Research Explorer

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Researcher

Lennart Martens

Publications & Research Data

Awards & Distinctions

351 Results

2026

Harnessing genomic and bioinformatics for surveillance of pathogens in Africa : a scoping review of existing training and gaps in training

Paul Tunde KingpriestJohn BokPalpouguini LompoEvodie NgelesiJoseph MwakaSainabou Laye NdureNyambura MoremiVito BarakaTim Van Den BosscheSakina Bombaywala et al.

A1 Journal Article in BMC INFECTIOUS DISEASES

iDeepLC : chemical structure information yields improved retention time prediction of peptides with unseen modifications

Alireza NameniArthur DeclercqRalf GabrielsRobbe DevreeseSven DegroeveAmélie De MaesschalckMaarten DhaenensCristina ChivaEduard SabidóLennart Martens et al.

A1 Journal Article in ANALYTICAL CHEMISTRY

InstaNovo-P : a de novo peptide sequencing model for phosphoproteomics

Jesper LauridsenVahap CanbayRachel CatzelPathmanaban RamasamyAmandla MabonaKevin EloffPaul FullwoodJennifer FergusonAnnekatrine Kirketerp-MøllerIda Sofie Goldschmidt et al.

A1 Journal Article in NATURE COMMUNICATIONS

Integrating multi-omics technologies to decipher microbiome functions

Tim Van Den BosscheEunice Adeline LazauVelma T. E. AhoJ. Alfredo Blakeley-RuizMaximilian WolfBenoit Josef KunathLuis E. Valentin-AlvaradoPatrick HellwigPieter VerschaffeltAndrew T. Rajczewski et al.

A1 Journal Article in NATURE COMMUNICATIONS

Large-scale proteomics profiling of peripheral blood of DM1 patients identifies biomarkers for disease severity and functional capacity

Daniël van AsTine ClaeysRenee SalzDelphi Van HaverSara DufourAmber van DeelenJolein GloerichRalf GabrielsPieter Jan VoldersVera Dobelmann et al.

A1 Journal Article in JOURNAL OF NEUROMUSCULAR DISEASES

MLMarker : a machine learning framework for tissue inference and biomarker discovery

Tine ClaeysSam van PuyenbroeckKris GevaertLennart Martens

A1 Journal Article in GENOME BIOLOGY

Project ODIN : advancing environmental genomic surveillance for public health across sub-Saharan Africa

Bonny BakerJosé Antonio Baz LombaJoseph Bitilinyu-BangohAndreas BerglöfSakina BombaywalaTracey Calvert-JoshuaBérenger KaboréPaul KingpriestTrudie LangJoshua I Levy et al.

A1 Journal Article in LANCET MICROBE

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

The need for standardization and improved open (meta)data practices in metaproteomics

Tim Van Den BosscheMaximilian WolfJean ArmengaudMagnus Ø. ArntzenDirk BenndorfDaniel FigeysLucia GrengaRobert L. HettichNithu Sara JohnPratik Jagtap et al.

A1 Journal Article in MICROBIOME

The Peptonizer2000 : bringing confidence to metaproteomics

Tanja HolsteinPieter VerschaffeltTim Van Den BosscheSimon Van de VyverLennart MartensBart MesuereThilo Muth

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

Unlocking the next decade of proteomics with standardized, structured metadata

Tim Van Den BosscheAnanth PrakashTine ClaeysJuan Antonio VizcaínoLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2025

Assessing the relation between protein phosphorylation, AlphaFold3 models and conformational variability

Pathmanaban RamasamyLennart MartensW. F. Vranken

Assessing the relation between protein phosphorylation, AlphaFold3 models, and conformational variability

Pathmanaban RamasamyJasper ZuallaertLennart MartensWim F. Vranken

A1 Journal Article in PROTEIN SCIENCE

Bringing confidence to species identification : probabilistic and proteogenomic approaches for single organism samples and metaproteomes

Tanja HolsteinThilo MuthLennart Martens

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

Epitope Odyssey : data-driven tools to extend the known immunopeptide universe

Arthur DeclercqLennart MartensFrancis Impens

High-coverage immunopeptidomics using timsTOF mass spectrometers with thunder-DDA-PASEF boosted by MS2Rescore

David Gomez-ZepedaJulian BeyrleAnnica PreikschatArthur DeclercqYannic ChenRalf GabrielsLennart MartensUte DistlerStefan Tenzer

Bookchapter in Immunoproteomics : methods and protocols

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

Metaproteomics beyond databases : addressing the challenges and potentials of de novo sequencing

Tim Van Den BosscheDenis BeslicSam van PuyenbroeckTomi SuomiTanja HolsteinLennart MartensLaura L. EloThilo Muth

Editorial material

MHCquant2 refines immunopeptidomics tumor antigen discovery

Jonas ScheidSteffen LemkeNaomi Hoenisch-GravelAnna DenglerTimo SachsenbergArthur DeclercqRalf GabrielsJens BauerMarcel WackerLeon Bichmann et al.

A1 Journal Article in GENOME BIOLOGY

msqrob2TMT : robust linear mixed models for inferring differential abundant proteins in labeled experiments with arbitrarily complex

Stijn VandenbulckeChristophe VanderaaOliver CrookLennart MartensLieven Clement

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

MzPeak : designing a scalable, interoperable, and future-ready mass spectrometry data format

Tim Van Den BosscheTheodore AlexandrovAivett BilbaoWout BittremieuxFederico Ivan BriganteMatthew Chase ChambersJoshua CharkowEric DeutschAndrew W. DowseyYasin El Abiead et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

omicsGMF : a multi-tool for dimensionality reduction, batch correction and imputation applied to bulk- and single cell proteomics data

Alexandre SegersCristian CastiglioneChristophe VanderaaElfride De BaereLennart MartensDavide RissoLieven Clement

PathwayPilot : a user-friendly tool for visualizing and navigating metabolic pathways

Tibo Vande MoortelePieter VerschaffeltQingyao HuangNadezhda T. DonchevaTanja HolsteinCaroline JachmannPeter DawyndtLennart MartensBart MesuereTim Van Den Bossche

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

PTMVision : an interactive visualization webserver for post-translational modifications of proteins

Simon HacklCaroline JachmannMathias Witte PazTheresa Anisja HarbigLennart MartensKay Nieselt

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

The microbiologist's guide to metaproteomics

Tim Van Den BosscheJean ArmengaudDirk BenndorfJose Alfredo Blakeley‐RuizMadita BrauerKai ChengMarybeth CreskeyDaniel FigeysLucia GrengaTimothy J. Griffin et al.

A1 Journal Article in IMETA

The microbiologist’s guide to metaproteomics

Tim Van Den BosscheJean ArmengaudDirk BenndorfJose Alfredo Blakeley-RuizMadita BrauerKai ChengMarybeth CreskeyDaniel FigeysLucia GrengaTimothy J Griffin et al.

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

Unipept in 2024 : expanding metaproteomics analysis with support for missed cleavages and semitryptic and nontryptic peptides

Tibo Vande MoorteleBram DevlaminckSimon Van de VyverTim Van Den BosscheLennart MartensPeter DawyndtBart MesuerePieter Verschaffelt

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2024

A tale of tissue and text : predictive proteome profiling and managing metadata mayhem

Tine ClaeysLennart MartensKris GevaertJuan Antonio Vizcaíno

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

Biodiversity analysis of metaproteomics samples with Unipept : a comprehensive tutorial

Tim Van Den BosschePieter VerschaffeltTibo Vande MoortelePeter DawyndtLennart MartensBart Mesuere

Bookchapter in Protein bioinformatics

Bioinformatics pipeline for processing single-cell data

Arthur DeclercqNina DemeulemeesterRalf GabrielsRobbin BouwmeesterSven DegroeveLennart Martens

Bookchapter in Mass spectrometry based single cell proteomics

Brain exposure to SARS-CoV-2 virions perturbs synaptic homeostasis

Emma PartiotAurélie HirschlerSophie ColombWilly LutzTine ClaeysFrançois DelalandeMaika S. DeffieuYonis BareJudith R. E. RoelsBarbara Gorda et al.

A1 Journal Article in NATURE MICROBIOLOGY

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

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

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

Novel statistical strategies for differential PTM abundance analysis in proteomics

Nina DemeulemeesterLennart MartensLieven Clement

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

The Peptonizer2000 : bringing confidence to metaproteomics

Tanja HolsteinPieter VerschaffeltTim Van Den BosscheSimon Van de VyverLennart MartensBart MesuereThilo Muth

Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model

David Gomez-ZepedaDanielle Arnold-SchildJulian BeyrleArthur DeclercqRalf GabrielsElena KummAnnica PreikschatMateusz Krzysztof ŁąckiAurélie HirschlerJeewan Babu Rijal et al.

