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Lennart Martens

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Thomas Fannes; Lennart Martens; Leander Schietgat; elien vandermarliere; Sven Degroeve; Jan Ramon
Predicting tryptic cleavage from proteomics data using decision tree ensembles.
Harald Barsnes; Lennart Martens
Crowdsourcing in proteomics: public resources lead to better experiments.
elien vandermarliere; Lennart Martens
Protein structure as a means to triage proposed PTM sites.

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2013: Thomas Fannes; Lennart Martens; Leander Schietgat; elien vandermarliere; Sven Degroeve; Jan Ramon
Predicting tryptic cleavage from proteomics data using decision tree ensembles.
Journal of proteome research 2013;12(5):2253-9.
2013: Harald Barsnes; Lennart Martens
Crowdsourcing in proteomics: public resources lead to better experiments.
Amino acids 2013;44(4):1129-37.
2013: elien vandermarliere; Lennart Martens
Protein structure as a means to triage proposed PTM sites.
Proteomics 2013;13(6):1028-35.
2013: Colaert Niklaas; Kris Gevaert; Kenny Helsens; Niels Hulstaert; Francis Impens; Davy Maddelein; Kim Plasman; Petra Van Damme; Joël Vandekerckhove; Lennart Martens
The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events.
Nucleic acids research 2013;41(Database issue):D333-7.
2012: Richard G Côté; Attila Csordas; José A Dianes; Johannes Griss; Albert J R Heck; Henning Hermjakob; Niels Hulstaert; Lennart Martens; David Ovelleiro; Yasset Perez-Rivevol; Florian Reisinger; Bas van Breukelen; Henk W P van den Toorn; Rui Wang; James C Wright; Harald Barsnes; Juan Antonio Vizcaino
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
Molecular & cellular proteomics : MCP 2012;11(12):1682-9.
2012: Sven Degroeve; Pieter-Jan De Bock; An Staes; Lennart Martens
The effect of peptide identification search algorithms on MS2-based label-free protein quantification.
Omics : a journal of integrative biology 2012;16(9):443-8.
2012: Giulia Gonnelli; Niels Hulstaert; Sven Degroeve; Lennart Martens
Towards a human proteomics atlas.
Analytical and bioanalytical chemistry 2012;404(4):1069-77.
2012: Luminita Moruz; An Staes; Evy Timmerman; Joseph M Foster; Maria Hatzou; Lennart Martens; Lukas Käll
Chromatographic retention time prediction for posttranslationally modified peptides.
Proteomics 2012;12(8):1151-9.
2012: Kenny Helsens; Niels Hulstaert; Michael Mueller; Lennart Martens
Sigpep: calculating unique peptide signature transition sets in a complete proteome background.
Proteomics 2012;12(8):1142-6.
2012: Kenny Helsens; Lennart Martens
Enabling computational proteomics by public and local data management systems.
Circulation. Cardiovascular genetics 2012;5(2):266.
2012: Rui Wang; Richard G Côté; Attila Csordas; Antonio Fabregat; Joseph M Foster; Johannes Griss; Henning Hermjakob; Lennart Martens; David Ovelleiro; Yasset Perez-Riverol; Florian Reisinger; Daniel Ríos; Juan Antonio Vizcaino
PRIDE Inspector: a tool to visualize and validate MS proteomics data.
Nature biotechnology 2012;30(2):135-7.
2011: Colaert Niklaas; Sven Degroeve; Kenny Helsens; Lennart Martens
Analysis of the resolution limitations of peptide identification algorithms.
Journal of proteome research 2011;10(12):5555-61.
2011: Kenny Helsens; Mi-Youn Brusniak; Eric Deutsch; Robert L Moritz; Lennart Martens
jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions.
Journal of proteome research 2011;10(11):5260-3.
2011: Colaert Niklaas; Kris Gevaert; Kenny Helsens; Albert Sickmann; Evy Timmerman; Marc Vaudel; Harald Barsnes; Lennart Martens
Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.
Journal of proteome research 2011;10(8):3840-3.
