Research Explorer

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Researcher

Petra Van Damme

Publications & Research Data

Awards & Distinctions

144 Results

2025

A guarded guest : unraveling tomato accommodation of arbuscular mycorrhiza at single-nucleus resolution

Naomi StuerSofie GoormachtigPetra Van DammeJudith Van Dingenen

BioID in bacteria : selection of a suitable biotin ligase for proxeome mapping

Laure SimoensVeronique JonckheerePetra Van Damme

Bookchapter in Proximity-dependent protein biotinylation : methods and protocols

Cross-species proximity-dependent protein biotinylation : a standardized approach for mapping proxeomes

Petra Van Damme

Bookchapter in Proximity-dependent protein biotinylation : methods and protocols

Endogenous HiBiT-tagging combined with affinity complementation : a new strategy for small open reading frame-encoded polypeptide detection in bacteria

Laure SimoensVeronique JonckheereDominiek CatteeuwPetra Van Damme

A2 Journal Article in ADVANCES IN SAMPLE PREPARATION

Exploring the tomato root protein network exploited by core type 3 effectors from the Ralstonia solanacearum species complex

Joren De RyckVeronique JonckheereBrigitte De PaepeAnnick De KeyserNemo PeetersJohan Van VaerenberghJane DebodePetra Van DammeSofie Goormachtig

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Melissospora conviva gen. nov., sp. nov., a novel actinobacterial genus isolated from beehive through cross-feeding interactions

Déborah TellatinLuc CornetValdes SnauwaertPhilippe CompèreMarc OngenaLoïc QuintonNudzejma StulanovicSilvia Ribeiro MonteiroAugustin RigoletPierre Burguet et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Methionyl aminopeptidase 1 (eukaryote)

Petra Van Damme

Bookchapter in Handbook of proteolytic enzymes : metallopeptidases

Proximal partners of the organellar N-terminal acetyltransferase NAA60 : insights into Golgi structure and transmembrane protein topology

Sebastian TancoVeronique JonckheereArun Kumar Tharkeshwar RaghunathAnnelies BogaertKris GevaertWim AnneartPetra Van Damme

A1 Journal Article in OPEN BIOLOGY

Proximity-dependent protein biotinylation : methods and protocols

Translon: a single term for translated regions

Michał I. ŚwirskiJack A. S. TierneyM. Mar AlbàDmitry E. AndreevJulie L. AspdenJohn F. AtkinsMichal Bassani-SternbergMarla J. BerryStefano BiffoKathleen Boris-Lawrie et al.

U Journal Article in Nature Methods

Unraveling N-terminal proteoform interactomes via multiplexed recombineering in Salmonella

Valdes SnauwaertVeronique JonckheerePetra Van Damme

Bookchapter in Proximity-dependent protein biotinylation : methods and protocols

2024

Characterization of newly discovered genomic elements in Enterobacteriaceae through advanced recombineering approaches

Valdes SnauwaertVeronique JonckheerePetra Van Damme

Distinct dynamics and proximity networks of hub proteins at the prey-invading cell pole in a predatory bacterium

Ophélie RemyYoann G. SantinVeronique JonckheereCoralie TesseurJovana KaljevićPetra Van DammeGéraldine Laloux

A1 Journal Article in JOURNAL OF BACTERIOLOGY

Proteins à la carte : riboproteogenomic exploration of bacterial N-terminal proteoform expression

Igor FijalkowskiValdes SnauwaertPetra Van Damme

A1 Journal Article in MBIO

2023

Cataloguing protein complexes in planta using TurboID-catalyzed proximity labeling

Lore GryffroyJoren De RyckVeronique JonckheereSofie GoormachtigAlain GoossensPetra Van Damme

Bookchapter in Protein-protein interactions : methods and protocols

Deciphering biological functions of newly discovered Salmonella N-terminal proteoforms with the use of multiplexed recombineering

Valdes SnauwaertVeronique JonckheerePetra Van Damme

Elucidating the tomato protein network exploited by core type 3 effectors from the Ralstonia solanacearum species complex