A1 Journal Article in NATURE COMMUNICATIONS

2023

Building the Unipept Ecosystem : empowering high-throughput metaproteomics data analysis for characterizing complex microbial communities

Pieter VerschaffeltPeter DawyndtLennart MartensBart Mesuere

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

Mikaela KoutrouliPau Piera LíndezKaterina NastouRobbin BouwmeesterSimon RasmussenLennart MartensLars Juhl Jensen

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

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

A1 Journal Article in BIOINFORMATICS

Large-scale proteomics profiling of peripheral blood of DM1 patients identifies biomarkers for disease severity and physical activity

P. 't HoenD. van AsTine ClaeysR. SalzRalf GabrielsFrancis ImpensPieter-Jan VoldersLennart MartensB. van Engelen

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

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

PepGM : a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores

Tanja HolsteinFranziska KistnerLennart MartensThilo Muth

A1 Journal Article in BIOINFORMATICS

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

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

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

Unipept Desktop 2.0 : construction of targeted reference protein databases for metaproteogenomics analyses

Pieter VerschaffeltAlessandro TancaMarcello AbbondioTim Van Den BosscheTibo Vande MoortelePeter DawyndtLennart MartensBart Mesuere

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

A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics

Bart Van PuyveldeSimon DaledSander WillemsRalf GabrielsAnne Gonzalez de PeredoKarima ChaouiEmmanuelle Mouton-BarbosaDavid BouyssiéKurt BoonenChristopher J. Hughes et al.

A1 Journal Article in SCIENTIFIC DATA

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 Martens et al.

A1 Journal Article in SCIENTIFIC DATA

Benchmark and improving methods in metaproteomics informatics

Tim Van Den BosscheLennart MartensBart MesuereThilo Muth

Cov²MS : an automated and quantitative matrix-independent assay for mass spectrometric measurement of SARS-CoV-2 nucleocapsid protein

Bart Van PuyveldeKatleen Van UytfangheLaurence Van OudenhoveRalf GabrielsTessa Van RoyenArne MatthysMorteza RazaviRichard YipTerry PearsonNicolas Drouin et al.

A1 Journal Article in ANALYTICAL CHEMISTRY

Data mining and modelling to understand cell migration heterogeneity and plasticity

Gwendolien SergeantLennart Martens

Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes

Rupert MayerRein VerbekeCaroline AsselmanIlke AernoutAdillah GulDenzel EggermontKatie BoucherFabien Henri TheryTeresa MaiaHans Demol et al.

A1 Journal Article in NATURE COMMUNICATIONS

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

Machine learning to the rescue : enabling novel proteomics workflows with data-driven bioinformatics methods

Ralf GabrielsLennart MartensSven Degroeve

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Arthur DeclercqRobbin BouwmeesterAurélie HirschlerChristine CarapitoSven DegroeveLennart MartensRalf Gabriels

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Orthogonal proteomics methods to unravel the HOTAIR interactome

Louis DelhayeEdith De BruyckerPieter-Jan VoldersDaria FijalkowskaDelphine De SutterSven DegroeveLennart MartensPieter MestdaghSven Eyckerman

Orthogonal proteomics methods to unravel the HOTAIR interactome

Louis DelhayeEdith De BruyckerPieter-Jan VoldersDaria FijalkowskaDelphine De SutterSven DegroeveLennart MartensPieter MestdaghSven Eyckerman

A1 Journal Article in SCIENTIFIC REPORTS

Panoramic perspective on human phosphosites

Pathmanaban RamasamyElien VandermarliereWim F. VrankenLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Pout2Prot : an efficient tool to create protein (sub)groups from Percolator Output Files

Kay SchallertPieter VerschaffeltBart MesuereDirk BenndorfLennart MartensTim Van Den Bossche

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

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

Uncovering new knowledge on protein post-translational modifications by large-scale reprocessing and analysis of public proteomics data

Pathmanaban RamasamyLennart MartensWim F. Vranken

Unipept visualizations : an interactive visualization library for biological data

Pieter VerschaffeltJames CollierAlexander BotzkiLennart MartensPeter DawyndtBart Mesuere

A1 Journal Article in BIOINFORMATICS

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

Critical assessment of metaproteome investigation (CAMPI) : a multi-lab comparison of established workflows

Tim Van Den BosscheBenoit J. KunathKay SchallertStephanie S. SchäpePaul E. AbrahamJean ArmengaudMagnus Ø. ArntzenAriane BassignaniDirk BenndorfStephan Fuchs et al.

Critical Assessment of MetaProteome Investigation (CAMPI) : a multi-laboratory comparison of established workflows

Tim Van Den BosscheBenoit J. KunathKay SchallertStephanie S. SchäpePaul E. AbrahamJean ArmengaudMagnus Ø. ArntzenAriane BassignaniDirk BenndorfStephan Fuchs et al.

A1 Journal Article in NATURE COMMUNICATIONS

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

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

MegaGO : a fast yet powerful approach to assess functional gene ontology similarity across meta-omics data sets

Pieter VerschaffeltTim Van Den BosscheWassim GabrielMichał BurdukiewiczAlessio SoggiuLennart MartensBernhard Y. RenardHenning SchiebenhoeferBart Mesuere

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

Pout2Prot : an efficient tool to create protein (sub)groups from Percolator output files

Tim Van Den BosscheKay SchallertPieter VerschaffeltBart MesuereDirk BenndorfLennart Martens

Spectral prediction features as a solution for the search space size problem in proteogenomics

Steven VerbruggenSiegfried GessulatRalf GabrielsAnna MatsarokiHendrik Van de VoordeBernhard KusterSven DegroeveLennart MartensWim Van CriekingeMathias Wilhelm et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

The RNA landscape of the human placenta in health and disease

Sungsam GongFrancesca GaccioliJustyna DopieralaUlla SovioEmma CookPieter-Jan VoldersLennart MartensPaul D. W. KirkSylvia RichardsonGordon C. S. Smith et al.

A1 Journal Article in NATURE COMMUNICATIONS

Unipept Desktop : a faster, more powerful metaproteomics results analysis tool

Pieter VerschaffeltTim Van Den BosscheLennart MartensPeter DawyndtBart Mesuere

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2020

Anatomy and evolution of database search engines : a central component of mass spectrometry based proteomic workflows

Kenneth VerheggenHelge RaederFrode S BervenLennart MartensHarald BarsnesMarc Vaudel

A1 Journal Article in MASS SPECTROMETRY REVIEWS

Community standards for open cell migration data

Alejandra N. Gonzalez-BeltranPaola MasuzzoChristophe AmpeGert-Jan BakkerSébastien BessonRobert H EiblPeter FriedlMatthias GunzerMark KittisopikulSylvia E. Le Dévédec et al.

A1 Journal Article in GIGASCIENCE

Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis

Tim Van Den BosschePieter VerschaffeltKay SchallertHarald BarsnesPeter DawyndtDirk BenndorfBernhard Y. RenardBart MesuereLennart MartensThilo Muth

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

COSS : a fast and user-friendly tool for spectral library searching

Genet Abay ShiferawElien VandermarliereNiels HulstaertRalf GabrielsLennart MartensPieter-Jan Volders

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

Robbin BouwmeesterLennart MartensSven Degroeve

A1 Journal Article in ANALYTICAL CHEMISTRY

MSqRob takes the missing hurdle : uniting intensity- and count-based proteomics

Ludger GoeminneAdriaan StickerLennart MartensKris GevaertLieven Clement

A1 Journal Article in ANALYTICAL CHEMISTRY

Pitfalls in re-analysis of observational omics studies: a post-mortem of the human pathology atlas

Jeroen GilisSteff TaelmanLucas DaveyLennart MartensLieven Clement

Precursor intensity-based label-free quantification software tools for proteomic and multi-omic analysis within the galaxy platform

Subina MehtaCaleb W. EasterlyRay SajulgaRobert J. MillikinAndrea ArgentiniIgnacio EguinoaLennart MartensMichael R. ShortreedLloyd M. SmithThomas McGowan et al.

A2 Journal Article in PROTEOMES

Removing the hidden data dependency of DIA with predicted spectral libraries

Bart Van PuyveldeSander WillemsRalf GabrielsSimon DaledLaura De ClerckSofie Vande CasteeleAn StaesFrancis ImpensDieter DeforceLennart Martens et al.