2011: Kenny Helsens; Lennart Martens; Petra Van Damme; Joël Vandekerckhove; Thomas Arnesen; Sven Degroeve; Kris Gevaert
Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation.
Journal of proteome research 2011;10(8):3578-89.
2011: Niklaas Colaert; Christophe Van Huele; Sven Degroeve; An Staes; Joël Vandekerckhove; Kris Gevaert; Lennart Martens
Combining quantitative proteomics data processing workflows for greater sensitivity.
Nature methods 2011;8(6):481-3.
2011: Joseph M Foster; Sven Degroeve; Laurent Gatto; Matthieu Visser; Rui Wang; Johannes Griss; Rolf Apweiler; Lennart Martens
A posteriori quality control for the curation and reuse of public proteomics data.
Proteomics 2011;11(11):2182-94.
2011: Colaert Niklaas; Joël Vandekerckhove; Kris Gevaert; Lennart Martens
A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision.
Proteomics 2011;11(6):1110-3.
2011: Harald Barsnes; Ingvar Eidhammer; Lennart Martens
A global analysis of peptide fragmentation variability.
Proteomics 2011;11(6):1181-8.
2011: Sven Degroeve; Colaert Niklaas; Joël Vandekerckhove; Kris Gevaert; Lennart Martens
A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods.
Proteomics 2011;11(6):1172-80.
2011: Niklaas Colaert; Joël Vandekerckhove; Lennart Martens; Kris Gevaert
A case study on the comparison of different software tools for automated quantification of peptides.
Methods in molecular biology (Clifton, N.J.) 2011;753():373-98.
2011: Lennart Martens
Bioinformatics challenges in mass spectrometry-driven proteomics.
Methods in molecular biology (Clifton, N.J.) 2011;753():359-71.
2011: Kenny Helsens; Lennart Martens; Joël Vandekerckhove; Kris Gevaert
Mass spectrometry-driven proteomics: an introduction.
Methods in molecular biology (Clifton, N.J.) 2011;753():1-27.
2011: Joseph M Foster; Lennart Martens
Bioinformatics challenges in the proteomic analysis of human plasma.
Methods in molecular biology (Clifton, N.J.) 2011;728():333-47.
2011: Lennart Martens
Data management in mass spectrometry-based proteomics.
Methods in molecular biology (Clifton, N.J.) 2011;728():321-32.
2011: Harald Barsnes; Marc Vaudel; Niklaas Colaert; Kenny Helsens; Albert Sickmann; Frode S Berven; Lennart Martens
compomics-utilities: an open-source Java library for computational proteomics.
BMC bioinformatics 2011;12():70.
2011: Harald Barsnes; Juan Antonio Vizcaíno; Florian Reisinger; Ingvar Eidhammer; Lennart Martens
Submitting proteomics data to PRIDE using PRIDE Converter.
Methods in molecular biology (Clifton, N.J.) 2011;694():237-53.
2011: Lennart Martens
Proteomics databases and repositories.
Methods in molecular biology (Clifton, N.J.) 2011;694():213-27.
2011: Lennart Martens; Matthew Chambers; Marc Sturm; Darren Kessner; Fredrik Levander; Jim Shofstahl; Wilfred H Tang; Andreas Römpp; Steffen Neumann; Angel Pizarro; Luisa Montecchi-Palazzi; Natalie Tasman; Mike Coleman; Florian Reisinger; Puneet Souda; Henning Hermjakob; Pierre-Alain Binz; Eric Deutsch
mzML--a community standard for mass spectrometry data.
Molecular & cellular proteomics : MCP 2011;10(1):R110.000133.
2010: Juan Antonio Vizcaino; Joseph M Foster; Lennart Martens
Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research.
Journal of proteomics 2010;73(11):2136-46.
2010: Richard G Côté; Florian Reisinger; Lennart Martens; Harald Barsnes; Juan Antonio Vizcaino; Henning Hermjakob
The Ontology Lookup Service: bigger and better.
Nucleic acids research 2010;38(Web Server issue):W155-60.
