Research Explorer

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Project

ProteinContour: proteome-scale unraveling of the relation between post-translational modifications, biophysical properties, interactions and sub-cellular location of proteins.

Outputs and Outcomes

Publications

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

msqrob2PTM : differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level

Nina DemeulemeesterMarie GébelinLucas Caldi GomesPaul LingorChristine CarapitoLennart MartensLieven Clement

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Conformational dynamics of α‐1 acid glycoprotein (AGP) in cancer : a comparative study of glycosylated and unglycosylated AGP

Bhawna DixitWim VrankenAn Ghysels

A1 Journal Article in PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ionmob : a Python package for prediction of peptide collisional cross-section values

David TeschnerDavid Gomez-ZepedaArthur DeclercqMateusz K ŁąckiSeymen AvciKonstantin BobUte DistlerThomas MichnaLennart MartensStefan TenzerAndreas HildebrandtJonathan Wren et al.

A1 Journal Article in BIOINFORMATICS

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

lesSDRF is more : maximizing the value of proteomics data through streamlined metadata annotation

Tine ClaeysTim Van Den BosscheYasset Perez-RiverolKris GevaertJuan Antonio VizcaínoLennart Martens

A1 Journal Article in NATURE COMMUNICATIONS

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

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

Challenges in describing the conformation and dynamics of proteins with ambiguous behavior

Joel Roca-MartinezTamas LazarJose Gavalda-GarciaDavid BickelRita PancsaBhawna DixitKonstantina TzavellaPathmanaban RamasamyMaite Sanchez-FornarisIsel GrauWim F. Vranken et al.

A1 Journal Article in FRONTIERS IN MOLECULAR BIOSCIENCES

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

An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia

Lien ProvezBart Van PuyveldeLaura CorveleynNina DemeulemeesterSigrid VerhelstBeatrice LintermansSimon DaledJuliette RoelsLieven ClementLennart MartensDieter DeforcePieter Van VlierbergheMaarten Dhaenens et al.

A1 Journal Article in SCIENTIFIC DATA

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

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Arthur DeclercqRobbin BouwmeesterAurélie HirschlerChristine CarapitoSven DegroeveLennart MartensRalf Gabriels

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

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