A1 Journal Article in PROTEOMICS

Robust summarization and inference in proteome-wide label-free quantification

Adriaan StickerLudger GoeminneLennart MartensLieven Clement

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Scop3P : a comprehensive resource of human phosphosites within their full context

Pathmanaban RamasamyDemet TuranNatalia TichshenkoNiels HulstaertElien VandermarliereWim VrankenLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Simple peptide quantification approach for MS-based proteomics quality control

Teresa MaiaAn StaesKim PlasmanJarne PauwelsKatie BoucherAndrea ArgentiniLennart MartensTony MontoyeKris GevaertFrancis Impens

A1 Journal Article in ACS OMEGA

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 CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis

Stephanie SmithShanshuo ZhuLisa JoosIanto RobertsNatalia NikonorovaLam Dai VuElisabeth StesHyunwoo ChoAntoine LarrieuWei Xuan et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

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

Robbin BouwmeesterLennart MartensSven Degroeve

ThermoRawFileParser : modular, scalable and cross-platform RAW file conversion

Niels HulstaertJim ShofstahlTimo SachsenbergMathias WalzerHarald BarsnesLennart MartensYasset Perez-Riverol

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Unipept CLI 2.0 : adding support for visualizations and functional annotations

Pieter VerschaffeltPhilippe Van ThienenTim Van Den BosscheFelix Van der JeugtCaroline De TenderLennart MartensPeter DawyndtBart Mesuere

A1 Journal Article in BIOINFORMATICS

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

A time of enlightenment : straightforward identification of protein modifications

Lennart Martens

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

An update on the moFF algorithm for label-free quantitative proteomics

Andrea ArgentiniAn StaesBjörn Andreas GrüningSubina MehtaCaleb EasterlyTimothy GriffinPratik JagtapFrancis ImpensLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Challenges and promise at the interface of metaproteomics and genomics : an overview of recent progress in metaproteogenomic data analysis

Henning SchiebenhoeferTim Van Den BosscheStephan FuchsBernhard Y RenardThilo MuthLennart Martens

A1 Journal Article in EXPERT REVIEW OF PROTEOMICS

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

Data-driven approaches for improved mass spectrometry-based analyte identification

Ana Sílvia Ferreira Diamantino Coelho e SilvaLennart MartensSven Degroeve

DoRes within CellMissy : dose-response analysis on cell migration and related data

Gwendolien SergeantLennart MartensMarleen Van TroysPaola Masuzzo

A1 Journal Article in BIOINFORMATICS

Fast and accurate MS² peak intensity predictions for multiple fragmentation methods, instruments and labeling techniques

Ralf GabrielsLennart MartensSven Degroeve

Keeping up appearances in the mumps vaccine : do antigenic differences matter?

Tessa VermeireLennart MartensSteven Van GuchtPaul RotaElien Vandermarliere

LNCipedia 5 : towards a reference set of human long non-coding RNAs

Pieter-Jan VoldersJasper AnckaertKenneth VerheggenJustine NuytensLennart MartensPieter MestdaghJo Vandesompele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

MS²PIP : fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

Ralf GabrielsLennart MartensSven Degroeve

Prediction-based reduction of the search space in metaproteomics

Tim Van Den BosscheLennart Martens

Rescoring peptide-to-spectrum-matches based on predicted fragment ion intensities leads to an increased identification rate in metaproteomics

Tim Van Den BosscheAna Sílvia Ferreira Diamantino Coelho e SilvaBernhard Y RenardThilo MuthLennart Martens

Robust summarisation and inference for Label-Free Quantification

Adriaan StickerLudger GoeminneLennart MartensLieven Clement

Scop3D : online visualization of mutation rates on protein structure

Lukasz KreftDemet TuranNiels HulstaertAlexander BotzkiLennart MartensElien Vandermarliere

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Unipept 4.0 : functional analysis of metaproteome data

Robbert Gurdeep SinghAlessandro TancaAntonio PalombaFelix Van der JeugtPieter VerschaffeltSergio UzzauLennart MartensPeter DawyndtBart Mesuere

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

Ralf GabrielsLennart MartensSven Degroeve

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2018

Adding new nodes to the protein association network

Surya GuptaLennart MartensJan Tavernier

Analysis of invasion dynamics of matrix-embedded cells in a multisample format

Marleen Van TroysPaola MasuzzoLynn HuyckKarima BakkaliDAVY WATERSCHOOTLennart MartensChristophe Ampe

Bookchapter in Cell migration : methods and protocols

Complementary use of ribosome profiling and proteomics for mapping the translation landscape

Elvis NdahPetra Van DammeGerben MenschaertLennart Martens

Cross-linked peptide identification : a computational forest of algorithms

Sule Yilmaz-RumpfGenet Abay ShiferawJosep RayoAnastassios EconomouLennart MartensElien Vandermarliere

A1 Journal Article in MASS SPECTROMETRY REVIEWS

Data-driven rescoring of metabolite annotations significantly improves sensitivity

Ana Sílvia Ferreira Diamantino Coelho e SilvaAndrew PalmerVitaly KovalevArtem TarasovTheodore AlexandrovLennart MartensSven Degroeve

A1 Journal Article in ANALYTICAL CHEMISTRY

Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins

Sigrid GoumaTessa VermeireSteven Van GuchtLennart MartensVeronik HutseJeroen CremerPaul A RotaGeert Leroux-RoelsMarion KoopmansRob van Binnendijk et al.

A1 Journal Article in SCIENTIFIC REPORTS

High-throughput metaproteomics data analysis with Unipept : a tutorial

Bart MesuereFelix Van der JeugtToon WillemsTom NaessensBart DevreeseLennart MartensPeter Dawyndt

A1 Journal Article in JOURNAL OF PROTEOMICS

How to till a growing field : large-scale re-analysis of public proteomics data

Kenneth VerheggenLennart MartensHarald Barsnes

Prediction-based reduction of the search space in metaproteomics

Tim Van Den BosscheLennart Martens

Prediction-based reduction of the search space in metaproteomics

Tim Van Den BosscheLennart Martens

SQANTI : extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

Manuel TardaguilaLorena de la FuenteCristina MartiCécile PereiraFrancisco Jose Pardo-PalaciosHector del RiscoMarc FerrellMaravillas MelladoMarissa MacchiettoKenneth Verheggen et al.

A1 Journal Article in GENOME RESEARCH

Surveillance of myelodysplastic syndrome via migration analyses of blood neutrophils : a potential prognostic tool

Marc SchusterMischa MoellerLea BornemannClara BessenCharlyn SobczakSaskia SchmitzLaura WitjesKatja KruithoffChristina KohnOlga Just et al.

A1 Journal Article in JOURNAL OF IMMUNOLOGY

The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease

Bram De WildeAnneleen BeckersSven LindnerKristina AlthoffKatleen De PreterPauline DepuydtPieter MestdaghTom SanteSteve LefeverFalk Hertwig et al.

A2 Journal Article in ONCOTARGET

The online Tabloid Proteome : an annotated database of protein associations

Surya GuptaDemet TuranJan TavernierLennart Martens

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The study of degradation mechanisms of glyco-engineered plant produced anti-rabies monoclonal antibodies E559 and 62-71-3

Sindisiwe G ButheleziHeini W DirrEreck ChakauyaRachel ChikwambaLennart MartensTsepo L TsekoaElien VandermarliereStoyan H Stoychev

A1 Journal Article in PLOS ONE

2017

A community proposal to integrate proteomics activities in ELIXIR

Juan Antonio VizcaínoMathias WalzerRafael C JiménezWout BittremieuxDavid BouyssiéChristine CarapitoFernando CorralesMyriam FerroAlbert JR HeckPeter Horvatovich et al.

A2 Journal Article in F1000RESEARCH

A golden age for working with public proteomics data

Lennart MartensJuan Antonio Vizcaíno

A1 Journal Article in TRENDS IN BIOCHEMICAL SCIENCES

An accessible proteogenomics informatics resource for cancer researchers

Matthew C ChambersPratik D JagtapJames E JohnsonThomas McGowanPraveen KumarGetiria OnsongoCandace R GuerreroHarald BarsnesMarc VaudelLennart Martens et al.

A1 Journal Article in CANCER RESEARCH

An end-to-end software solution for the analysis of high-throughput single-cell migration data

Paola MasuzzoLynn HuyckAleksandra SimiczyjewChristophe AmpeLennart MartensMarleen Van Troys

A1 Journal Article in SCIENTIFIC REPORTS

Computational quality control tools for mass spectrometry proteomics

Wout BittremieuxDirk ValkenborgLennart MartensKris Laukens

A1 Journal Article in PROTEOMICS

MAPPI-DAT : data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform

Surya GuptaVeronic De PuysseleyrJosé Van Der HeydenDavy MaddeleinIrma LemmensSam LievensSven DegroeveJan TavernierLennart Martens

A1 Journal Article in BIOINFORMATICS

Mass spectrometrists should search for all peptides, but assess only the ones they care about

Adriaan StickerLennart MartensLieven Clement

A1 Journal Article in NATURE METHODS

Methods to calculate spectrum similarity

Sule Yilmaz-RumpfElien VandermarliereLennart Martens

Bookchapter in Proteome bioinformatics

MPA Portable : a stand-alone software package for analyzing metaproteome samples on the go

Thilo MuthFabian KohrsRobert HeyerDirk BenndorfErdmann RappUdo ReichlLennart MartensBernhard Y Renard

A1 Journal Article in ANALYTICAL CHEMISTRY

N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana

Patrick WillemsElvis NdahVeronique JonckheereSimon StaelAdriaan StickerLennart MartensFrank Van BreusegemKris GevaertPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Noncoding after all : biases in proteomics data do not explain observed absence of lncRNA translation products

Kenneth VerheggenPieter-Jan VoldersPieter MestdaghGerben MenschaertPetra Van DammeKris GevaertLennart MartensJo Vandesompele

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Novel algorithms for two interesting challenges in proteomics : unsequenced organisms and cross-linked peptide identification

Sule Yilmaz-RumpfLennart MartensElien Vandermarliere

Protein complex analysis : from raw protein lists to protein interaction networks