2010: Lennart Martens
A report on the ESF workshop on quality control in proteomics.
Molecular bioSystems 2010;6(6):935-8.
2010: Juan Antonio Vizcaíno; Florian Reisinger; Richard Côté; Lennart Martens
PRIDE: Data submission and analysis.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] 2010;Chapter 25():Unit 25.4.
2010: Richard G Côté; Florian Reisinger; Lennart Martens
jmzML, an open-source Java API for mzML, the PSI standard for MS data.
Proteomics 2010;10(7):1332-5.
2010: Kenny Helsens; Colaert Niklaas; Harald Barsnes; Thilo Muth; Kristian Flikka; An Staes; Evy Timmerman; Steffi Wortelkamp; Albert Sickmann; Joël Vandekerckhove; Kris Gevaert; Lennart Martens
ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics.
Proteomics 2010;10(6):1261-4.
2010: Harald Barsnes; Ingvar Eidhammer; Lennart Martens
FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data.
Proteomics 2010;10(5):1087-90.
2010: Harald Barsnes; Richard G Côté; Ingvar Eidhammer; Lennart Martens
OLS dialog: an open-source front end to the ontology lookup service.
BMC bioinformatics 2010;11():34.
2010: Philip Jones; Lennart Martens
Using the PRIDE proteomics identifications database for knowledge discovery and data analysis.
Methods in molecular biology (Clifton, N.J.) 2010;604():297-307.
2010: Juan Antonio Vizcaino; Richard Côté; Florian Reisinger; Harald Barsnes; Joseph M Foster; Jonathan Rameseder; Henning Hermjakob; Lennart Martens
The Proteomics Identifications database: 2010 update.
Nucleic acids research 2010;38(Database issue):D736-42.
2009: Colaert Niklaas; Kenny Helsens; Lennart Martens; Joël Vandekerckhove; Kris Gevaert
Improved visualization of protein consensus sequences by iceLogo.
Nature methods 2009;6(11):786-7.
2009: Luisa Montecchi-Palazzi; Samuel Kerrien; Florian Reisinger; Bruno Aranda; Andrew R Jones; Lennart Martens; Henning Hermjakob
The PSI semantic validator: a framework to check MIAPE compliance of proteomics data.
Proteomics 2009;9(22):5112-9.
2009: Florian Reisinger; Lennart Martens
Database on Demand - an online tool for the custom generation of FASTA-formatted sequence databases.
Proteomics 2009;9(18):4421-4.
2009: Juan Antonio Vizcaino; Richard Côté; Florian Reisinger; Joseph M Foster; Michael Mueller; Jonathan Rameseder; Henning Hermjakob; Lennart Martens
A guide to the Proteomics Identifications Database proteomics data repository.
Proteomics 2009;9(18):4276-83.
2009: Martin Eisenacher; Lennart Martens; Tanja Hardt; Michael Kohl; Harald Barsnes; Kenny Helsens; Jari Häkkinen; Fredrik Levander; Ruedi Aebersold; Joël Vandekerckhove; Michael J Dunn; Frederique Lisacek; Jennifer A Siepen; Simon J Hubbard; Pierre-Alain Binz; Martin Blüggel; Herbert Thiele; John Cottrell; Helmut E Meyer; Rolf Apweiler; Christian Stephan
Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).
Proteomics 2009;9(15):3928-33.
2009: Harald Barsnes; Steffen Huber; Albert Sickmann; Ingvar Eidhammer; Lennart Martens
OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results.
Proteomics 2009;9(14):3772-4.
2009: Martin Eisenacher; Lennart Martens; Harald Barsnes; Tanja Hardt; Michael Kohl; Jari Häkkinen; Rolf Apweiler; Helmut E Meyer; Christian Stephan
Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece.
Proteomics 2009;9(14):3626-9.
2009: Harald Barsnes; Juan Antonio Vizcaíno; Ingvar Eidhammer; Lennart Martens
PRIDE Converter: making proteomics data-sharing easy.
Nature biotechnology 2009;27(7):598-9.