Joren De RyckSofie GoormachtigPetra Van DammeJane Debode

Expanded in vivo substrate profile of the yeast N-terminal acetyltransferase NatC

Petra Van DammeCamilla OsbergVeronique JonckheereNina GlomnesKris GevaertThomas ArnesenHenriette Aksnes

A1 Journal Article in JOURNAL OF BIOLOGICAL CHEMISTRY

Exposing the small protein load of bacterial life

Laure SimoensIgor FijalkowskiPetra Van Damme

A1 Journal Article in FEMS MICROBIOLOGY REVIEWS

From prediction to function : current practices and challenges towards the functional characterization of type III effectors

Joren De RyckPetra Van DammeSofie Goormachtig

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Gasdermin D independent canonical inflammasome responses cooperate with caspase-8 to establish host defense against gastrointestinal Citrobacter rodentium infection

Elien EeckhoutLisa HamerlinckVeronique JonckheerePetra Van DammeGeert van LooAndy Wullaert

A1 Journal Article in CELL DEATH & DISEASE

Identification of plant protein-metabolite interactions by limited proteolysis-coupled mass spectrometry (LiP-MS)

Jhon Jairo Venegas MolinaPetra Van DammeAlain Goossens

Bookchapter in Cell-wide identification of metabolite-protein interactions

Proximity mapping of CCP6 reveals its association with centrosome organization and cilium assembly

Sergi Rodriguez-CaladoPetra Van DammeFrancesc Xavier AvilésAna Paula CandiotaSebastian TancoJulia Lorenzo

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Rhizogenic agrobacterium protein RolB interacts with the TOPLESS repressor proteins to reprogram plant immunity and development

Lore GryffroyEvi CeulemansNicolás Manosalva PérezJhon Jairo Venegas MolinaAna JaramilloSavio D. RodriguesLiesbeth De MildeVeronique JonckheereMarc Van MontaguBarbara De Coninck et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Seeking the interspecies crosswalk for filamentous microbe effectors

Naomi StuerPetra Van DammeSofie GoormachtigJudith Van Dingenen

A1 Journal Article in TRENDS IN PLANT SCIENCE

Shift in vacuolar to cytosolic regime of infecting Salmonella from a dual proteome perspective

Ursula FelsPatrick WillemsMargaux De MeyerKris GevaertPetra Van Damme

A1 Journal Article in PLOS PATHOGENS

Virotrap : trapping protein complexes in virus-like particles

Georgios MoschonasMargaux De MeyerDelphine De SutterEvy TimmermanPetra Van DammeSven Eyckerman

Bookchapter in Mass spectrometry-based proteomics

2022

Combining selection and Oligo-Mediated Allelic-Replacement (OMAR) based recombineering to steer expression of newly discovered Salmonella N-terminal proteoforms

Valdes SnauwaertVeronique JonckheerePetra Van Damme

Hidden in plain sight : challenges in proteomics detection of small ORF-encoded polypeptides

Igor FijalkowskiPatrick WillemsVeronique JonckheereLaure SimoensPetra Van Damme

A2 Journal Article in MICROLIFE

Mapping the protein interaction landscape of T-DNA proteins in tomato hairy root development

Lore GryffroyAlain GoossensPetra Van Damme

Recent advancements in tracking bacterial effector protein translocation

Julie BraetDominiek CatteeuwPetra Van Damme

A1 Journal Article in MICROORGANISMS

Selective ribosome profiling reveals a role for SecB in the co-translational inner membrane protein biogenesis

Lena EismannIgor FijalkowskiCarla Verónica GalmozziJiří KoubekFrank TippmannPetra Van DammeGünter Kramer

A1 Journal Article in CELL REPORTS

To new beginnings : riboproteogenomics discovery of N-terminal proteoforms in Arabidopsis thaliana

Patrick WillemsElvis NdahVeronique JonckheereFrank Van BreusegemPetra Van Damme

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

2021

Capturing salmonella SspH2 host targets in virus-like particles

Margaux De MeyerIgor FijalkowskiVeronique JonckheereDelphine De SutterSven EyckermanPetra Van Damme

A1 Journal Article in FRONTIERS IN MEDICINE

Charting the N-terminal acetylome : a comprehensive map of human NatA substrates

Petra Van Damme

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Mechanisms of congenital heart disease caused by NAA15 haploinsufficiency

Tarsha L. WardWarren TaiSarah U. MortonFrancis ImpensPetra Van DammeDelphi Van HaverEvy TimmermanGabriela VenturiniKehan ZhangMin Young Jang et al.