Pieter MeysmanKevin TitecaSven EyckermanJan TavernierBart GoethalsLennart MartensDirk ValkenborgKris Laukens

A1 Journal Article in MASS SPECTROMETRY REVIEWS

Quality control in mass spectrometry-based proteomics

Wout BittremieuxDavid L TabbFrancis ImpensAn StaesEvy TimmermanLennart MartensKris Laukens

A1 Journal Article in MASS SPECTROMETRY REVIEWS

sfinx : an R package for the elimination of false positives from affinity purification-mass spectrometry datasets

Kevin TitecaPieter MeysmanKris LaukensLennart MartensJan TavernierSven Eyckerman

A1 Journal Article in BIOINFORMATICS

Unbiased protein association study on the public human proteome reveals biological connections between co-occurring protein pairs

Surya GuptaKenneth VerheggenJan TavernierLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2016

A pipeline for differential proteomics in unsequenced species

Sule Yilmaz-RumpfBjorn VictorNiels HulstaertElien VandermarliereHarald BarsnesSven DegroeveSurya GuptaAdriaan StickerSarah GabriëlPierre Dorny et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics

Giel VandemoorteleAn StaesGiulia GonnelliNoortje SamynDelphine De SutterElien VandermarliereEvy TimmermanKris GevaertLennart MartensSven Eyckerman

A1 Journal Article in SCIENTIFIC REPORTS

Database search engines : paradigms, challenges and solutions

Kenneth VerheggenLennart MartensFrode S. BervenHarald BarsnesMarc Vaudel

A1 Journal Article in Modern proteomics : sample preparation, analysis and practical applications

Designing biomedical proteomics experiments : state-of-the-art and future perspectives

Evelyne MaesPieter KelchtermansWout BittremieuxKurt De GraveSven DegroeveJef HooyberghsInge MertensGeert BaggermanJan RamonKris Laukens et al.

A1 Journal Article in EXPERT REVIEW OF PROTEOMICS

Exploring the potential of public proteomics data

Marc VaudelKenneth VerheggenAttila CsordasHelge RaederFrode S BervenLennart MartensJuan A VizcaínoHarald Barsnes

A1 Journal Article in PROTEOMICS

Human proteome project mass spectrometry data interpretation guidelines 2.1

Eric W DeutschChristopher M OverallJennifer E Van EykMark S BakerYoung-Ki PaikSusan T WeintraubLydie LaneLennart MartensYves VandenbrouckUlrike Kusebauch et al.

Editorial material

Identification of quantitative proteomic differences between Mycobacterium tuberculosis lineages with altered virulence

Julian S PetersBridget CalderGiulia GonnelliSven DegroeveElinambinina RajaonarifaraNicola MulderNelson C SoaresLennart MartensJonathan M Blackburn

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Metaproteomic data analysis at a glance : advances in computational microbial community proteomics

Thilo MuthBernhard Y RenardLennart Martens

A1 Journal Article in EXPERT REVIEW OF PROTEOMICS

moFF : a robust and automated approach to extract peptide ion intensities

Andrea ArgentiniLudger GoeminneKenneth VerheggenNiels HulstaertAn StaesLieven ClementLennart Martens

A1 Journal Article in NATURE METHODS

Proteome-scale binary interactomics in human cells

Sam LievensJosé Van Der HeydenDelphine MasschaeleLeentje De CeuninckIoanna PettaSurya GuptaVeronic De PuysseleyrVirginie VauthierIrma LemmensDries De Clercq et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Resolution of protein structure by mass spectrometry

Elien VandermarliereElisabeth StesKris GevaertLennart Martens

A1 Journal Article in MASS SPECTROMETRY REVIEWS

SFINX : straightforward filtering index for affinity purification mass spectrometry data analysis

Kevin TitecaPieter MeysmanKris GevaertJan TavernierKris LaukensLennart MartensSven Eyckerman

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Taking aim at moving targets in computational cell migration

Paola MasuzzoMarleen Van TroysChristophe AmpeLennart Martens

A1 Journal Article in TRENDS IN CELL BIOLOGY

The impact of sequence database choice on metaproteomic results in gut microbiota studies

Alessandro TancaAntonio PalombaCristina FraumeneDaniela PagnozziValeria ManghinaMassimo DeligiosThilo MuthErdmann RappLennart MartensMaria Filippa Addis et al.

A1 Journal Article in MICROBIOME

The Lyssavirus glycoprotein : a key to cross-immunity

Sindisiwe G ButheleziHeini W DirrEreck ChakauyaRachel ChikwambaLennart MartensTsepo L TsekoaStoyan H StoychevElien Vandermarliere

A1 Journal Article in VIROLOGY

Towards an open data exchange ecosystem : forging a new path for cell migration data analysis and mining

Paola MasuzzoChristophe AmpeLennart MartensMarleen Van Troys

Unsupervised quality assessment of mass spectrometry proteomics experiments by multivariate quality control metrics

Wout BittremieuxPieter MeysmanLennart MartensDirk ValkenborgKris Laukens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Up-to-date workflow for plant (phospho)proteomics identifies differential drought-responsive phosphorylation events in maize leaves

Lam Dai VuElisabeth StesMichiel Van BelHilde NelissenDavy MaddeleinDirk InzéFrederik CoppensLennart MartensKris GevaertIve De Smet

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Xilmass: a new approach toward the identification of cross-linked peptides

Sule Yilmaz-RumpfFriedel DrepperNiels HulstaertMaša ČerničKris GevaertAnastassios EconomouBettina WarscheidLennart MartensElien Vandermarliere

A1 Journal Article in ANALYTICAL CHEMISTRY

2015

A decoy-free approach to the identification of peptides

Giulia GonnelliMichiel StockJan VerwaerenDavy MaddeleinBernard De BaetsLennart MartensSven Degroeve

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes

Jelle Van LeeneDominique EeckhoutBernard CannootNancy De WinneGeert PersiauEveline Van De SlijkeLeen VercruysseMaarten DedeckerAurine VerkestKlaas Vandepoele et al.

A1 Journal Article in NATURE PROTOCOLS

An open data ecosystem for cell migration research

Paola MasuzzoLennart Martensthe 2014 Cell Migration workshop participantsChristophe AmpeOlivier De WeverMarleen Van Troys

Editorial material

An update on LNCipedia : a database for annotated human lncRNA sequences

Pieter-Jan VoldersKenneth VerheggenGerben MenschaertKlaas VandepoeleLennart MartensJo VandesompelePieter Mestdagh

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Ariadne's thread : a robust software solution leading to automated absolute and relative quantification of SRM data

Sara NassoSandra GoetzeLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Colonic metaproteomic signatures of active bacteria and the host in obesity

Carolin A KolmederJarmo RitariFroukje J VerdamThilo MuthSalla KeskitaloMarkku VarjosaloSusana FuentesJan Willem GreveWim A BuurmanUdo Reichl et al.

A1 Journal Article in PROTEOMICS

iMonDB : mass spectrometry quality control through instrument monitoring

Wout BittremieuxHanny WillemsPieter KelchtermansLennart MartensKris LaukensDirk Valkenborg

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

JSparklines : making tabular proteomics data come alive

Harald BarsnesMarc VaudelLennart Martens

A1 Journal Article in PROTEOMICS

Limited proteolysis combined with stable isotope labeling reveals conformational changes in protein (pseudo)kinases upon binding small molecules

Michela Di MicheleElisabeth StesElien VandermarliereRohit AroraJuan Astorga-WellsJonathan VandenbusscheErika van HeerdeRoman ZubarevPascal BonnetJoannes TM Linders et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Managing expectations when publishing tools and methods for computational proteomics

Lennart MartensOliver KohlbacherSusan T Weintraub

Editorial material

MS²PIP prediction server : compute and visualize MS² peak intensity predictions for CID and HCD fragmentation

Sven DegroeveDavy MaddeleinLennart Martens

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Navigating through metaproteomics data : a logbook of database searching

Thilo MuthCarolin A KolmederJarkko SalojärviSalla KeskitaloMarkku VarjosaloFroukje J VerdamSander S RensenUdo ReichlWillem M de VosErdmann Rapp et al.