2009: Juan Antonio Vizcaino; Michael Mueller; Henning Hermjakob; Lennart Martens
Charting online OMICS resources: A navigational chart for clinical researchers.
Proteomics. Clinical applications 2009;3(1):18-29.
2009: Lennart Martens; Rolf Apweiler
Algorithms and databases.
Methods in molecular biology (Clifton, N.J.) 2009;564():245-59.
2009: Martin Eisenacher; Michael Kohl; Lennart Martens; Harald Barsnes; Tanja Hardt; Fredrik Levander; Jari Häkkinen; Rolf Apweiler; Helmut E Meyer; Christian Stephan
Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands.
Proteomics 2009;9(2):218-22.
2008: Kenny Helsens; Evy Timmerman; Joël Vandekerckhove; Kris Gevaert; Lennart Martens
Peptizer, a tool for assessing false positive peptide identifications and manually validating selected results.
Molecular & cellular proteomics : MCP 2008;7(12):2364-72.
2008: Martin Eisenacher; Tanja Hardt; Lennart Martens; Jari Häkkinen; Rolf Apweiler; Michael Hamacher; Helmut E Meyer; Christian Stephan
Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain.
Proteomics 2008;8(20):4163-7.
2008: Richard G Côté; Philip Jones; Lennart Martens; Rolf Apweiler; Henning Hermjakob
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.
Nucleic acids research 2008;36(Web Server issue):W372-6.
2008: Ravi Tharakan; Lennart Martens; Jennifer E Van Eyk; David Raymond Graham
OMSSAGUI: An open-source user interface component to configure and run the OMSSA search engine.
Proteomics 2008;8(12):2376-8.
2008: Michael Hamacher; Martin Eisenacher; Florian Tribl; Christian Stephan; Katrin Marcus; Tanja Hardt; Jens Wiltfang; Lennart Martens; Dominic Desiderio; Howard B Gutstein; Young Mok Park; Helmut E Meyer
The HUPO Brain Proteome project wish list--summary of the 9(th) HUPO BPP Workshop 9-10 January 2008, Barbados.
Proteomics 2008;8(11):2160-4.
2008: Martin Eisenacher; Tanja Hardt; Michael Hamacher; Lennart Martens; Jari Häkkinen; Fredrik Levander; Rolf Apweiler; Helmut E Meyer; Christian Stephan
Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea.
Proteomics 2008;8(7):1326-30.
2008: Sandra Orchard; Lennart Martens; Joshua Tasman; Pierre-Alain Binz; Juan Pablo Albar; Henning Hermjakob
6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea.
Proteomics 2008;8(7):1331-3.
2008: Lennart Martens; Phil Jones; Richard Côté
Using the Proteomics Identifications Database (PRIDE).
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2008;Chapter 13():Unit 13.8.
2008: Michael Mueller; Juan Antonio Vizcaino; Philip Jones; Richard Côté; David Thorneycroft; Rolf Apweiler; Henning Hermjakob; Lennart Martens
Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets.
Proteomics 2008;8(6):1138-48.