A1 Journal Article in CIRCULATION RESEARCH

N-terminal acetyltransferase Naa40p whereabouts put into N-terminal proteoform perspective

Veronique JonckheerePetra Van Damme

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Small protein enrichment improves proteomics detection of sORF encoded polypeptides

Igor FijalkowskiMarlies PeetersPetra Van Damme

A1 Journal Article in FRONTIERS IN GENETICS

Use of hybrid data-dependent and -independent acquisition spectral libraries empowers dual-proteome profiling

Patrick WillemsUrsula FelsAn StaesKris GevaertPetra Van Damme

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2020

Bacterial genetic engineering by means of recombineering for reverse genetics

Ursula FelsKris GevaertPetra Van Damme

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Bacterial riboproteogenomics : the era of N-terminal proteoform existence revealed

Daria FijalkowskaIgor FijalkowskiPatrick WillemsPetra Van Damme

A1 Journal Article in FEMS MICROBIOLOGY REVIEWS

Establishment of proximity-dependent biotinylation approaches in different plant model systems

Deepanksha AroraNikolaj B. AbelChen LiuPetra Van DammeKlaas YpermanDominique EeckhoutLam Dai VuJie WangAnna TornkvistFrancis Impens et al.

A1 Journal Article in PLANT CELL

Keeping in touch with type-III secretion system effectors : mass spectrometry-based proteomics to study effector-host protein-protein interactions

Margaux De MeyerJoren De RyckSofie GoormachtigPetra Van Damme

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Lost and found : re-searching and re-scoring proteomics data aids genome annotation and improves proteome coverage

Patrick WillemsIgor FijalkowskiPetra Van Damme

A1 Journal Article in MSYSTEMS

Method optimization for unveiling the proteome landscape of bacterial pathogens in the context of the infected host

Ursula FelsPetra Van DammeKris Gevaert

The proteogenomic hunt for new proteoforms using ribosome profiling

Steven VerbruggenWim Van CriekingeGerben MenschaertPetra Van Damme

2019

Ablation of elongation factor 2 kinase enhances heat-shock protein 90 chaperone expression and protects cells under proteotoxic stress

Jianling XiePetra Van DammeDanielle FangChristopher G. Proud

A1 Journal Article in JOURNAL OF BIOLOGICAL CHEMISTRY

PROTEOFORMER 2.0 : further developments in the ribosome profiling-assisted proteogenomic hunt for new proteoforms

Steven VerbruggenElvis NdahWim Van CriekingeSiegfried GessulatBernhard KusterMathias WilhelmGerben MenschaertPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

2018

Cell-intrinsic control of interneuron migration drives cortical morphogenesis

Carla G SilvaElise PeyreMohit H AdhikariSylvia TielensSebastian TancoPetra Van DammeLorenza MagnoNathalie KrusyGulistan AgirmanMaria M Magiera et al.

A1 Journal Article in CELL

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

Elvis NdahPetra Van DammeGerben MenschaertLennart Martens

Limitless translation limits translation

Petra Van Damme

Editorial material

N-terminal acetylation levels are maintained during acetyl-CoA deficiency in Saccharomyces cerevisiae

Sylvia VarlandHenriette AksnesFedor KryuchkovFrancis ImpensDelphi Van HaverVeronique JonckheereMathias ZieglerKris GevaertPetra Van DammeThomas Arnesen

