Research Explorer

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Researcher

Robbin Bouwmeester

Publications & Research Data

Awards & Distinctions

40 Results

2026

The Escherichia coli PeptideAtlas build : characterizing the observed Escherichia coli pan-proteome and its post-translational modifications

Caroline JachmannZhi SunKevin VelgheFlorence Arsène-PloetzeAurélie HirschlerJasper ZuallaertChristine CarapitoRobbin BouwmeesterKay NieseltEric W. Deutsch et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setups

Robbin BouwmeesterAlireza NameniArthur DeclercqRobbe DevreeseKevin VelgheVladimir GorshkovPelayo A. PenanesFrank KjeldsenMagali RompaisChristine Carapito et al.

A1 Journal Article in NATURE COMMUNICATIONS

2025

Classification of collagens via peptide ambiguation, in a paleoproteomic LC-MS/MS-based taxonomic pipeline

Ian EngelsAlexandra BurnettPrudence RobertCamille PironneauGrégory AbramsRobbin BouwmeesterPeter Van Der PlaetsenKévin Di ModicaMarcel OtteLawrence Guy Straus et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Collisional cross-section prediction for multiconformational peptide ions with IM2Deep

Robbe DevreeseAlireza NameniArthur DeclercqEmmy TerrynRalf GabrielsFrancis ImpensKris GevaertLennart MartensRobbin Bouwmeester

A1 Journal Article in ANALYTICAL CHEMISTRY

Koina : democratizing machine learning for proteomics research

Ludwig LautenbacherKevin L. YangTobias KockmannChristian PanseWassim GabrielDulguun BoldElias KahlMatthew ChambersBrendan X. MacLeanKai Li et al.

A1 Journal Article in NATURE COMMUNICATIONS

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 Bouwmeester et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Potential of proteomics in forensic phenotyping : a focus on biological sex estimation

Shirin AlexRuben AlmeyRachel Sian DennisOlivier TytgatRobbin BouwmeesterDieter DeforceMarcel De PuitMaarten DhaenensLaura De Clerck

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. Krieger et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2024

Benefit of in silico predicted spectral libraries in data-independent acquisition data analysis workflows

An StaesTeresa MaiaSara DufourRobbin BouwmeesterRalf GabrielsLennart MartensKris GevaertFrancis ImpensSimon Devos

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Bioinformatics pipeline for processing single-cell data

Arthur DeclercqNina DemeulemeesterRalf GabrielsRobbin BouwmeesterSven DegroeveLennart Martens

Bookchapter in Mass spectrometry based single cell proteomics

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

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

A1 Journal Article in 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

Predicting ion mobility collision cross sections and assessing prediction variation by combining conventional and data driven modeling

Robbin BouwmeesterKeith RichardsonRichard DennyIan D. WilsonSven DegroeveLennart MartensJohannes P.C. Vissers

A1 Journal Article in TALANTA

2023

FAVA : high-quality functional association networks inferred from scRNA-seq and proteomics data

Mikaela KoutrouliPau Piera LíndezKaterina NastouRobbin BouwmeesterSimon RasmussenLennart MartensLars Juhl Jensen

Machine learning on large-scale proteomics data identifies tissue and cell-type specific proteins

Tine ClaeysMaxime MenuRobbin BouwmeesterKris GevaertLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

PhosphoLingo : protein language models for phosphorylation site prediction

Jasper ZuallaertPathmanaban RamasamyRobbin BouwmeesterNico CallewaertSven Degroeve

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

The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions

Myrsini SakarikaFrederiek-Maarten KerckhofLotte Van PeteghemAlexandra Pinto Martins PereiraTim Van Den BosscheRobbin BouwmeesterRalf GabrielsDelphi Van HaverBarbara UlčarLennart Martens et al.

A1 Journal Article in MICROBIAL CELL FACTORIES

Toward an integrated machine learning model of a proteomics experiment

Benjamin A. NeelyViktoria DorferLennart MartensIsabell BludauRobbin BouwmeesterSven DegroeveEric W. DeutschSiegfried GessulatLukas KaellPawel Palczynski et al.