2008: M Suresh; Mukhtar Ahmed; Natalie G Ahn; Hainard Alexandre; Ramars Amanchy; Philip C Andrews; Joel S Bader; Brian M Balgley; Marcus Bantscheff; Keiryn Bennett; Erik Björling; Blagoy Blagoev; Ron Bose; Samir K Brahmachari; Alma S Burlingame; Xosé R Bustelo; Gerard Cagney; Greg T Cantin; Helene L Cardasis; Julio E Celis; Raghothama Chaerkady; Feixia Chu; Philip A Cole; Catherine E Costello; Robert J Cotter; David Crockett; James P DeLany; Angelo M DeMarzo; Leroi V DeSouza; Eric W Deutsch; Eric Dransfield; Gerard Drewes; Arnaud Droit; Michael J Dunn; Kojo Seys John Elenitoba-Johnson; Rob M Ewing; Jennifer E Van Eyk; Vitor Faca; Jayson Falkner; Xiangming Fang; Catherine Fenselau; Daniel Figeys; Pierre Gagné; Cecilia Gelfi; Kris Gevaert; Jeffrey M Gimble; Florian Gnad; renu goel; Pavel Gromov; Samir M Hanash; William S Hancock; H C Harsha; Gerald W Hart; Faith Hays; Fuchu He; Prashantha Hebbar; Kenny Helsens; Heiko Hermeking; Winston Hide; Karin Hjernø; Denis F Hochstrasser; Oliver Hofmann; David M Horn; Ralph Hruban; Nieves Ibarrola; Peter James; Ole N Jensen; Pia Hønnerup Jensen; Peter Jung; Richard Kumaran Kandasamy; Indu Kheterpal; Reiko F Kikuno; Ulrike Korf; Roman Körner; Bernhard Kuster; Min-Seok Kwon; Hyoung-Joo Lee; Young-Jin Lee; Michael Lefevre; Minna Lehvaslaiho; Pierre Lescuyer; Fredrik Levander; Megan S Lim; Christian Löbke; Joseph A Loo; Matthias Mann; Lennart Martens; Juan Martinez-Heredia; Mark McComb; James McRedmond; Alexander Mehrle; Rajasree Menon; Christine A Miller; Harald Mischak; S Sujatha Mohan; Riaz Mohmood; Henrik Molina; Michael F Moran; James D Morgan; Robert Moritz; Martine Morzel; David C Muddiman; Anuradha Nalli; J Daniel Navarro; Thomas A Neubert; Osamu Ohara; Rafael Oliva; Gilbert S Omenn; Masaaki Oyama; Young-Ki Paik; Kyla Pennington; Rainer Pepperkok; Balamurugan Periaswamy; Emanuel F Petricoin; Guy G Poirier; T S Keshava Prasad; Samuel O Purvine; B Abdul Rahiman; Prasanna Ramachandran; Y L Ramachandra; Robert H Rice; Jens Rick; Ragna H Ronnholm; Johanna Salonen; jean-charles sanchez; Thierry Sayd; Beerelli Seshi; Kripa Shankari; Shi Jun Sheng; Vivekananda Shetty; K Shivakumar; Richard J Simpson; Ravi Sirdeshmukh; K W Michael Siu; Jeffrey Smith; Richard D Smith; David J States; Sumio Sugano; Matthew Sullivan; Giulio Superti-Furga; Maarit Takatalo; Visith Thongboonkerd; Jonathan C Trinidad; Mathias Uhlen; Joël Vandekerckhove; Julian Vasilescu; Timothy D Veenstra; José-Manuel Vidal-Taboada; Mauno Vihinen; Robin Wait; Xiaoyue Wang; Stefan Wiemann; Billy Wu; Tao Xu; John R Yates; Jun Zhong; Ming Zhou; Yunping Zhu; Petra Zurbig; Akhilesh Pandey
Human Proteinpedia enables sharing of human protein data.
Nature biotechnology 2008;26(2):164-7.
2008: Lennart Martens; Luisa Montecchi Palazzi; Henning Hermjakob
Data standards and controlled vocabularies for proteomics.
Methods in molecular biology (Clifton, N.J.) 2008;484():279-86.
2008: Sebastian Klie; Lennart Martens; Juan Antonio Vizcaino; Richard Côté; Philip Jones; Rolf Apweiler; Alexander Hinneburg; Henning Hermjakob
Analyzing large-scale proteomics projects with latent semantic indexing.
Journal of proteome research 2008;7(1):182-91.
2008: Philip Jones; Richard G Côté; Sang Yun Cho; Sebastian Klie; Lennart Martens; Antony F Quinn; David Thorneycroft; Henning Hermjakob
PRIDE: new developments and new datasets.
Nucleic acids research 2008;36(Database issue):D878-83.
2007: Lennart Martens; Sandra Orchard; Rolf Apweiler; Henning Hermjakob
Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy.
Molecular & cellular proteomics : MCP 2007;6(9):1666-7.