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

N-terminal acetylation modulates Bax targeting to mitochondria

Sara AlvesLeire NeiriSusana Rodrigues ChavesSelma VieiraDário TrindadeStephen ManonVeronica DominguezBelen PintadoVeronique JonckheerePetra Van Damme et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Omics assisted N-terminal proteoform and protein expression profiling on methionine aminopeptidase 1 (MetAP1) deletion

Veronique JonckheereDaria FijalkowskaPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

2017

eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs

Daria FijalkowskaSteven VerbruggenElvis NdahVeronique JonckheereGerben MenschaertPetra Van Damme

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Identification of carboxypeptidase substrates by C-terminal COFRADIC

Sebastian TancoFrancesc Xavier AvilesKris GevaertJulia LorenzoPetra Van Damme

Bookchapter in Protein terminal profiling : methods and protocols

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

Protease substrate profiling by N-terminal COFRADIC

An StaesPetra Van DammeEvy TimmermanBart RuttensElisabeth StesKris GevaertFrancis Impens

Bookchapter in Protein terminal profiling : methods and protocols

Proteogenomics in aid of host-pathogen interaction studies : a bacterial perspective

Ursula FelsKris GevaertPetra Van Damme

A2 Journal Article in PROTEOMES

REPARATION : ribosome profiling assisted (re-)annotation of bacterial genomes

Elvis NdahVeronique JonckheereAdam GiessEivind ValenGerben MenschaertPetra Van Damme

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Ribosome signatures aid bacterial translation initiation site identification

Adam GiessVeronique JonckheereElvis NdahKatarzyna ChyżyńskaPetra Van DammeEivind Valen

A1 Journal Article in BMC BIOLOGY

2016

A role for human N-alpha acetyltransferase 30 (Naa30) in maintaining mitochondrial integrity

Petra Van DammeThomas V KalvikKristian W StarheimVeronique JonckheereLine M MyklebustGerben MenschaertJan Erik VarhaugKris GevaertThomas Arnesen

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms

Om Singh RathoreAlexandra FaustinoPedro PrudêncioPetra Van DammeCymon J CoxRui Gonçalo Martinho

A1 Journal Article in SCIENTIFIC REPORTS

Alternative translation initiation unraveled by N-terminomics and ribosome profiling

Daria FijalkowskaPetra Van DammeKris Gevaert

Positional proteomics reveals differences in N-terminal proteoform stability

Daria FijalkowskaElvis NdahKris GevaertPetra Van Damme

A1 Journal Article in MOLECULAR SYSTEMS BIOLOGY

2015

An organellar Nα-acetyltransferase, Naa60, acetylates cytosolic N termini of transmembrane proteins and maintains Golgi integrity

Henriette AksnesPetra Van DammeMarianne GorisKristian K StarheimMichaël MarieSvein Isungset StøveCamilla HoelThomas Vikestad KalvikKristine HoleNina Glomnes et al.

A1 Journal Article in CELL REPORTS

Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects

Line M MyklebustPetra Van DammeSvein I StøveMax J DörfelAngèle AbboudThomas V KalvikCedric GrauffelVeronique JonckheereYiyang WuJeffrey Swensen et al.

A1 Journal Article in HUMAN MOLECULAR GENETICS

C-terminomics screen for natural substrates of cytosolic carboxypeptidase 1 reveals processing of acidic protein C termini

Sebastian TancoOlivia TortHans DemolFrancesc Xavier AvilesKris GevaertPetra Van DammeJulia Lorenzo

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

C-terminomics: targeted analysis of natural and posttranslationally modified protein and peptide C-termini

Sebastian TancoKris GevaertPetra Van Damme

A1 Journal Article in PROTEOMICS

Metabolic regulation of N-terminal acetylation in Saccharomyces cerevisiae

Sylvia VarlandPetra Van DammeJolien HollebekeHenriette AksnesKris GevaertThomas Arnesen

N-terminal acetylome analysis reveals the specificity of Naa50 (Nat5) and suggests a kinetic competition between N-terminal acetyltransferases and methionine aminopeptidases