A1 Journal Article in PROTEOMICS

On the assessment of the reliability of peptide-to-spectrum matches in mass-spectrometry-based proteomics

Giulia GonnelliLennart MartensBernard De Baets

Open-source, platform-independent library and online scripting environment for accessing thermo scientific RAW files

Pieter KelchtermansAna Sílvia Ferreira Diamantino Coelho e SilvaAndrea ArgentiniAn StaesJonathan VandenbusscheKris LaukensDirk ValkenborgLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

PepShell : visualization of conformational proteomics data

Elien VandermarliereDavy MaddeleinNiels HulstaertElisabeth StesMichela Di MicheleKris GevaertEdgar JacobyDirk BrehmerLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

PeptideShaker enables reanalysis of MS-derived proteomics data sets

Marc VaudelJulia M BurkhartRené P ZahediEystein OvelandFrode S BervenAlbert SickmannLennart MartensHarald Barsnes

A1 Journal Article in NATURE BIOTECHNOLOGY

Phospho-iTRAQ : assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry

Pieter GlibertPaulien MeertKatleen Van SteendamFilip Van NieuwerburghDieter De ConinckLennart MartensMaarten DhaenensDieter Deforce

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Phospho-iTRAQ data article : assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry

Pieter GlibertPaulien MeertKatleen Van SteendamLennart MartensDieter DeforceMaarten Dhaenens

A2 Journal Article in DATA IN BRIEF

Pladipus enables universal distributed computing in proteomics bioinformatics

Kenneth VerheggenDavy MaddeleinNiels HulstaertLennart MartensHarald BarsnesMarc Vaudel

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Ryanodine receptors are targeted by anti-apoptotic Bcl-X-L involving its BH4 domain and Lys87 from its BH3 domain

Tim VervlietIrma LemmensElien VandermarliereElke DecrockHristina IvanovaGiovanni MonacoVincenzo SorrentinoNael Nadif KasriLudwig MissiaenLennart Martens et al.

A1 Journal Article in SCIENTIFIC REPORTS

Scop3D : three-dimensional visualization of sequence conservation

Tessa VermeireStijn VermaereBert SchepensXavier SaelensSteven Van GuchtLennart MartensElien Vandermarliere

A1 Journal Article in PROTEOMICS

sORFs.org : a repository of small ORFs identified by ribosome profiling

Volodimir OlexioukJeroen CrappéSteven VerbruggenKenneth VerheggenLennart MartensGerben Menschaert

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Structural investigation of B-Raf paradox breaker and inducer inhibitors

Rohit AroraMichela Di MicheleElisabeth StesElien VandermarliereLennart MartensKris GevaertErika Van HeerdeJoannes TM LindersDirk BrehmerEdgar Jacoby et al.

A1 Journal Article in JOURNAL OF MEDICINAL CHEMISTRY

Summarization vs. peptide-based models in label-free quantitative proteomics : performance, pitfalls, and data analysis guidelines

Ludger GoeminneAndrea ArgentiniLennart MartensLieven Clement

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

The iceLogo web server and SOAP service for determining protein consensus sequences

Davy MaddeleinNiklaas ColaertIain BuchananNiels HulstaertKris GevaertLennart Martens

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The MetaProteomeAnalyzer : a powerful open-source software suite for metaproteomics data analysis and interpretation

Thilo MuthAlexander BehneRobert HeyerFabian KohrsDirk BenndorfMarcus HoffmannMiro LehtevaUdo ReichlLennart MartensErdmann Rapp

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Viewing the proteome : how to visualize proteomics data?

Eystein OvelandThilo MuthErdmann RappLennart MartensFrode S BervenHarald Barsnes

A1 Journal Article in PROTEOMICS

2014

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra

Thilo MuthLisa WeilnböckErdmann RappChristian G HuberLennart MartensMarc VaudelHarald Barsnes

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory

Kenneth VerheggenHarald BarsnesLennart Martens

A1 Journal Article in PROTEOMICS

Informaticawetenschappen in het leerplichtonderwijs

Giovanni SamaeyJacques Van RemortelHugues BersiniYvan BruynseraedeJan DekelverFrederik De LaenderDirk DeschoolmeesterPaul GistelinckBern MartensLennart Martens et al.

Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics

Marc VaudelAlbert SickmannLennart Martens

A1 Journal Article in BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

jqcML: an open-source Java API for mass spectrometry quality control data in the qcML format

Wout BittremieuxPieter KelchtermansDirk VakenborgLennart MartensKris Laukens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Machine learning applications in proteomics research: how the past can boost the future

Pieter KelchtermansWout BittremieuxKurt De GraveSven DegroeveJan RamonKris LaukensDirk ValkenborgHarald BarsnesLennart Martens

A1 Journal Article in PROTEOMICS

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

Juan A VizcainoEric W DeutschRui WangAttila CsordasFlorian ReisingerDaniel RíosJosé A DianesZhi SunTerry FarrahNuno Bandeira et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

qcML: an exchange format for quality control metrics from mass spectrometry experiments

Mathias WalzerLucia Espona PernasSara NassoWout BittremieuxSven NahnsenPieter KelchtermansPeter PichlerHenk WP van den ToornAn StaesJonathan Vandenbussche et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Shedding light on black boxes in protein identification

Marc VaudelA Saskia VenneFrode S BervenRené P ZahediLennart MartensHarald Barsnes

A1 Journal Article in PROTEOMICS

Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways

Florian BeckJörg GeigerStepan GambaryanJohannes VeitMarc VaudelPeter NollauOliver KohlbacherLennart MartensUlrich WalterAlbert Sickmann et al.

A1 Journal Article in BLOOD

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications

Eugene KolkerVural ÖzdemirLennart MartensWilliam HancockGordon AndersonNathaniel AndersonSukru AynaciogluAncha BaranovaShawn R CampagnaRui Chen et al.

Editorial material

Unraveling the specificities of the different human methionine sulfoxide reductases

Elien VandermarliereBart GhesquièreVeronique JonckheereKris GevaertLennart Martens

A1 Journal Article in PROTEOMICS

2013

About dice, bouldering, and team empowerment: running the CompOmics group at VIB and Ghent University, Belgium

Lennart Martens

A1 Journal Article in PLOS COMPUTATIONAL BIOLOGY

Asn₃, a reliable, robust, and universal lock mass for improved accuracy in LC-MS and LC-MS/MS

An StaesJonathan VandenbusscheHans DemolMarc GoethalsSule Yilmaz-RumpfNiels HulstaertSven DegroevePieter KelchtermansLennart MartensKris Gevaert

A1 Journal Article in ANALYTICAL CHEMISTRY

Bringing proteomics into the clinic: the need for the field to finally take itself seriously

Lennart Martens

A1 Journal Article in PROTEOMICS CLINICAL APPLICATIONS

CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays

Paola MasuzzoNiels HulstaertLynn HuyckChristophe AmpeMarleen Van TroysLennart Martens

A1 Journal Article in BIOINFORMATICS

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report

Yasset Perez-RiverolHenning HermjakobOliver KohlbacherLennart MartensDavid CreasyJürgen CoxFelipe LeprevostBaozhen Paul ShanVioleta I Pérez-NuenoMichal Blazejczyk et al.

A1 Journal Article in JOURNAL OF PROTEOMICS

Crowdsourcing in proteomics: public resources lead to better experiments

Harald BarsnesLennart Martens

A1 Journal Article in AMINO ACIDS

D-score: a search engine independent MD-score

Marc VaudelDaniela BreiterFlorian BeckJörg RahnenführerLennart MartensRené P Zahedi

A1 Journal Article in PROTEOMICS

Delsa workshop IV : launching the Quantified Human Initiative

Elizabeth StewartTodd SmithAndrea De SouzaJack FarisLennart MartensSophie MohinVural OzdemirCourtney MacNealy-KochEugene Kolker

A1 Journal Article in BIG DATA

Early targets of MIR-34A in neuroblastoma

P De AntonellisM CarotenutoG De VitaJonathan VandenbusscheC MedagliaJ VandesopeleP MestdaghLennart MartensAn StaesKathleen Moens et al.

Getting intimate with trypsin, the leading protease in proteomics

Elien VandermarliereMichael MuellerLennart Martens

A1 Journal Article in MASS SPECTROMETRY REVIEWS

In praise of open research measures

Eugene KolkerIlkay AltintasPhilip BourneJack FarisGeoffrey FoxDmitrij FrishmanChristy GeraciWilliam HancockBiaoyang LinDoron Lancet et al.

A1 Journal Article in NATURE

LNCipedia 2.0: a database for annotated human lncRNA transcript sequences and structures

Pieter-Jan VoldersKenny HelsensXiaowei WangLennart MartensKris GevaertJo VandesompelePieter Mestdagh

LNCipedia 2.0: a database for annotated human lncRNA transcript sequences and structures

Pieter-Jan VoldersKenny HelsensXiaowei WangLennart MartensKris GevaertJo VandesompelePieter Mestdagh

LNCipedia : a database for annotated human lncRNA transcript sequences and structures

Pieter-Jan VoldersKenny HelsensXiaowei WangBjörn MentenLennart MartensKris GevaertJo VandesompelePieter Mestdagh

A1 Journal Article in NUCLEIC ACIDS RESEARCH

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

Pieter-Jan VoldersKenny HelsensXiaowei WangLennart MartensKris GevaertJo VandesompelePieter Mestdagh

MS²PIP: a tool for MS/MS peak intensity prediction

Sven DegroeveLennart Martens

A1 Journal Article in BIOINFORMATICS

PiTRAQ, a strategy to simultaneously correlate protein expression and phosphorylation stoichiometry between different samples : evaluation on different mass spectrometers

Pieter GlibertMaarten DhaenensPaulien MeertNiklaas ColaertFilip Van NieuwerburghLennart MartensDieter Deforce

Predicting tryptic cleavage from proteomics data using decision tree ensembles

Thomas FannesElien VandermarliereLeander SchietgatSven DegroeveLennart MartensJan Ramon