2007: Kristian Flikka; Jeroen Meukens; Kenny Helsens; Joël Vandekerckhove; Ingvar Eidhammer; Kris Gevaert; Lennart Martens
Implementation and application of a versatile clustering tool for tandem mass spectrometry data.
Proteomics 2007;7(18):3245-58.
2007: Martin Eisenacher; Tanja Hardt; Michael Hamacher; Lennart Martens; Jari Häkkinen; Fredrik Levander; Rolf Apweiler; Helmut E Meyer; Christian Stephan
Proteomics Data Collection - the 1st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France.
Proteomics 2007;7(17):3034-7.
2007: Christopher Taylor; Norman W Paton; Kathryn S Lilley; Pierre-Alain Binz; Randall K Julian; Andrew R Jones; Weimin Zhu; Rolf Apweiler; Ruedi Aebersold; Eric Deutsch; Michael J Dunn; albert heck; Alexander Leitner; Marcus Macht; Matthias Mann; Lennart Martens; Thomas A Neubert; Scott D Patterson; Peipei Ping; Sean L Seymour; Puneet Souda; Akira Tsugita; Joel Vandekerckhove; Thomas M Vondriska; Julian P Whitelegge; Marc R Wilkins; Ioannnis Xenarios; John R Yates; Henning Hermjakob
The minimum information about a proteomics experiment (MIAPE).
Nature biotechnology 2007;25(8):887-93.
2007: Kris Gevaert; Petra Van Damme; Bart Ghesquière; Francis Impens; Lennart Martens; Kenny Helsens; Joël Vandekerckhove
A la carte proteomics with an emphasis on gel-free techniques.
Proteomics 2007;7(16):2698-718.
2007: Lennart Martens; Henning Hermjakob
Proteomics data validation: why all must provide data.
Molecular bioSystems 2007;3(8):518-22.
2007: Michael Hamacher; Christian Stephan; Martin Eisenacher; Piotr Lewczuk; Jens Wiltfang; Lennart Martens; Juan Antonio Vizcaino; Kyung-Hoon Kwon; Jong Shin Yoo; Young Mok Park; Johannes Beckers; Marion Horsch; Martin Hrabé De Angelis; Zang-Hee Cho; Rolf Apweiler; Helmut E Meyer
High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK.
Proteomics 2007;7(15):2490-6.
2007: Juan Antonio Vizcaino; Lennart Martens; Henning Hermjakob; Randall K Julian; Norman W Paton
The PSI formal document process and its implementation on the PSI website.
Proteomics 2007;7(14):2355-7.
2007: Michalis Aivaliotis; Kris Gevaert; Michaela Falb; Andreas Tebbe; Kosta Konstantinidis; Birgit Bisle; Christian Klein; Lennart Martens; An Staes; Evy Timmerman; Jozef Van Damme; Frank Siedler; Friedhelm Pfeiffer; Joël Vandekerckhove; Dieter Oesterhelt
Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis.
Journal of proteome research 2007;6(6):2195-204.
2007: Michael Hamacher; Christian Stephan; Martin Eisenacher; Andre van Hall; Katrin Marcus; Lennart Martens; Young Mok Park; Howard B Gutstein; Friedrich W Herberg; Helmut E Meyer
Proteomics for everyday use: activities of the HUPO Brain Proteome Project during the 5th HUPO World Congress.
Proteomics 2007;7(7):1012-5.
2007: Michael Mueller; Lennart Martens; Rolf Apweiler
Annotating the human proteome: beyond establishing a parts list.
Biochimica et biophysica acta 2007;1774(2):175-91.
2007: Kenny Helsens; Lennart Martens; Joël Vandekerckhove; Kris Gevaert
MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results.
Proteomics 2007;7(3):364-6.
2007: Richard G Côté; Philip Jones; Lennart Martens; Samuel Kerrien; Florian Reisinger; Quan Lin; Rasko Leinonen; Rolf Apweiler; Henning Hermjakob
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
BMC bioinformatics 2007;8():401.
2006: Xavier Hanoulle; Jozef Van Damme; An Staes; Lennart Martens; Marc Goethals; Joël Vandekerckhove; Kris Gevaert
A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes.
