· 1 shared Caroline JachmanniD· 1 shared

Activity by Year

2023-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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2 shared papersBiochemistry

Jonathan R. KriegerORCID

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Author profile →

3 papers

Recent·Most cited

Enhanced Identifications and Quantification through Retention Time Down-Sampling in Fast-Cycling diagonal-PASEF Methods

Christopher Below, Oliver M. Bernhardt, Stephanie Kaspar-Schönefeld, Sander Willems, E. Coronado‐Barrientos, Ino D. Karemaker, Bettina Streckenbach, Monika Pepelnjak, Luca Raess, Sandra Schär, Dennis Trede, Jonathan R. Krieger, Tejas Gandhi, Roland Bruderer, Lukas Reiter

This paper optimizes diagonal-PASEF mass spectrometry with retention time down-sampling, improving identifications and quantification in proteomics.

Molecular & Cellular Proteomics · Dec 10, 2025Peer-reviewedBiochemistry

TIMS2Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS2Rescore

Arthur Declercq, Robbe Devreese, Jonas Scheid, Caroline Jachmann, Tim Van Den Bossche, Annica Preikschat, David Gomez‐Zepeda, Jeewan Babu Rijal, Aurélie Hirschler, Jonathan R. Krieger, Tharan Srikumar, George Rosenberger, Dennis Trede, Christine Carapito, Stefan Tenzer, , Ralf Gabriels

TIMS2Rescore is a data-driven rescoring pipeline optimized for DDA-PASEF data that improves protein identification in proteomics analyses.

bioRxiv · May 29, 2024 · PreprintBioinformatics

The GlycoPaSER prototype as a real-time N-glycopeptide identification tool based on the PaSER parallel computing platform

Gad Armony, Sven Brehmer, Tharan Srikumar, Lennard Pfennig, Fokje Zijlstra, Dennis Trede, Gary H. Kruppa, Dirk J. Lefeber, Alain J. van Gool, Hans J. C. T. Wessels

The paper introduces GlycoPaSER, a real-time glycopeptide identification tool that decomposes spectra and uses specialized algorithms for real-time analysis, matching performance with existing software.

International Journal of Molecular Sciences · Apr 26, 2023Peer-reviewedBioinformatics