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Pride-asap: automatic fragment ion annotation of identified PRIDE spectra

Niels HulstaertFlorian ReisingerJonathan RamesederHarald BarsnesJuan Antonio VizcaínoLennart Martens

A1 Journal Article in JOURNAL OF PROTEOMICS

Protein structure as a means to triage proposed PTM sites

Elien VandermarliereLennart Martens

A1 Journal Article in PROTEOMICS

ProteoCloud: a full-featured open source proteomics cloud computing pipeline

Thilo MuthJulian PetersJonathan BlackburnErdmann RappLennart Martens

A1 Journal Article in JOURNAL OF PROTEOMICS

Proteome-derived peptide libraries to study the substrate specificity profiles of carboxypeptidases

Sebastian TancoJulia LorenzoJavier Garcia-PardoSven DegroeveLennart MartensFrancesc Xavier AvilesKris GevaertPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Resilience in the proteomics data ecosystem: how the field cares for its data

Lennart Martens

A1 Journal Article in PROTEOMICS

Searching for a needle in a stack of needles: challenges in metaproteomics data analysis

Thilo MuthDirk BenndorfUdo ReichlErdmann RappLennart Martens

A1 Journal Article in MOLECULAR BIOSYSTEMS

The Online Protein Processing Resource (TOPPR) : a database and analysis platform for protein processing events

Niklaas ColaertDavy MaddeleinFrancis ImpensPetra Van DammeKim PlasmanKenny HelsensNiels HulstaertJoël VandekerckhoveKris GevaertLennart Martens

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2012

A complex standard for protein identification, designed by evolution

Marc VaudelJulia M BurkhartDaniela BreiterRené P ZahediAlbert SickmannLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Chromatographic retention time prediction for posttranslationally modified peptides

Luminita MoruzAn StaesJoseph M FosterMaria HatzouEvy TimmermanLennart MartensLukas Käll

A1 Journal Article in PROTEOMICS

Current methods for global proteome identification

Marc VaudelAlbert SickmannLennart Martens

A1 Journal Article in EXPERT REVIEW OF PROTEOMICS

Detailed analysis of the blood platelet proteome through the use of innovative bioinformatics methods for protein identification, quantification and post-translational modification localization

Marc VaudelLennart MartensAlbert Sickmann

Enabling computational proteomics by public and local data management systems

Kenny HelsensLennart Martens

A1 Journal Article in CIRCULATION-CARDIOVASCULAR GENETICS

Evaluation of a strategy for parallel protein phosphorylation and expression analysis

Pieter GlibertMaarten DhaenensPaulien MeertNiklaas ColaertFilip Van NieuwerburghLennart MartensDieter Deforce

Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI)

Marc VaudelJulia M BurkhartSonja RadauRené P ZahediLennart MartensAlbert Sickmann

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

iTRAQ data interpretation

Marc VaudelJulia Maria BurkhartRené Peiman ZahediLennart MartensAlbert Sickmann

Bookchapter in Quantitative methods in proteomics

Lncipedia: a novel database for annotated lncRNA sequences and structures

Pieter-Jan VoldersKenny HelsensXiaowei WangLennart MartensKris GevaertJo VandesompelePieter Mestdagh

PRIDE Inspector: a tool to visualize and validate MS proteomics data

Rui WangAntonio FabregatDaniel RíosDavid OvelleiroJoseph M FosterRichard G CôtéJohannes GrissAttila CsordasYasset Perez-RiverolFlorian Reisinger et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

Sigpep: calculating unique peptide signature transition sets in a complete proteome background

Kenny HelsensMichael MuellerNiels HulstaertLennart Martens

A1 Journal Article in PROTEOMICS

The effect of peptide identification search algorithms on MS2-based label-free protein quantification

Sven DegroeveAn StaesPieter-Jan De BockLennart Martens

A1 Journal Article in OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways

Julia M BurkhartMarc VaudelStepan GambaryanSonja RadauUlrich WalterLennart MartensJörg GeigerAlbert SickmannRené P Zahedi

A1 Journal Article in BLOOD

The HUPO initiative on Model Organism Proteomes, iMOP

Alexandre ME JonesRuedi AebersoldChristian H AhrensRolf ApweilerKatja BaerenfallerMark BakerEmøke BendixenSteve BriggsPhilip BrownridgeErich Brunner et al.

A1 Journal Article in PROTEOMICS

The PRoteomics IDEntification (PRIDE) converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium

Richard G CôtéJohannes GrissJosé A DianesRui WangJames C WrightHenk WP van den ToornBas van BreukelenAlbert JR HeckNiels HulstaertLennart Martens et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Towards a human proteomics atlas

Giulia GonnelliNiels HulstaertSven DegroeveLennart Martens

A1 Journal Article in ANALYTICAL AND BIOANALYTICAL CHEMISTRY

TraML: a standard format for exchange of selected reaction monitoring transition lists

Eric W DeutschMatthew ChambersSteffen NeumannFredrik LevanderPierre-Alain BinzJim ShofstahlDavid S CampbellLuis MendozaDavid OvelleiroKenny Helsens et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

2011

'4D Biology for health and disease' workshop report

Jan-Pieter AbrahamsRolf ApweilerRudi BallingMichela G BerteroJanusz M BujnickiNaomi E ChayenPatrick ChèneGary L CorthalsTomasz DylągFriedrich Förster et al.

A1 Journal Article in NEW BIOTECHNOLOGY

A case study on the comparison of different software tools for automated quantification of peptides

Niklaas ColaertJoël VandekerckhoveLennart MartensKris Gevaert

Bookchapter in Gel-free proteomics : methods and protocols

A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision

Niklaas ColaertJoël VandekerckhoveKris GevaertLennart Martens

A1 Journal Article in PROTEOMICS

A global analysis of peptide fragmentation variability

Harald BarsnesIngvar EidhammerLennart Martens

A1 Journal Article in PROTEOMICS

A posteriori quality control for the curation and reuse of public proteomics data

Joseph M FosterSven DegroeveLaurent GattoMatthieu VisserRui WangJohannes GrissRolf ApweilerLennart Martens

A1 Journal Article in PROTEOMICS

A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods

Sven DegroeveNiklaas ColaertJoël VandekerckhoveKris GevaertLennart Martens

A1 Journal Article in PROTEOMICS

Analysis of the resolution limitations of peptide identification algorithms

Niklaas ColaertSven DegroeveKenny HelsensLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation

Kenny HelsensPetra Van DammeSven DegroeveLennart MartensThomas ArnesenJoël VandekerckhoveKris Gevaert

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Combining quantitative proteomics data processing workflows for greater sensitivity

Niklaas ColaertChristophe Van HueleSven DegroeveAn StaesJoël VandekerckhoveKris GevaertLennart Martens

A1 Journal Article in NATURE METHODS

compomics-utilities: an open-source Java library for computational proteomics

Harald BarsnesMarc VaudelNiklaas ColaertKenny HelsensAlbert SickmannFrode S BervenLennart Martens

A1 Journal Article in BMC BIOINFORMATICS

Digging deeper in the data, novel approaches and analysis methods in quantitative peptide-centric proteomics

Niklaas ColaertKris GevaertLennart Martens

iTRAQ protein quantification: a quality-controlled workflow

Julia M BurkhartMarc VaudelReneP ZahediLennart MartensAlbert Sickmann

A1 Journal Article in PROTEOMICS

jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions

Kenny HelsensMi-Youn BrusniakEric DeutschRobert L MoritzLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

mzML: a community standard for mass spectrometry data

Lennart MartensMatthew ChambersMarc SturmDarren KessnerFredrik LevanderJim ShofstahlWilfred H TangAndreas RoppSteffen NeumannAngel D Pizarro et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

N-Terminal combined fractional diagonal chromatographic (COFRADIC) analysis of the human platelet proteome

Francis ImpensKenny HelsensNiklaas ColaertLennart MartensJoël VandekerckhoveKris Gevaert

Bookchapter in Platelet proteomics : principles, analysis, and applications

Peptide identification quality control

Marc VaudelJulia M BurkhartAlbert SickmannLennart MartensRene P Zahedi

A1 Journal Article in PROTEOMICS

Quality control in proteomics

Lennart MartensJuan Antonio VizcainoRoz Banks

Editorial material

RIBAR and xRIBAR: methods for reproducible relative MS/MS-based label-free protein quantification

Niklaas ColaertKris GevaertLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

Marc VaudelHarald BarsnesFrode S BervenAlbert SickmannLennart Martens

A1 Journal Article in PROTEOMICS

thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files

Niklaas ColaertHarald BarsnesMarc VaudelKenny HelsensEvy TimmermanAlbert SickmannKris GevaertLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2010

A report on the ESF workshop on quality control in proteomics

Lennart Martens

Editorial material

FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data

Harald BarsnesIngvar EidhammerLennart Martens

A1 Journal Article in PROTEOMICS

High-throughput proteomics and bioinformatics : joined at the hip

Lennart MartensHenning Hermjakob

Editorial material

Increasing the specificity and the sensitivity in peptide centric proteomics

Kenny HelsensKris GevaertLennart Martens

jmzML, an open-source Java API for mzML, the PSI standard for MS data

Richard G CôtéFlorian ReisingerLennart Martens

A1 Journal Article in PROTEOMICS

jTraqX: a free, platform independent tool for isobaric tag quantitation at the protein level

Thilo MuthDaniela KellerStephanie Michaela PuetzLennart MartensAlbert SickmannAndreas M Boehm

A1 Journal Article in PROTEOMICS

ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics

Kenny HelsensNiklaas ColaertHarald BarsnesThilo MuthKristian FlikkaAn StaesEvy TimmermanSteffi WortelkampAlbert SickmannJoël Vandekerckhove et al.