Journal of proteome research 2006;5(12):3438-45.
2006: Bart Ghesquière; Jozef Van Damme; Lennart Martens; Joël Vandekerckhove; Kris Gevaert
Proteome-wide characterization of N-glycosylation events by diagonal chromatography.
Journal of proteome research 2006;5(9):2438-47.
2006: Michael Hamacher; Rolf Apweiler; Georg Arnold; Albert Becker; Martin Blüggel; Odile Carrette; Christine Colvis; Michael J Dunn; Thomas Fröhlich; Michael Fountoulakis; André van Hall; Friedrich Herberg; Jianguo Ji; Juango Ji; Hans A Kretzschmar; Piotr Lewczuk; Gert Lubec; Katrin Marcus; Lennart Martens; Nadine Palacios Bustamante; Young Mok Park; Stephen R Pennington; Johan Robben; Kai Stühler; Kai A Reidegeld; Peter Riederer; Jean Rossier; jean-charles sanchez; Michael Schrader; Christian Stephan; Danilo Tagle; Herbert Thiele; Jing Wang; Jens Wiltfang; Jong Shin Yoo; Chenggang Zhang; Joachim Klose; Helmut E Meyer
HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy.
Proteomics 2006;6(18):4890-8.
2006: Christian Stephan; Kai A Reidegeld; Michael Hamacher; Andre van Hall; Katrin Marcus; Chris Taylor; Philip Jones; Michael Müller; Rolf Apweiler; Lennart Martens; Gerhard Körting; Daniel C Chamrad; Herbert Thiele; Martin Blüggel; David Parkinson; Pierre-Alain Binz; Andrew Lyall; Helmut E Meyer
Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.
Proteomics 2006;6(18):5015-29.
2006: Kai A Reidegeld; Michael Müller; Christian Stephan; Martin Blüggel; Michael Hamacher; Lennart Martens; Gerhard Körting; Daniel C Chamrad; David Parkinson; Rolf Apweiler; Helmut E Meyer; Katrin Marcus
The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results.
Proteomics 2006;6(18):4997-5014.
2006: Lennart Martens; Michael Müller; Christian Stephan; Michael Hamacher; Kai A Reidegeld; Helmut E Meyer; Martin Blüggel; Joël Vandekerckhove; Kris Gevaert; Rolf Apweiler
A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies.
Proteomics 2006;6(18):5076-86.
2006: Michael Mueller; Lennart Martens; Kai A Reidegeld; Michael Hamacher; Christian Stephan; Martin Blüggel; Gerhard Körting; Daniel C Chamrad; Christian Scheer; Katrin Marcus; Helmut E Meyer; Rolf Apweiler
Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study.
Proteomics 2006;6(18):5059-75.
2006: Kris Gevaert; Jef Pinxteren; Hans Demol; Koen Hugelier; An Staes; Jozef Van Damme; Lennart Martens; Joël Vandekerckhove
Four stage liquid chromatographic selection of methionyl peptides for peptide-centric proteome analysis: the proteome of human multipotent adult progenitor cells.
Journal of proteome research 2006;5(6):1415-28.
2006: Kristian Flikka; Lennart Martens; Joël Vandekerckhove; Kris Gevaert; Ingvar Eidhammer
Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering.
Proteomics 2006;6(7):2086-94.
2006: Michael Hamacher; Christian Stephan; Martin Blüggel; Daniel C Chamrad; Gerhard Körting; Lennart Martens; Michael Müller; Henning Hermjakob; David Parkinson; Andrew W Dowsey; Kai A Reidegeld; Katrin Marcus; Michael J Dunn; Helmut E Meyer; Rolf Apweiler
The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies.
Proteomics 2006;6(6):1719-21.
2006: Lennart Martens; Geert Monsieur; Christophe Ampe; Kris Gevaert; Joël Vandekerckhove
Cell_motility: a cross-platform, open source application for the study of cell motion paths.
BMC bioinformatics 2006;7():289.