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

2022

How sticky are our proteins? Quantifying hydrophobicity of the human proteome

Juami Hermine Mariama van GilsDea GogishviliJan van EckRobbin BouwmeesterErik van DijkSanne Abeln

A2 Journal Article in BIOINFORMATICS ADVANCES

Ionbot : a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification

Sven DegroeveRalf GabrielsKevin VelgheRobbin BouwmeesterNatalia TichshenkoLennart Martens

Machine learning on large-scale proteomics data identifies tissue- and cell type-specific proteins

Tine ClaeysMaxime MenuRobbin BouwmeesterKris GevaertLennart Martens

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Arthur DeclercqRobbin BouwmeesterAurélie HirschlerChristine CarapitoSven DegroeveLennart MartensRalf Gabriels

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

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

Tobias RehfeldtRalf GabrielsRobbin BouwmeesterSiegfried GessulatBenjamin NeelyMagnus PalmbladYasset Perez-RiverolTobias SchmidtJuan Antonio VizcaínoEric Deutsch

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

Ralf GabrielsArthur DeclercqRobbin BouwmeesterSven DegroeveLennart Martens

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

Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator

Genet Abay ShiferawRalf GabrielsRobbin BouwmeesterTim Van Den BosscheElien VandermarliereLennart MartensPieter-Jan Volders

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2021

Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients

Bart Van PuyveldeKatleen Van UytfangheOlivier TytgatLaurence Van OudenhoveRalf GabrielsRobbin BouwmeesterSimon DaledTim Van Den BosschePathmanaban RamasamySigrid Verhelst et al.

A2 Journal Article in JACS AU

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

Robbin BouwmeesterRalf GabrielsNiels HulstaertLennart MartensSven Degroeve

A1 Journal Article in NATURE METHODS

Graph convolutional networks for improved prediction and interpretability of chromatographic retention data

Alexander KensertRobbin BouwmeesterKyriakos EfthymiadisPeter Van BroeckGert DesmetDeirdre Cabooter

A1 Journal Article in ANALYTICAL CHEMISTRY

Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

Morgane BoonePathmanaban RamasamyJasper ZuallaertRobbin BouwmeesterBerre Van MoerDavy MaddeleinDemet TuranNiels HulstaertHannah EeckhautElien Vandermarliere et al.

A1 Journal Article in NATURE COMMUNICATIONS

MS²DIP : highly accurate MS2 spectrum prediction for modified peptides & MS²Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Ralf GabrielsRobbin BouwmeesterJasper ZuallaertLennart MartensSven Degroeve

Personalized proteome : comparing proteogenomics and open variant search approaches for single amino acid variant detection

Renee SalzRobbin BouwmeesterRalf GabrielsSven DegroeveLennart MartensPieter-Jan VoldersPeter A.C. ’t Hoen

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2020

Generalized calibration across liquid chromatography setups for generic prediction of small-molecule retention times

Robbin BouwmeesterLennart MartensSven Degroeve

A1 Journal Article in ANALYTICAL CHEMISTRY

The age of data-driven proteomics : how machine learning enables novel workflows

Robbin BouwmeesterRalf GabrielsTim Van Den BosscheLennart MartensSven Degroeve

A1 Journal Article in PROTEOMICS

The difference is in the details : predicting the LC-IM-MS behaviour of metabolites and peptides

Robbin BouwmeesterLennart MartensSven Degroeve

2019

A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry : application to the characterisation of metabolites in rat urine

Leanne C NyeJonathan P WilliamsNyasha C MunjomaMarine PM LetertreMuireann CoenRobbin BouwmeesterLennart MartensJonathan R SwannJeremy K NicholsonRobert S Plumb et al.

A1 Journal Article in JOURNAL OF CHROMATOGRAPHY A

Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions

Ana Sílvia Ferreira Diamantino Coelho e SilvaRobbin BouwmeesterLennart MartensSven Degroeve

A1 Journal Article in BIOINFORMATICS

Comprehensive and empirical evaluation of machine learning algorithms for small molecule LC retention time prediction

Robbin BouwmeesterLennart MartensSven Degroeve

A1 Journal Article in ANALYTICAL CHEMISTRY