A1 Journal Article in PROTEOMICS

OLS Dialog : an open-source front end to the Ontology Lookup Service

Harald BarsnesRichard G CôtéIngvar EidhammerLennart Martens

A1 Journal Article in BMC BIOINFORMATICS

Peptide and protein quantification: A map of the minefield

Marc VaudelAlbert SickmannLennart Martens

A1 Journal Article in PROTEOMICS

Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research

Juan Antonio VizcaínoJoseph M FosterLennart Martens

A1 Journal Article in JOURNAL OF PROTEOMICS

The Ontology Lookup Service : bigger and better

Richard CôtéFlorian ReisingerLennart MartensHarald BarsnesJuan Antonio VizcaínoHenning Hermjakob

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The Proteomics Identifications database : 2010 update

Juan Antonio VizcaínoRichard CôtéFlorian ReisingerHarald BarsnesJoseph M FosterJonathan RamesederHenning HermjakobLennart Martens

A1 Journal Article in NUCLEIC ACIDS RESEARCH

XTandem parser: an open-source library to parse and analyse X!Tandem MS/MS search results

Thilo MuthMarc VaudelHarald BarsnesLennart MartensAlbert Sickmann

A1 Journal Article in PROTEOMICS

2009

A guide to the Proteomics Identifications Database proteomics data repository

JA VizcainoR CoteF ReisingerJM FosterM MuellerJ RamesederH HermjakobLennart Martens

A1 Journal Article in PROTEOMICS

A HUPO test sample study reveals common problems in mass spectrometry-based proteomics

Alexander W BellEric W DeutschCatherine E AuRobert E KearneyRon BeavisSalvatore SechiTommy NilssonJohn J M Bergeron- HUPO Test Sample Working GroupLennart Martens

A1 Journal Article in NATURE METHODS

Charting online OMICS resources: a navigational chart for clinical researchers

Juan Antonio VizcaMichael MuellerHenning HermjakobLennart Martens

A1 Journal Article in PROTEOMICS CLINICAL APPLICATIONS

Database on Demand: an online tool for the custom generation of FASTA-formatted sequence databases

Florian ReisingerLennart Martens

A1 Journal Article in PROTEOMICS

Getting a grip on proteomics data: Proteomics Data Collection (ProDaC)

Martin EisenacherLennart MartensMichael KohlHarald BarsnesKenny HelsensJari HäkkinenFredrik LevanderRuedi AebersoldJoël VandekerckhoveMichael J. Dunn et al.

A1 Journal Article in PROTEOMICS

Improved visualization of protein consensus sequences by iceLogo

Niklaas ColaertKenny HelsensLennart MartensJoël VandekerckhoveKris Gevaert

A1 Journal Article in NATURE METHODS

OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results

Harald BarsnesSteffen HuberAlbert SickmannIngvar EidhammerLennart Martens

A1 Journal Article in PROTEOMICS

PRIDE Converter: making proteomics data-sharing easy

Harald BarsnesJuan Antonio VizcaínoIngvar EidhammerLennart Martens

A1 Journal Article in NATURE BIOTECHNOLOGY

Proteomics data collection : 4th ProDaC workshop: 15 August 2008, Amsterdam, The Netherlands

Martin EisenacherMichael KohlLennart MartensHarald BarsnesTanja HardtFredrik LevanderJari HäkkinenRolf ApweilerHelmut E MeyerChristian Stephan

Editorial material

Proteomics data collection: 5th ProDaC workshop: 4 March 2009, Kolympari, Crete, Greece

Martin EisenacherLennart MartensHarald BarsnesTanja HardtMichael KohlJari HäkkinenRolf ApweilerHelmut E MeyerChristian Stephan

A1 Journal Article in PROTEOMICS

The PSI semantic validator: a framework to check MIAPE compliance of proteomics data

Luisa Montecchi-PalazziSamuel KerrienFlorian ReisingerBruno ArandaAndrew R JonesLennart MartensHenning Hermjakob

A1 Journal Article in PROTEOMICS

Toward a successful clinical neuroproteomics : the 11th HUPO Brain Proteome Project Workshop 3 March, 2009, Kolymbari, Greece

Young Hye KimKatrin MarcusLea Tenenholz GrinbergHeike GoehlerJens WiltfangChristian StephanMartin EisenacherTanja HardtLennart MartensMichael J Dunn et al.

A1 Journal Article in PROTEOMICS CLINICAL APPLICATIONS

2008

6th HUPO Annual World Congress : Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea

Sandra OrchardLennart MartensJoshua TasmanPierre-Alain BinzJuan Pablo AlbarHenning Hermjakob

Editorial material

Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets

Michael MuellerJuan Antonio VizcaínoPhilip JonesRichard CôtéDavid ThorneycroftRolf ApweilerHenning HermjakobLennart Martens

A1 Journal Article in PROTEOMICS

Analyzing large-scale proteomics projects with latent semantic indexing

Sebastian KlieLennart MartensJuan Antonio VizcaínoRichard CôtéPhil JonesRolf ApweilerAlexander HinneburgHenning Hermjakob

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Human Proteinpedia enables sharing of human protein data

Suresh MathivananMukhtar AhmedNatalie G AhnHainard AlexandreRamars AmanchyPhilip C AndrewsJoel S BaderBrian M BalgleyMarcus BantscheffKeiryn L Bennett et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

OMSSAGUI: an open-source user interface component to configure and run the OMSSA search engine

Ravi TharakanLennart MartensJennifer E Van EykDavid R Graham

A1 Journal Article in PROTEOMICS

Peptizer: a tool for assessing false positive peptide identifications and manually validating selected results

Kenny HelsensEvy TimmermanJoël VandekerckhoveKris GevaertLennart Martens

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

PRIDE : new developments and new datasets

Philip JonesRichard G CôtéSang Yun ChoSebastian KlieLennart MartensAntony F QuinnDavid ThorneycroftHenning Hermjakob

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Proteomics data collection : 2nd ProDaC workshop : 5 October 2007, Seoul, Korea

Martin EisenacherTanja HardtMichael HamacherLennart MartensJari HäkkinenFredrik LevanderRolf ApweilerHelmut E MeyerChristian Stephan

A1 Journal Article in PROTEOMICS

Proteomics data collection: 3rd ProDaC workshop April 22nd 2008, Toledo, Spain

Martin EisenacherTanja HardtLennart MartensJari HäkkinenRolf ApweilerMichael HamacherHelmut E MeyerChristian Stephan

A1 Journal Article in PROTEOMICS

The HUPO Brain Proteome project wish list : summary of the 9th HUPO BPP Workshop 9-10 January 2008, Barbados

Michael HamacherMartin EisenacherFlorian TriblChristian StephanKatrin MarcusTanja HardtJens WiltfangLennart MartensDominic DesiderioHoward Gutstein et al.

A1 Journal Article in PROTEOMICS

The Ontology Lookup Service : more data and better tools for controlled vocabulary queries

Richard G CôtéPhilip JonesLennart MartensRolf ApweilerHenning Hermjakob

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2007

A la carte proteomics with an emphasis on gel-free techniques

Kris GevaertPetra Van DammeBart GhesquièreFrancis ImpensLennart MartensKenny HelsensJoël Vandekerckhove

A1 Journal Article in PROTEOMICS

Annotating the human proteome: beyond establishing a parts list

Michael MuellerLennart MartensRolf Apweiler

A1 Journal Article in BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

High performance proteomics : 7th HUPO Brain Proteome project workshop, March 7-9, 2007, Wellcome Trust Conference Centre, Hinxton, UK

Michael HamacherChristian StephanMartin EisenacherPiotr LewczukJens WiltfangLennart MartensJuan Antonio VizcaínoKyung-Hoon KwonJong Shin YooYoung Mok Park et al.