Petra Van DammeKristine HoleKris GevaertThomas Arnesen

A1 Journal Article in PROTEOMICS

OMICS views on protein N-terminal biology

Petra Van DammeKris Gevaert

Editorial material

PROTEOFORMER : deep proteome coverage through ribosome profiling and MS integration

Jeroen CrappéElvis NdahAlexander KochSandra SteyaertDaria FijalkowskaSarah De KeulenaerEllen De MeesterTim De MeyerWim Van CriekingePetra Van Damme et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Proteomic identification of cysteine cathepsin substrates shed from the surface of cancer cells

Barbara SobotičMatej VizovišekRobert VidmarPetra Van DammeVasilena GochevaJohanna A JoyceKris GevaertVito TurkBoris TurkMarko Fonović

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

2014

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

Alexander KochDaria FijalkowskaSandra SteyaertElvis NdahJeroen CrappéSarah De KeulenaerEllen De MeesterMing MaBen ShenKris Gevaert et al.

A1 Journal Article in PROTEOMICS

A Saccharomyces cerevisiae model reveals in vivo functional impairment of the Ogden syndrome N-Terminal Acetyltransferase NAA10 Ser37Pro Mutant

Petra Van DammeSvein I. StøveNina GlomnesKris GevaertThomas Arnesen

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Granzyme M targets topoisomerase II alpha to trigger cell cycle arrest and caspase-dependent apoptosis

SAH de PootKW LaiL van der WalKim PlasmanPetra Van DammeAC PorterKris GevaertN Bovenschen

A1 Journal Article in CELL DEATH AND DIFFERENTIATION

Holistic view on the extended substrate specificities of orthologous granzymes

Kim PlasmanSebastian Maurer-StrohKris GevaertPetra Van Damme

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Identification of Serpinb6b as a species-specific mouse granzyme A inhibitor suggests functional divergence between human and mouse granzyme A

Dion KaisermanSarah E StewartKim PlasmanKris GevaertPetra Van DammePhillip I Bird

A1 Journal Article in JOURNAL OF BIOLOGICAL CHEMISTRY

Importance of extended protease substrate recognition motifs in steering BNIP-2 cleavage by human and mouse granzymes B

Petra Van DammeKim PlasmanGiel VandemoorteleVeronique JonckheereSebastian Maurer-StrohKris Gevaert

A1 Journal Article in BMC BIOCHEMISTRY

N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men

Petra Van DammeDaria FijalkowskaWim Van CriekingeGerben Menschaert

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Preparation of Arabidopsis thaliana seedling proteomes for identifying metacaspase substrates by N-terminal COFRADIC

Liana TsiatsianiSimon StaelPetra Van DammeFrank Van BreusegemKris Gevaert

Bookchapter in Caspases, paracaspases, and metacaspases : methods and protocols

Substrate specificities of the granzyme tryptases A and K

Kim PlasmanHans DemolPhilip I BirdKris GevaertPetra Van Damme

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

The proteome under translational control

Daria FijalkowskaKris GevaertPetra Van Damme

A1 Journal Article in PROTEOMICS

2013

Conservation of the extended substrate specificity profiles among homologous granzymes across species

Kim PlasmanSebastian Maurer-StrohJamshaid AhmadHan HaoDion KaisermanFernanda L SirotaVeronique JonckheerePhilip I BirdKris GevaertPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Contemporary positional proteomics strategies to study protein processing

Kim PlasmanPetra Van DammeKris Gevaert

A1 Journal Article in CURRENT OPINION IN CHEMICAL BIOLOGY

Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events

Gerben MenschaertWim Van CriekingeTineke NotelaersAlexander KochJeroen CrappéKris GevaertPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Dissecting apoptosis the omics way

Petra Van Damme

Editorial material

HPLC-based quantification of in vitro N-terminal acetylation

Rune H. EvjenthPetra Van DammeKris GevaertThomas Arnesen

Bookchapter in Protein Acetylation : Methods and Protocols

In-gel N-acetylation for the quantification of the degree of protein in vivo N-terminal acetylation

