Publications

Peer-reviewed papers and preprints from the CompOmics computational proteomics group at Ghent University / VIB.

Research output

Publications

Peer-reviewed papers and preprints from CompOmics group members. For a complete list, see our Google Scholar page or individual ORCID profiles.

All people Sakina Bombaywala Tim Van Den Bossche Robbin Bouwmeester Toon Callens Tine Claeys Arthur Declercq Robbe Devreese Daria Fijalkowska Ralf Gabriels Sude Güneş Sander Heyndrickx Caroline Jachmann Alexander Kensert Lyudmila Kovalchuke Patricia Lefèvre Xuxa Malliet Lennart Martens Enrico Massignani Alireza Nameni Sam Van Puyenbroeck Harikrishnan Ramadasan Pathmanaban Ramasamy Natalia Tichshenko Kevin Velghe Pieter Verschaffelt Jasper Zuallaert

2026

1. Evaluation of Protein Reference Database Reduction and Its Impact on Peptide-Centric MetaproteomicsTibo Vande Moortele, Simon Vande Vyver, Ben-Björn Binke, Tim Van Den Bossche, Peter Dawyndt, Lennart Martens, Bart Mesuere, Pieter Verschaffelt

   Preprint
2. Hardware Software Synergy in Proteomics: Systematic Evaluation Across Mass Spectrometry Platforms, Search Engines, and Rescoring MethodsSander Heyndrickx, Robbin Bouwmeester, Arthur Declercq, Robbe Devreese, Magnus Palmblad, Wout Bittremieux, Tess AV Afanasyeva, Joel Lapin

   Preprint
3. High-Throughput Quantification of Spike Protein Expression by LC–MS for mRNA-LNP Evaluation and Immune Response ProfilingRuben Almey, Kevin Mwangi, Amélie De Maesschalck, Thomas Ehouarne, Sieglinde de Cae, Pathmanaban Ramasamy, Marijn Van Hulle, Ine Lentacker

   Analytical Chemistry, 98(17):13134-13143
4. LFQ Benchmark Dataset - Generation Beta: Assessing Modern Proteomics Instruments and Acquisition Workflows with High-Throughput LC GradientsBart Van Puyvelde, Robbe Devreese, Cristina Chiva, Eduard Sabidó, Sibylle Pfammatter, Christian Panse, Jeewan Babu Rijal, Charline Keller

   Preprint
5. MoDPA: Inferring Modification-dependent Protein Associations from Uniformly Reprocessed Mass SpectrometryEnrico Massignani, Natalia Tichshenko, Kevin Velghe, Lennart Martens

   Preprint
6. Predicting and Elucidating Peptide Retention Mechanisms with Graph Attention NetworksAlexander Kensert, Katerina Hruzova, Robbe Devreese, Alireza Nameni, Arthur Declercq, Ralf Gabriels, Lennart Martens, Robbin Bouwmeester

   Preprint
7. The <i>Escherichia coli</i> PeptideAtlas Build: Characterizing the Observed <i>Escherichia coli</i> Pan-Proteome and Its Post-Translational ModificationsCaroline Jachmann, Zhi Sun, Kevin Velghe, Florence Arsène-Ploetze, Aurélie Hirschler, Jasper Zuallaert, Christine Carapito, Robbin Bouwmeester

   Journal of Proteome Research, 25(2):1027-1041
8. The Peptonizer2000: Bringing Confidence to MetaproteomicsTanja Holstein, Pieter Verschaffelt, Tim Van Den Bossche, Simon Van de Vyver, Lennart Martens, Bart Mesuere, Thilo Muth

   Journal of Proteome Research, 25(4):1831-1845
9. Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setupsRobbin Bouwmeester, Alireza Nameni, Arthur Declercq, Robbe Devreese, Kevin Velghe, Vladimir Gorshkov, Pelayo A. Penanes, Frank Kjeldsen

   Nature Communications, 17(1)
10. Unlocking the Next Decade of Proteomics with Standardized, Structured MetadataTim Van Den Bossche, Ananth Prakash, Tine Claeys, Juan Antonio Vizcaíno, Lennart Martens

    Journal of Proteome Research, 25(2):556-561
11. iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen ModificationsAlireza Nameni, Arthur Declercq, Ralf Gabriels, Robbe Devreese, Sven Degroeve, Amélie De Maesschalck, Maarten Dhaenens, Cristina Chiva