Editorial material

Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy

Lennart MartensSandra OrchardRolf ApweilerHenning Hermjakob

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Implementation and application of a versatile clustering tool for tandem mass spectrometry data

Kristian FlikkaJeroen MeukensKenny HelsensJoël VandekerckhoveIngvar EidhammerKris GevaertLennart Martens

A1 Journal Article in PROTEOMICS

Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis

Michalis AivaliotisKris GevaertMichaela FalbAndreas TebbeKosta KonstantinidisBirgit BisleChristian KleinLennart MartensAn StaesEvy Timmerman et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results

Kenny HelsensLennart MartensJoël VandekerckhoveKris Gevaert

A1 Journal Article in PROTEOMICS

Proteomics data collection : the 1st ProDaC workshop: 26 April 2007, Ecole Normale Supérieur, Lyon, France

Martin EisenacherTanja HardtMichael HamacherLennart MartensJari HäkkinenFredrik LevanderRolf ApweilerHelmut E MeyerChristian Stephan

A1 Journal Article in PROTEOMICS

Proteomics data validation: why all must provide data

Lennart MartensHenning Hermjakob

A1 Journal Article in MOLECULAR BIOSYSTEMS

Proteomics for everyday use : activities of the HUPO Brain Proteome project during the 5th HUPO world congress

Michael HamacherChristian StephanMartin EisenacherAndre van HallKatrin MarcusLennart MartensYoung Mok ParkHoward B GutsteinFriedrich HerbergHelmut E Meyer

Editorial material

The minimum information about a proteomics experiment (MIAPE)

Chris F TaylorNorman W PatonKathryn S LilleyPierre-Alain BinzRandall K, Jr JulianAndrew R JonesWeimin ZhuRolf ApweilerRuedi AebersoldEric W Deutsch et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

The Protein Identifier Cross-Referencing (PICR) service : reconciling protein identifiers across multiple source databases

Richard G CôtéPhilip JonesLennart MartensSamuel KerrienFlorian ReisingerQuan LinRasko LeinonenRolf ApweilerHenning Hermjakob

A1 Journal Article in BMC BIOINFORMATICS

The PSI formal document process and its implementation on the PSI website

Juan Antonio VizcaínoLennart MartensHenning HermjakobRandall K JulianNorman W Paton

A1 Journal Article in PROTEOMICS

2006

A comparison of the HUPO Brain Proteome project pilot with other proteomics studies

Lennart MartensMichael MüllerChristian StephanMichael HamacherKai A ReidegeldHelmut E MeyerMartin BlüggelJoël VandekerckhoveKris GevaertRolf Apweiler

A1 Journal Article in PROTEOMICS

A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes

Xavier HanoulleJozef Van DammeAn StaesLennart MartensMarc GoethalsJoël VandekerckhoveKris Gevaert

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome project pilot phase

Christian StephanKai A ReidegeldMichael HamacherAndré van HallKatrin MarcusChris TaylorPhilip JonesMichael MüllerRolf ApweilerLennart Martens et al.

A1 Journal Article in PROTEOMICS

Cell_motility : a cross-platform, open source application for the study of cell motion paths

Lennart MartensGeert MonsieurChristophe AmpeKris GevaertJoël Vandekerckhove

A1 Journal Article in BMC BIOINFORMATICS

Four stage liquid chromatographic selection of methionyl peptides for peptide-centric proteome analysis: the proteome of human multipotent adult progenitor cells

Kris GevaertJozef PinxterenHans DemolKoen HugelierAn StaesJozef Van DammeLennart MartensJoël Vandekerckhove

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Functional annotation of proteins identified in human brain during the HUPO Brain Proteome project pilot study

Michael MuellerLennart MartensKai A ReidegeldMichael HamacherChristian StephanMartin BlüggelGerhard KörtingDaniel ChamradChristian ScheerKatrin Marcus et al.

A1 Journal Article in PROTEOMICS

HUPO Brain Proteome Project : summary of the pilot phase and introduction of a comprehensive data reprocessing strategy

Michael HamacherRolf ApweilerGeorg ArnoldAlbert BeckerMartin BlüggelOdile CarretteChristine ColvisMichael J. DunnThomas FröhlichMichael Fountoulakis et al.

HUPO Brain Proteome Project : summary of the pilot phase and introduction of a comprehensive data reprocessing strategy

Michael HamacherRolf ApweilerGeorg ArnoldAlbert BeckerMartin BlüggelOdile CarretteChristine ColvisMichael J DunnThomas FröhlichMichael Fountoulakis et al.

Editorial material

Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering

Kristian FlikkaLennart MartensJoël VandekerckhoveKris GevaertIngvar Eidhammer

A1 Journal Article in PROTEOMICS

Novel bioinformatics tools assisting targeted peptide-centric proteomics and global proteomics data dissemination

Lennart MartensJ Vandekerckhove

PRIDE : a public repository of protein and peptide identifications for the proteomics community

Philip JonesRichard G CôtéLennart MartensAntony F QuinnChris F TaylorWilliam DeracheHenning HermjakobRolf Apweiler

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Proteome-wide characterization of N-glycosylation events by diagonal chromatography

Bart GhesquièreJozef Van DammeLennart MartensJoël VandekerckhoveKris Gevaert

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

The HUPO Brain Proteome Project

Kai ReidegeldHemut MeyerChristian StephanMartin BlüggelGerhard KörtingDaniel ChamradChristian ScheerHerbert ThieleBruker DaltonikChris Taylor et al.

A2 Journal Article in EUROPEAN PHARMACEUTICAL REVIEW

The HUPO Brain Proteome project jamboree: centralised summary of the pilot studies

Michael HamacherChristian StephanMartin BlüggelDaniel ChamradGerhard KörtingLennart MartensMichael MüllerHenning HermjakobDavid ParkinsonAndrew Dowsey et al.

A1 Journal Article in PROTEOMICS

The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome project pilot study results

Kai A ReidegeldMichael MüllerChristian StephanMartin BlüggelMichael HamacherLennart MartensGerhard KörtingDaniel C ChamradDavid ParkinsonRolf Apweiler et al.

A1 Journal Article in PROTEOMICS

2005

5th HUPO BPP bioinformatics meeting at the European Bioinformatics Institute in Hinxton, UK : setting the analysis frame

Christian StephanMichael HamacherMartin BlüggelGerhard KörtingDaniel ChamradChristian ScheerKatrin MarcusKai A ReidegeldChristiane LohausHeike Schäfer et al.

A1 Journal Article in PROTEOMICS

Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis

Petra Van DammeLennart MartensJozef Van DammeKoen HugelierAn StaesJoël VandekerckhoveKris Gevaert

A1 Journal Article in NATURE METHODS

Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome project

Marcin AdamskiThomas BlackwellRajasree MenonLennart MartensHenning HermjakobChris TaylorGilbert S OmennDavid J States

A1 Journal Article in PROTEOMICS

DBToolkit: processing protein databases for peptide-centric proteomics

Lennart MartensJoël VandekerckhoveKris Gevaert

A1 Journal Article in BIOINFORMATICS

Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics?

Kris GevaertPetra Van DammeLennart MartensJoël Vandekerckhove

A1 Journal Article in ANALYTICAL BIOCHEMISTRY

Do we want our data raw?: including binary mass spectrometry data in public proteomics data repositories

Lennart MartensAlexey I NesvizhskiiHenning HermjakobMarcin AdamskiGilbert S OmennJoël VandekerckhoveKris Gevaert

A1 Journal Article in PROTEOMICS

Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC

Kris GevaertAn StaesJozef Van DammeSara De GrootKoen HugelierHans DemolLennart MartensMarc GoethalsJoël Vandekerckhove

A1 Journal Article in PROTEOMICS

PRIDE: The proteomics identification database (vol 5, pg 3537, 2005)

Lennart Martens

PRIDE: the proteomics identifications database

Lennart MartensHenning HermjakobPhilip JonesMarcin AdamskiChris TaylorDavid StatesKris GevaertJoël VandekerckhoveRolf Apweiler

A1 Journal Article in PROTEOMICS

The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile

Lennart MartensPetra Van DammeJozef Van DammeAn StaesEvy TimmermanBart GhesquièreGrégoire R ThomasJoël VandekerckhoveKris Gevaert

A1 Journal Article in PROTEOMICS

2004

Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18

An StaesHans DemolJozef Van DammeLennart MartensJoël VandekerckhoveKris Gevaert

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies

Kris GevaertBart GhesquièreAn StaesLennart MartensJozef Van DammeGrégoire ThomasJoël Vandekerckhove

A1 Journal Article in PROTEOMICS

2003

Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides

Kris GevaertMarc GoethalsLennart MartensJozef Van DammeAn StaesGrégoire ThomasJoël Vandekerckhove

A1 Journal Article in NATURE BIOTECHNOLOGY

IL-29 Is proteomics heading towards medicine?

Joël VandekerckhoveJozef Van DammeLennart MartensGrégoire ThomasAn StaesMarc GoethalsBart GhesquièreMagda PuypeHans DemolKris Gevaert

A2 Journal Article in PIGMENT CELL RESEARCH

2002

Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins

Kris GevaertJozef Van DammeMarc GoethalsGrégoire ThomasBart HoorelbekeHans DemolLennart MartensMagda PuypeAn StaesJoël Vandekerckhove

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

2001

Protein identification based on matrix assisted laser desorption/ionization-post source decay-mass spectrometry.

Kris GevaertHans DemolLennart MartensB HOORELBEKEMagda PuypeM GOETHALSJozef Van DammeStefaan De BoeckJoël Vandekerckhove

A1 Journal Article in ELECTROPHORESIS