Petra Van DammeThomas ArnesenBart RuttensKris Gevaert

Bookchapter in Protein Acetylation : Methods and Protocols

Mass spectrometry and ribosome profiling, a perfect combination towards a more comprehensive identification strategy of true in vivo protein forms

Jeroen CrappéAlexander KochSandra SteyaertWim Van CriekingePetra Van DammeGerben Menschaert

Protein identification based on Ribosome targeted mRNA Fragments

Elvis NdahJeroen CrappéAlexander KochGerben MenschaertSandra SteyaertPetra Van Damme

Protein N-terminal acetyltransferases act as N-terminal propionyltransferases in vitro and in vivo

Håvard FoynPetra Van DammeSvein I StøveNina GlomnesRune EvjenthKris GevaertThomas Arnesen

A1 Journal Article in MOLECULAR & CELLULAR 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

Reviving nuclear translation

Petra Van DammeGerben Menschaert

The Arabidopsis METACASPASE9 degradome

Liana TsiatsianiEvy TimmermanPieter-Jan De BockDominique VercammenSimon StaelBrigitte Van De CotteAn StaesMarc GoethalsTine BeunensPetra Van Damme et al.

A1 Journal Article in PLANT CELL

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

Unraveling substrate repertoires and specificities of orthologous granzymes by peptide-based, gel-free proteomics

Kim PlasmanKris GevaertPetra Van Damme

Vpr content of HIV-1 virions determines infection of resting peripheral blood CD4⁺ lymphocytes

Anouk Van NuffelFrancis ImpensAnn BaeyensStijn VanheeWojciech WitkowskiElien VandermarliereHanne VanderstraetenEvelien NaessensKathleen Van LandeghemSophie Vermaut et al.

2012

Degradomics reveals that cleavage specificity profiles of caspase-2 and effector caspases are alike

Magdalena WejdaFrancis ImpensNozomi TakahashiPetra Van DammeKris GevaertPeter Vandenabeele

A1 Journal Article in JOURNAL OF BIOLOGICAL CHEMISTRY

N-terminal acetylation and other functions of Nα-acetyltransferases

Jolien HollebekePetra Van DammeKris Gevaert

A1 Journal Article in BIOLOGICAL CHEMISTRY

N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB

Petra Van DammeMarta LasaBogdan PolevodaCristina GazquezAlberto Elosegui-ArtolaDuk Soo KimElena De Juan-PardoKimberly DemeyerKristine HoleEsther Larrea et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

2011

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

Caspase-14 is required for filaggrin degradation to natural moisturizing factors in the skin

Esther HostePatrick KempermanMichael DevosGeertrui DeneckerSanja KezicNico YauBarbara GilbertSaskia LippensPhilippe De GrooteRia Roelandt et al.

A1 Journal Article in JOURNAL OF INVESTIGATIVE DERMATOLOGY

Human and mouse granzyme M display divergent and species-specific substrate specificities

Stefanie AH de PootMarijn WestgeestDaniel R HostetterPetra Van DammeKim PlasmanKimberly DemeyerRoel BroekhuizenKris GevaertCharles S CraikNiels Bovenschen

A1 Journal Article in BIOCHEMICAL JOURNAL

NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation

Petra Van DammeKristine HoleAna Pimenta-MarquesKenny HelsensJoël VandekerckhoveRui G MartinhoKris GevaertThomas Arnesen

A1 Journal Article in PLOS GENETICS

Probing the efficiency of proteolytic events by positional proteomics

Kim PlasmanPetra Van DammeDion KaisermanFrancis ImpensKimberly DemeyerKenny HelsensMarc GoethalsPhillip I BirdJoël VandekerckhoveKris Gevaert

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Protein alpha-N-acetylation studied by N-terminomics

Petra Van DammeThomas ArnesenKris Gevaert

A1 Journal Article in FEBS JOURNAL

Proteome-derived peptide libraries allow detailed analysis of the substrate specificities of Nα-acetyltransferases and point to hNaa10p as the post-translational actin Nα-acetyltransferase