    Analytical Chemistry
12. omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation in bulk- and single-cell proteomicsAlexandre Segers, Cristian Castiglione, Christophe Vanderaa, Lennart Martens, Davide Risso, Lieven Clement

    Nature Communications
13. quantms-rescoring enables deep proteome coverage across protein quantification, immunopeptidomics, and post-translational modifications experimentsChengxin Dai, Ralf Gabriels, Robbin Bouwmeester, Asier Larrea, Jonas Scheid, Henry Webel, Fuchu He, Lennart Martens

    Preprint

2025

1. Assessing the relation between protein phosphorylation, <scp>AlphaFold3</scp> models, and conformational variabilityPathmanaban Ramasamy, Jasper Zuallaert, Lennart Martens, Wim F. Vranken

   Protein Science, 35(1)
2. BioSamples database: the global hub for sample metadata and multi-omics integrationDipayan Gupta, Isuru Liyanage, Yasset Perez-Riverol, Enrique Sapena Ventura, Wei Kheng Teh, Tim Van Den Bossche, Senthilnathan Vijayaraja, Amnon Khen

   Nucleic Acids Research, 54(D1):D1761-D1767
3. Classification of Collagens via Peptide Ambiguation, in a Paleoproteomic LC-MS/MS-Based Taxonomic PipelineIan Engels, Alexandra Burnett, Prudence Robert, Camille Pironneau, Grégory Abrams, Robbin Bouwmeester, Peter Van der Plaetsen, Kévin Di Modica

   Journal of Proteome Research, 24(4):1907-1925
4. Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2DeepRobbe Devreese, Alireza Nameni, Arthur Declercq, Emmy Terryn, Ralf Gabriels, Francis Impens, Kris Gevaert, Lennart Martens

   Analytical Chemistry, 97(28):15113-15121
5. Creating a supportive academic culture by preventing and responding to transgressive behaviorTim Van Den Bossche, Dries H. Bostyn, Femke De Backere, Sean Bex

   Nature Mental Health, 3(5):481-482
6. Data‐Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model MicrobiomeAndrew T. Rajczewski, J. Alfredo Blakeley‐Ruiz, Annaliese Meyer, Simina Vintila, Matthew R. McIlvin, Tim Van Den Bossche, Brian C. Searle, Timothy J. Griffin

   PROTEOMICS, 25(9-10)
7. DeepLC introduces transfer learning for accurate LC retention time prediction and adaptation to substantially different modifications and setupsRobbin Bouwmeester, Alireza Nameni, Arthur Declercq, Robbe Devreese, Kevin Velghe, Vladimir Gorshkov, Pelayo A. Penanes, Frank Kjeldsen

   Preprint
8. Development of a General Purpose Targeted LC-MS Method for Accurate Quantification of the SARS-CoV-2 Spike Protein ExpressionRuben Almey, Kevin Mwangi, Siegliende de Cae, Pathmanaban Ramasamy, Marijn Van Hulle, Ine Lentacker, Bert Schepens, Dieter Deforce

   Preprint
9. Direct construction of sparse suffix arrays with LibsaisSimon Van de Vyver, Tibo Vande Moortele, Peter Dawyndt, Bart Mesuere, Pieter Verschaffelt

   Preprint
10. Emergence and Global Spread of Mpox Clade Ib: Challenges and the Role of Wastewater and Environmental SurveillanceAnanda Tiwari, Thierry Kalonji, Taru Miller, Tim Van Den Bossche, Adriana Krolicka, Hypolite Muhindo-Mavoko, Patrick Mitashi, Marc Christian Tahita

    The Journal of Infectious Diseases, 231(5):e825-e829
11. Establishing the ELIXIR Microbiome CommunityRobert D. Finn, Bachir Balech, Josephine Burgin, Physilia Chua, Erwan Corre, Cymon J. Cox, Claudio Donati, Vitor Martins dos Santos

    F1000Research, 13:50
12. Evaluation Metrics in Saliency Maps Applied to Graph RegressionNatàlia Segura-Alabart, Alberto Fernández, Alexander Kensert, Deirdre Cabooter, Francesc Serratosa

    Lecture Notes in Computer Science, 62-71
13. Illuminating the Invisible: Green Fluorescent Protein as a Beacon for Antibiotic-Induced Phage Activity in Escherichia coliMaria João Silva, Tim Van Den Bossche, Mattias Collin, Rolf Lood

