| PeptideShaker enables reanalysis of MS-derived proteomics data sets M Vaudel, JM Burkhart, RP Zahedi, E Oveland, FS Berven, A Sickmann, ... Nature biotechnology 33 (1), 22-24, 2015 | 600 | 2015 |
| BioContainers: an open-source and community-driven framework for software standardization F da Veiga Leprevost, BA Grüning, S Alves Aflitos, HL Röst, J Uszkoreit, ... Bioinformatics 33 (16), 2580-2582, 2017 | 598 | 2017 |
| SearchGUI: An open‐source graphical user interface for simultaneous OMSSA and X! Tandem searches M Vaudel, H Barsnes, FS Berven, A Sickmann, L Martens Proteomics 11 (5), 996-999, 2011 | 428 | 2011 |
| The proteomics identifications database: 2010 update JA Vizcaíno, R Coˆte, F Reisinger, H Barsnes, JM Foster, J Rameseder, ... Nucleic acids research 38 (suppl_1), D736-D742, 2010 | 251 | 2010 |
| SearchGUI: a highly adaptable common interface for proteomics search and de novo engines H Barsnes, M Vaudel Journal of proteome research 17 (7), 2552-2555, 2018 | 210 | 2018 |
| ThermoRawFileParser: modular, scalable, and cross-platform RAW file conversion N Hulstaert, J Shofstahl, T Sachsenberg, M Walzer, H Barsnes, L Martens, ... Journal of proteome research 19 (1), 537-542, 2019 | 207 | 2019 |
| PRIDE Converter: making proteomics data-sharing easy H Barsnes, JA Vizcaino, I Eidhammer, L Martens Nature biotechnology 27 (7), 598-599, 2009 | 185 | 2009 |
| In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR) A Guldbrandsen, H Vethe, Y Farag, E Oveland, H Garberg, M Berle, ... Molecular & cellular proteomics 13 (11), 3152-3163, 2014 | 155 | 2014 |
| Anatomy and evolution of database search engines—a central component of mass spectrometry based proteomic workflows K Verheggen, H Ræder, FS Berven, L Martens, H Barsnes, M Vaudel Mass spectrometry reviews 39 (3), 292-306, 2020 | 150 | 2020 |
| The ontology lookup service: bigger and better R Cï¿ ½tï¿ ½, F Reisinger, L Martens, H Barsnes, JA Vizcaino, ... Nucleic acids research 38 (suppl_2), W155-W160, 2010 | 142 | 2010 |
| The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium RG Côté, J Griss, JA Dianes, R Wang, JC Wright, HWP van den Toorn, ... Molecular & Cellular Proteomics 11 (12), 1682-1689, 2012 | 114 | 2012 |
| compomics-utilities: an open-source Java library for computational proteomics H Barsnes, M Vaudel, N Colaert, K Helsens, A Sickmann, FS Berven, ... BMC bioinformatics 12, 1-6, 2011 | 110 | 2011 |
| Exploring the potential of public proteomics data M Vaudel, K Verheggen, A Csordas, H Ræder, FS Berven, L Martens, ... Proteomics 16 (2), 214-225, 2016 | 101 | 2016 |
| IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT MØ Arntzen, CJ Koehler, H Barsnes, FS Berven, A Treumann, B Thiede Journal of proteome research 10 (2), 913-920, 2011 | 97 | 2011 |
| ms_lims, a simple yet powerful open source laboratory information management system for MS‐driven proteomics K Helsens, N Colaert, H Barsnes, T Muth, K Flikka, A Staes, E Timmerman, ... Proteomics 10 (6), 1261-1264, 2010 | 94 | 2010 |
| DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra T Muth, L Weilnböck, E Rapp, CG Huber, L Martens, M Vaudel, ... Journal of proteome research 13 (2), 1143-1146, 2014 | 87 | 2014 |
| Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM AC Kroksveen, E Aasebø, H Vethe, V Van Pesch, D Franciotta, ... Journal of proteomics 78, 312-325, 2013 | 81 | 2013 |
| Machine learning applications in proteomics research: How the past can boost the future P Kelchtermans, W Bittremieux, K De Grave, S Degroeve, J Ramon, ... Proteomics 14 (4-5), 353-366, 2014 | 77 | 2014 |
| The mzIdentML data standard version 1.2, supporting advances in proteome informatics JA Vizcaíno, G Mayer, S Perkins, H Barsnes, M Vaudel, Y Perez-Riverol, ... Molecular & cellular proteomics 16 (7), 1275-1285, 2017 | 67 | 2017 |
| XTandem Parser: an open‐source library to parse and analyse X! Tandem MS/MS search results T Muth, M Vaudel, H Barsnes, L Martens, A Sickmann Proteomics 10 (7), 1522-1524, 2010 | 67 | 2010 |
Lennart MartensSenior Full Professor of Systems Biology, Ghent University and VIB, Ghent, BelgiumVerified email at UGent.be