Petra Van DammeRune EvjenthHavard FoynKimberly DemeyerPieter-Jan De BockJohan R LillehaugJoël VandekerckhoveThomas ArnesenKris Gevaert

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Selecting protein N-terminal peptides by combined fractional diagonal chromatography

An StaesFrancis ImpensPetra Van DammeBart RuttensMarc GoethalsHans DemolEvy TimmermanJoël VandekerckhoveKris Gevaert

A1 Journal Article in NATURE PROTOCOLS

T-cell receptor-induced JNK activation requires proteolytic inactivation of CYLD by MALT1

Jens StaalYasmine DriegeTine BekaertAnnelies DemeyerDavid MuyllaertPetra Van DammeKris GevaertRudi Beyaert

A1 Journal Article in EMBO JOURNAL

The human N-alpha-acetyltransferase 40 (hNaa40p/hNatD) is conserved from yeast and N-terminally acetylates histones H2A and H4

Kristine HolePetra Van DammeMonica DalvaHenriette AksnesNina GlomnesJan Erik VarhaugJohan R LillehaugKris GevaertThomas Arnesen

A1 Journal Article in PLOS ONE

2010

Complementary positional proteomics for screening substrates of endo- and exoproteases

Petra Van DammeAn StaesSilvia BronsomsKenny HelsensNiklaas ColaertEvy TimmermanFrancesc X AvilesJoël VandekerckhoveKris Gevaert

A1 Journal Article in NATURE METHODS

MS-driven protease substrate degradomics

Francis ImpensNiklaas ColaertKenny HelsensKim PlasmanPetra Van DammeJoël VandekerckhoveKris Gevaert

A1 Journal Article in PROTEOMICS

The chaperone-like Protein HYPK acts together with NatA in cotranslational N-terminal acetylation and prevention of Huntingtin aggregation

Thomas ArnesenKristian K StarheimPetra Van DammeRune EvjenthHuyen DinhMatthew J BettsAnita RyningenJoël VandekerckhoveKris GevaertDave Anderson

A1 Journal Article in MOLECULAR AND CELLULAR BIOLOGY

The substrate specificity profile of human granzyme A

Petra Van DammeSebastian Maurer-StrohHan HaoNiklaas ColaertEvy TimmermanFrank EisenhaberJoël VandekerckhoveKris Gevaert

A1 Journal Article in BIOLOGICAL CHEMISTRY

2009

A review of COFRADIC techniques targeting protein N-terminal acetylation

Petra Van DammeJozef Van DammeHans DemolAn StaesJoël VandekerckhoveKris Gevaert

Analysis of Protein Processing by N-terminal Proteomics Reveals Novel Species-specific Substrate Determinants of Granzyme B Orthologs

Petra Van DammeSebastian Maurer-StrohKim PlasmanJoost Van DurmeNiklaas ColaertEvy TimmermanPieter-Jan De BockMarc GoethalsFrederic RousseauJoost Schymkowitz et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Caspase substrates: easily caught in deep waters?

Dieter DemonPetra Van DammeTom Vanden BergheJoël VandekerckhoveWim DeclercqKris GevaertPeter Vandenabeele

A1 Journal Article in TRENDS IN BIOTECHNOLOGY

Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity

Dieter DemonPetra Van DammeTom Vanden BergheAnnelies DeceuninckJoost Van DurmeJelle VerspurtenKenny HelsensFrancis ImpensMagdalena WejdaJoost Schymkowitz et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans

Thomas ArnesenPetra Van DammeBogdan PolevodaKenny HelsensRune EvjenthNiklaas ColaertJan Erik VarhaugJoël VandekerckhoveJohan LillehaugFred Sherman et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of granzyme C reveals an unusual mechanism of protease autoinhibition

Dion KaisermanAshley M BucklePetra Van DammeJames A. IrvingRuby H. P. LawAntony Y. MatthewsTanya Bashtannyk-PuhalovichChris LangendorfPhilip ThompsonJoël Vandekerckhove et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

2008

Abolition of stress-induced protein synthesis sensitizes leukemia cells to anthracycline-induced death

Gro GausdalBjøorn Tore GjertsenEmmet McCormackPetra Van DammeRandi HovlandCamilla KrakstadØystein BruserudKris GevaertJoël VandekerckhoveStein Ove Døskeland

A1 Journal Article in BLOOD

Caspase-14 is a crucial protease in proper stratum corneum formation

E HOSTEG DENECKERPetra Van DammeJ HACHEMB GILBERTPetra OvaereRB PRESLANDT MAKINON HUHPM ELIAS et al.