    Antibiotics, 14(7):714
14. InstaNovo-P: A de novo peptide sequencing model for phosphoproteomicsJesper Lauridsen, Pathmanaban Ramasamy, Rachel Catzel, Vahap Canbay, Amandla Mabona, Kevin Eloff, Paul Fullwood, Jennifer Ferguson

    Preprint
15. Limitations of <i>de novo</i> sequencing in resolving sequence ambiguitySam van Puyenbroeck, Denis Beslic, Tomi Suomi, Tanja Holstein, Thilo Muth, Laura L. Elo, Lennart Martens, Robbin Bouwmeester

    Preprint
16. MLMarker: A machine learning framework for tissue inference and biomarker discoveryTine Claeys, Sam van Puyenbroeck, Kris Gevaert, Lennart Martens

    Preprint
17. Machine learning-based rescoring with MS²Rescore boosts peptide identification and taxonomic specificity in metaproteomicsXuxa Malliet, Arthur Declercq, Ralf Gabriels, Tanja Holstein, Bart Mesuere, Thilo Muth, Pieter Verschaffelt, Lennart Martens

    Preprint
18. Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and RescoringPatrick Willems, Fabien Thery, Laura Van Moortel, Margaux De Meyer, An Staes, Adillah Gul, Lyudmila Kovalchuke, Arthur Declercq

    Journal of Proteome Research, 24(4):2141-2151
19. Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo SequencingTim Van Den Bossche, Denis Beslic, Sam van Puyenbroeck, Tomi Suomi, Tanja Holstein, Lennart Martens, Laura L. Elo, Thilo Muth

    PROTEOMICS, 25(17-18):51-61
20. Metaproteomics in the One Health Framework for Unraveling Microbial Effectors in MicrobiomesRobert Heyer, Maximilian Wolf, Dirk Benndorf, Sergio Uzzau, Jana Seifert, Lucia Grenga, Martin Pabst, Heike Schmitt

    Preprint
21. Molecular attributes of intrinsically disordered regions in secretomes influence fungal pathogenesisAnkita Mohapatra, Rajashekar Varma Kadumuri, Ashwin Sharma, Anita P Saju, Harikrishnan Ramadasan, Anushka Agrawal, Vaidehi Sharma, Sreenivas Chavali

    Preprint
22. MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using ProteogenomicsJulian Pipart, Tanja Holstein, Lennart Martens, Thilo Muth

    Journal of Proteome Research, 24(6):2643-2656
23. Open-Source and FAIR Research Software for ProteomicsYasset Perez-Riverol, Wout Bittremieux, William S. Noble, Lennart Martens, Aivett Bilbao, Michael R. Lazear, Bjorn Grüning, Daniel S. Katz

    Journal of Proteome Research, 24(5):2222-2234
24. PTMVision: An Interactive Visualization Webserver for Post-translational Modifications of ProteinsSimon Hackl, Caroline Jachmann, Mathias Witte Paz, Theresa Anisja Harbig, Lennart Martens, Kay Nieselt

    Journal of Proteome Research, 24(2):919-928
25. PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic PathwaysTibo Vande Moortele, Pieter Verschaffelt, Qingyao Huang, Nadezhda T. Doncheva, Tanja Holstein, Caroline Jachmann, Peter Dawyndt, Lennart Martens

    Molecular &amp; Cellular Proteomics, 24(3):100918
26. Potential of Proteomics in Forensic Phenotyping: A Focus on Biological Sex EstimationShirin Alex, Ruben Almey, Rachel Sian Dennis, Olivier Tytgat, Robbin Bouwmeester, Dieter Deforce, Marcel De Puit, Maarten Dhaenens

    Journal of Proteome Research, 24(10):4888-4899
27. ProteoBench: the community-curated platform for comparing proteomics data analysis workflowsRobbe Devreese, Caroline Jachmann, Bart Van Puyvelde, Holda A. Anagho-Mattanovich, Witold E. Wolski, Henry Webel, Matthias Anagho-Mattanovich, Wout Bittremieux

    Preprint
28. TIMS²Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS²RescoreArthur Declercq, Robbe Devreese, Jonas Scheid, Caroline Jachmann, Tim Van Den Bossche, Annica Preikschat, David Gomez-Zepeda, Jeewan Babu Rijal

    Journal of Proteome Research, 24(3):1067-1076
29. Target acquired: Lock-on bacterial immunopeptidesPatrick Willems, Lyudmila Kovalchuke, Francis Impens