2006: Philip Jones; Richard G Côté; Lennart Martens; Antony F Quinn; Christopher Taylor; William Derache; Henning Hermjakob; Rolf Apweiler
PRIDE: a public repository of protein and peptide identifications for the proteomics community.
Nucleic acids research 2006;34(Database issue):D659-63.
2005: Kris Gevaert; Petra Van Damme; Lennart Martens; Joël Vandekerckhove
Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics?
Analytical biochemistry 2005;345(1):18-29.
2005: Petra Van Damme; Lennart Martens; Jozef Van Damme; Koen Hugelier; An Staes; Joël Vandekerckhove; Kris Gevaert
Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis.
Nature methods 2005;2(10):771-7.
2005: Christian Stephan; Michael Hamacher; Martin Blüggel; Gerhard Körting; Daniel C Chamrad; Christian Scheer; Katrin Marcus; Kai A Reidegeld; Christiane Lohaus; Heike Schäfer; Lennart Martens; Philip Jones; Michael Müller; Kevin Auyeung; Chris Taylor; Pierre-Alain Binz; Herbert Thiele; David Parkinson; Helmut E Meyer; Rolf Apweiler
5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.
Proteomics 2005;5(14):3560-2.
2005: Kris Gevaert; An Staes; Jozef Van Damme; Sara De Groot; Koen Hugelier; Hans Demol; Lennart Martens; Marc Goethals; Joël Vandekerckhove
Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC.
Proteomics 2005;5(14):3589-99.
2005: Lennart Martens; Joël Vandekerckhove; Kris Gevaert
DBToolkit: processing protein databases for peptide-centric proteomics.
Bioinformatics (Oxford, England) 2005;21(17):3584-5.
2005: Marcin Adamski; Thomas Blackwell; Rajasree Menon; Lennart Martens; Henning Hermjakob; Chris Taylor; Gilbert S Omenn; David States
Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project.
Proteomics 2005;5(13):3246-61.
2005: Lennart Martens; Henning Hermjakob; Philip Jones; Marcin Adamski; Chris Taylor; David States; Kris Gevaert; Joël Vandekerckhove; Rolf Apweiler
PRIDE: the proteomics identifications database.
Proteomics 2005;5(13):3537-45.
2005: Lennart Martens; Alexey I Nesvizhskii; Henning Hermjakob; Marcin Adamski; Gilbert S Omenn; Joël Vandekerckhove; Kris Gevaert
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories.
Proteomics 2005;5(13):3501-5.
2005: Lennart Martens; Petra Van Damme; Jozef Van Damme; An Staes; Evy Timmerman; Bart Ghesquière; Grégoire Thomas; Joël Vandekerckhove; Kris Gevaert
The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile.
Proteomics 2005;5(12):3193-204.
2004: An Staes; Hans Demol; Jozef Van Damme; Lennart Martens; Joël Vandekerckhove; Kris Gevaert
Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18.
Journal of proteome research 2004;3(4):786-91.
2004: Kris Gevaert; Bart Ghesquière; An Staes; Lennart Martens; Jozef Van Damme; Grégoire Thomas; Joël Vandekerckhove
Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies.
Proteomics 2004;4(4):897-908.
2003: Kris Gevaert; Marc Goethals; Lennart Martens; Jozef Van Damme; An Staes; Grégoire Thomas; Joël Vandekerckhove
Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides.
Nature biotechnology 2003;21(5):566-9.
2002: Kris Gevaert; Jozef Van Damme; Marc Goethals; Grégoire Thomas; Bart Hoorelbeke; Hans Demol; Lennart Martens; Magda Puype; An Staes; Joël Vandekerckhove
Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins.
Molecular & cellular proteomics : MCP 2002;1(11):896-903.
2001: Kris Gevaert; Hans Demol; Lennart Martens; Bart Hoorelbeke; Magda Puype; Marc Goethals; Jozef Van Damme; S De Boeck; Joël Vandekerckhove
Protein identification based on matrix assisted laser desorption/ionization-post source decay-mass spectrometry.
Electrophoresis 2001;22(9):1645-51.