Disentanglement of protease substrate repertoires

Petra Van DammeJ VANDELKERCKHOVEKris Gevaert

A1 Journal Article in BIOLOGICAL CHEMISTRY

Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)

An StaesPetra Van DammeKenny HelsensHans DemolJoël VandekerckhoveKris Gevaert

A1 Journal Article in PROTEOMICS

Mechanistic insight into taxol-induced cell death

Francis ImpensPetra Van DammeHans DemolJozef Van DammeJoël VandekerckhoveKris Gevaert

A1 Journal Article in ONCOGENE

Protein processing characterized by a gel-free proteomics approach

Petra Van DammeFrancis ImpensJoël VandekerckhoveKris Gevaert

Bookchapter in Functional proteomics, part III

Stable isotopic labeling in proteomics

Kris GevaertFrancis ImpensBart GhesquièrePetra Van DammeAnja LambrechtsJoël Vandekerckhove

A1 Journal Article in PROTEOMICS

Targeted peptidecentric proteomics reveals caspase-7 as a substrate of the caspase-1 inflammasomes

Mohamed LamkanfiThirumala-Devi KannegantiPetra Van DammeTom Vanden BergheIsabel VanoverbergheJoël VandekerckhovePeter VandenabeeleKris GevaertGabriel Nuñez

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

The substrate repertoire and the specificity of proteases assessed by peptide-centric proteomics

Petra Van DammeKris Gevaert

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

Applications of diagonal chromatography for proteome-wide characterization of protein modifications and activity-based analyses

Kris GevaertFrancis ImpensPetra Van DammeBart GhesquièreXavier HanoulleJoël Vandekerckhove

A1 Journal Article in FEBS JOURNAL

Caspase-14 protects against epidermal UVB photo-damage and water loss

Geertrui DeneckerEsther HosteBarbara GilbertTino HochepiedPetra OvaereSaskia LippensC VAN DEN BROUCKEPetra Van DammeKatharina D'HerdeJ HACHEM et al.

Caspase-14 protects against epidermal UVB photo-damage and water loss.

Geertrui DeneckerEsther HosteBarbara GilbertTino HochepiedPetra OvaereSaskia LippensC VAN DEN BROUCKEPetra Van DammeKatharina D'HerdeJ HACHEM et al.

Caspase-14 protects against epidermal UVB photodamage and water loss

Geertrui DeneckerEsther HosteBarbara GilbertTino HochepiedPetra OvaereSaskia LippensCaroline Van den broeckePetra Van DammeKatharina D'HerdeJP HACHEM et al.

A1 Journal Article in NATURE CELL BIOLOGY

Identification and characterization of filaggrin as a caspase-14 substrate

Esther HosteGeertrui DeneckerPetra Van DammeRB PRESLANDJoël VandekerckhoveKris GevaertPeter VandenabeeleWim Declercq

Proteome-wide identification of HtrA2/Omi substrates

Lieselotte Vande WallePetra Van DammeMohamed LamkanfiXavier SaelensJoël VandekerckhoveKris GevaertPeter Vandenabeele

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2006

Protein processing and other modifications analyzed by diagonal peptide chromatography

Kris GevaertPetra Van DammeBart GhesquièreJoël Vandekerckhove

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

2005

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

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

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

2003

Transcriptional activation of the NF-kappa B p65 subunit by mitogen- and stress-activated protein kinase-1 (MSK1)

Linda VermeulenGert De WildePetra Van DammeWim Vanden BergheGuy Haegeman

A1 Journal Article in EMBO JOURNAL