    Journal of Experimental Medicine, 222(10)
30. The microbiologist's guide to metaproteomicsTim Van Den Bossche, Jean Armengaud, Dirk Benndorf, Jose Alfredo Blakeley‐Ruiz, Madita Brauer, Kai Cheng, Marybeth Creskey, Daniel Figeys

    iMeta, 4(3)
31. Unipept in 2024: Expanding Metaproteomics Analysis with Support for Missed Cleavages and Semitryptic and Nontryptic PeptidesTibo Vande Moortele, Bram Devlaminck, Simon Van de Vyver, Tim Van Den Bossche, Lennart Martens, Peter Dawyndt, Bart Mesuere, Pieter Verschaffelt

    Journal of Proteome Research, 24(2):949-954
32. msqrob2TMT: Robust Linear Mixed Models for Inferring Differential Abundant Proteins in Labeled Experiments With Arbitrarily Complex DesignStijn Vandenbulcke, Christophe Vanderaa, Oliver Crook, Lennart Martens, Lieven Clement

    Molecular &amp; Cellular Proteomics, 24(7):101002
33. mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data FormatTim Van Den Bossche, Theodore Alexandrov, Aivett Bilbao, Wout Bittremieux, Federico Ivan Brigante, Matthew Chase Chambers, Joshua Charkow, Eric Deutsch

    Journal of Proteome Research, 24(11):5329-5335
34. omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation applied to bulk- and single cell proteomics dataAlexandre Segers, Cristian Castiglione, Christophe Vanderaa, Lennart Martens, Davide Risso, Lieven Clement

    Preprint

2024

1. A hands-on tutorial on quantitative structure-activity relationships using fully expressive graph neural networksAlexander Kensert, Gert Desmet, Deirdre Cabooter

   Analytica Chimica Acta, 1331:343046
2. Automated method development in high-pressure liquid chromatographyEmery Bosten, Alexander Kensert, Gert Desmet, Deirdre Cabooter

   Journal of Chromatography A, 1714:464577
3. Biodiversity Analysis of Metaproteomics Samples with Unipept: A Comprehensive TutorialTim Van Den Bossche, Pieter Verschaffelt, Tibo Vande Moortele, Peter Dawyndt, Lennart Martens, Bart Mesuere

   Methods in Molecular Biology, 183-215
4. Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and JavaChris Bielow, Nils Hoffmann, David Jimenez-Morales, Tim Van Den Bossche, Juan Antonio Vizcaíno, David L. Tabb, Wout Bittremieux, Mathias Walzer

   Journal of the American Society for Mass Spectrometry, 35(8):1875-1882
5. Deep reinforcement learning for the direct optimization of gradient separations in liquid chromatographyAlexander Kensert, Pieter Libin, Gert Desmet, Deirdre Cabooter

   Journal of Chromatography A, 1720:464768
6. Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree speciesLydia Kipping, Nico Jehmlich, Julia Moll, Matthias Noll, Martin M Gossner, Tim Van Den Bossche, Pascal Edelmann, Werner Borken

   The ISME Journal, 18(1)
7. High-coverage immunopeptidomics using timsTOF mass spectrometers with Thunder-DDA-PASEF boosted by MS2RescoreDavid Gomez-Zepeda, Julian Beyrle, Annica Preikschat, Arthur Declercq, Yannic Chen, Ralf Gabriels, Lennart Martens, Ute Distler

   Preprint
8. Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐linksArslan Siraj, Robbin Bouwmeester, Arthur Declercq, Luisa Welp, Aleksandar Chernev, Alexander Wulf, Henning Urlaub, Lennart Martens

   PROTEOMICS, 24(8)
9. MHCquant2 refines immunopeptidomics tumor antigen discoveryJonas Scheid, Steffen Lemke, Naomi Hoenisch-Gravel, Anna Dengler, Timo Sachsenberg, Arthur Declerq, Ralf Gabriels, Jens Bauer

   Preprint
10. MS²Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0Louise M. Buur, Arthur Declercq, Marina Strobl, Robbin Bouwmeester, Sven Degroeve, Lennart Martens, Viktoria Dorfer, Ralf Gabriels

    Journal of Proteome Research, 23(8):3200-3207
11. MultiStageSearch: a multi-step proteogenomic workflow for taxonomic identification of viral proteome samples adressing database biasJulian Pipart, Tanja Holstein, Lennart Martens, Thilo Muth

    Preprint
12. Predicting ion mobility collision cross sections and assessing prediction variation by combining conventional and data driven modelingRobbin Bouwmeester, Keith Richardson, Richard Denny, Ian D. Wilson, Sven Degroeve, Lennart Martens, Johannes P.C. Vissers

    Talanta, 274:125970
13. Proceedings of the EuBIC-MS developers meeting 2023Pedro Beltrao, Tim Van Den Bossche, Ralf Gabriels, Tanja Holstein, Tobias Kockmann, Alireza Nameni, Christian Panse, Ralph Schlapbach

    Journal of Proteomics, 305:105246
14. Proteogenomics analysis of human tissues using pangenomesDong Wang, Robbin Bouwmeester, Ping Zheng, Chengxin Dai, Aniel Sanchez, Kunxian Shu, Mingze Bai, Husen M. Umer

    Preprint
15. TIMS ² Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS ² RescoreArthur Declercq, Robbe Devreese, Jonas Scheid, Caroline Jachmann, Tim Van Den Bossche, Annica Preikschat, David Gomez-Zepeda, Jeewan Babu Rijal

    Preprint
16. Unraveling Microbial Effectors: Metaproteomics in the One Health FrameworkRobert Heyer, Maximilian Wolf, Dirk Benndorf, Sergio Uzzau, Jana Seifert, Lucia Grenga, Martin Pabst, Heike Schmitt

    Preprint
17. msqrob2PTM: Differential Abundance and Differential Usage Analysis of MS-Based Proteomics Data at the Posttranslational Modification and Peptidoform LevelNina Demeulemeester, Marie Gébelin, Lucas Caldi Gomes, Paul Lingor, Christine Carapito, Lennart Martens, Lieven Clement

    Molecular &amp; Cellular Proteomics, 23(2):100708

2023

1. Benchmarking DIA data analysis workflowsAn Staes, Teresa Maia, Sara Dufour, Robbin Bouwmeester, Ralf Gabriels, Lennart Martens, Francis Impens, Simon Devos

   Preprint
2. Ionmob: a Python package for prediction of peptide collisional cross-section valuesDavid Teschner, David Gomez-Zepeda, Arthur Declercq, Mateusz K Łącki, Seymen Avci, Konstantin Bob, Ute Distler, Thomas Michna

   Bioinformatics, 39(9)
3. Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific ProteinsTine Claeys, Maxime Menu, Robbin Bouwmeester, Kris Gevaert, Lennart Martens

   Journal of Proteome Research, 22(4):1181-1192
4. O15 Large-scale proteomics profiling of peripheral blood of DM1 patients identifies biomarkers for disease severity and physical activityP. 't Hoen, D. van As, T. Claeys, R. Salz, R. Gabriels, F. Impens, P. Volders, L. Martens

   Neuromuscular Disorders, 33:S132-S133
5. Proteins with amino acid repeats constitute a rapidly evolvable and human-specific essentialomeAnjali K. Singh, Ishita Amar, Harikrishnan Ramadasan, Keertana S. Kappagantula, Sreenivas Chavali

   Cell Reports, 42(7):112811
6. ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in ProteomicsTobias G. Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A. Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt

   Journal of Proteome Research, 22(2):632-636
7. Quality Control for the Target Decoy Approach for Peptide IdentificationElke Debrie, Milan Malfait, Ralf Gabriels, Arthur Declerq, Adriaan Sticker, Lennart Martens, Lieven Clement

   Journal of Proteome Research, 22(2):350-358
8. Toward an Integrated Machine Learning Model of a Proteomics ExperimentBenjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat

   Journal of Proteome Research, 22(3):681-696
9. Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics AnalysesPieter Verschaffelt, Alessandro Tanca, Marcello Abbondio, Tim Van Den Bossche, Tibo Vande Moortele, Peter Dawyndt, Lennart Martens, Bart Mesuere

   Journal of Proteome Research, 22(8):2620-2628
10. Updated MS²PIP web server supports cutting-edge proteomics applicationsArthur Declercq, Robbin Bouwmeester, Cristina Chiva, Eduard Sabidó, Aurélie Hirschler, Christine Carapito, Lennart Martens, Sven Degroeve

    Nucleic Acids Research, 51(W1):W338-W342
11. lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotationTine Claeys, Tim Van Den Bossche, Yasset Perez-Riverol, Kris Gevaert, Juan Antonio Vizcaíno, Lennart Martens

    Nature Communications, 14(1)

2022

1. <i>Pout2Prot</i> : An Efficient Tool to Create Protein (Sub)groups from Percolator Output FilesKay Schallert, Pieter Verschaffelt, Bart Mesuere, Dirk Benndorf, Lennart Martens, Tim Van Den Bossche

   Journal of Proteome Research, 21(4):1175-1180
2. A Comprehensive Evaluation of Consensus Spectrum Generation Methods in ProteomicsXiyang Luo, Wout Bittremieux, Johannes Griss, Eric W. Deutsch, Timo Sachsenberg, Lev I. Levitsky, Mark V. Ivanov, Julia A. Bubis

   Journal of Proteome Research, 21(6):1566-1574
3. A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomicsBart Van Puyvelde, Simon Daled, Sander Willems, Ralf Gabriels, Anne Gonzalez de Peredo, Karima Chaoui, Emmanuelle Mouton-Barbosa, David Bouyssié

   Scientific Data, 9(1)
4. A study on experimental bias in post-translational modification predictorsJasper Zuallaert, Pathmanaban Ramasamy, Robbin Bouwmeester, Nico Callewaert, Sven Degroeve

   Preprint
5. An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemiaLien Provez, Bart Van Puyvelde, Laura Corveleyn, Nina Demeulemeester, Sigrid Verhelst, Béatrice Lintermans, Simon Daled, Juliette Roels

   Scientific Data, 9(1)
6. Challenges in describing the conformation and dynamics of proteins with ambiguous behaviorJoel Roca-Martinez, Tamas Lazar, Jose Gavalda-Garcia, David Bickel, Rita Pancsa, Bhawna Dixit, Konstantina Tzavella, Pathmanaban Ramasamy

   Frontiers in Molecular Biosciences, 9
7. Clinical improvement of DM1 patients reflected by reversal of disease-induced gene expression in bloodRemco T. P. van Cruchten, Daniël van As, Jeffrey C. Glennon, Baziel G. M. van Engelen, Peter A. C. ‘t Hoen, K Okkersen, C Jimenez-Moreno, S Wenninger

   BMC Medicine, 20(1)
8. Convolutional neural network for automated peak detection in reversed-phase liquid chromatographyAlexander Kensert, Emery Bosten, Gilles Collaerts, Kyriakos Efthymiadis, Peter Van Broeck, Gert Desmet, Deirdre Cabooter

   Journal of Chromatography A, 1672:463005
9. Cov ² MS: an automated matrix-independent assay for mass spectrometric detection and measurement of SARS-CoV-2 nucleocapsid protein in infectious patientsBart Van Puyvelde, Katleen Van Uytfanghe, Laurence Van Oudenhove, Ralf Gabriels, Tessa Van Royen, Arne Matthys, Morteza Razavi, Richard Yip

   Preprint
10. Cov²MS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid ProteinBart Van Puyvelde, Katleen Van Uytfanghe, Laurence Van Oudenhove, Ralf Gabriels, Tessa Van Royen, Arne Matthys, Morteza Razavi, Richard Yip

    Analytical Chemistry, 94(50):17379-17387
11. Differential colonization and functioning of microbial community in response to phosphate levelsVarsha Jha, Sakina Bombaywala, Hemant Purohit, Nishant A. Dafale

    Journal of Environmental Management, 321:115856
12. Efficacy of microbes in removal of pesticides from watershed systemAshootosh Mandpe, Sakina Bombaywala, Sonam Paliya, Sunil Kumar

    Synergistic Approaches for Bioremediation of Environmental Pollutants : Recent Advances and Challenges, 27-51
13. Genome plasticity as a paradigm of antibiotic resistance spread in ESKAPE pathogensSanchita Das, Sakina Bombaywala, Shweta Srivastava, Atya Kapley, Rita Dhodapkar, Nishant A. Dafale

    Environmental Science and Pollution Research, 29(27):40507-40519
14. MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification RatesArthur Declercq, Robbin Bouwmeester, Aurélie Hirschler, Christine Carapito, Sven Degroeve, Lennart Martens, Ralf Gabriels

    Molecular &amp; Cellular Proteomics, 21(8):100266
15. Machine learning on large-scale proteomics data identifies tissue- and cell type-specific proteinsTine Claeys, Maxime Menu, Robbin Bouwmeester, Kris Gevaert, Lennart Martens

    Preprint
16. Multi‐model averaging improves the performance of model‐guided infliximab dosing in patients with inflammatory bowel diseasesWannee Kantasiripitak, An Outtier, Sebastian G. