Research Explorer

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Project

A novel era in proteomics-based protein PTM discovery through deep learning approaches

Outputs and Outcomes

Publications

Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring

Patrick WillemsFabien Henri TheryLaura Van MoortelMargaux De MeyerAn StaesAdillah GulLyudmila KovalchukeArthur DeclercqRobbe DevreeseRobbin BouwmeesterRalf GabrielsLennart MartensFrancis Impens et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

TIMS2Rescore : a data dependent acquisition-parallel accumulation and serial fragmentation-optimized data-driven rescoring pipeline based on MS2Rescore

Arthur DeclercqRobbe DevreeseJonas ScheidCaroline JachmannTim Van Den BosscheAnnica PreikschatDavid Gomez-ZepedaJeewan Babu RijalAurelie HirschlerJonathan R. KriegerTharan SrikumarGeorge RosenbergerClaudia MartelliDennis TredeChristine CarapitoStefan TenzerJuliane S. WalzSven DegroeveRobbin BouwmeesterLennart MartensRalf Gabriels et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links

Arslan SirajRobbin BouwmeesterArthur DeclercqLuisa WelpAleksandar ChernevAlexander WulfHenning UrlaubLennart MartensSven DegroeveOliver KohlbacherTimo Sachsenberg et al.

A1 Journal Article in PROTEOMICS

Bioinformatics pipeline for processing single-cell data

Arthur DeclercqNina DemeulemeesterRalf GabrielsRobbin BouwmeesterSven DegroeveLennart Martens

Bookchapter in Mass spectrometry based single cell proteomics

MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0

Louise M. BuurArthur DeclercqMarina StroblRobbin BouwmeesterSven DegroeveLennart MartensViktoria DorferRalf Gabriels

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Updated MS²PIP web server supports cutting-edge proteomics applications

Arthur DeclercqRobbin BouwmeesterCristina ChivaEduard SabidoAurelie HirschlerChristine CarapitoLennart MartensSven DegroeveRalf Gabriels

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Quality control for the target decoy approach for peptide identification

Elke DebrieMilan MalfaitRalf GabrielsArthur DeclercqAdriaan StickerLennart MartensLieven Clement

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

ProteomicsML : an online platform for community-curated data sets and tutorials for machine learning in proteomics

Tobias G. RehfeldtRalf GabrielsRobbin BouwmeesterSiegfried GessulatBenjamin A. NeelyMagnus PalmbladYasset Perez-RiverolTobias SchmidtJuan Antonio VizcaínoEric W. Deutsch

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

psm_utils : a high-level python API for parsing and handling peptide-spectrum matches and proteomics search results

Ralf GabrielsArthur DeclercqRobbin BouwmeesterSven DegroeveLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH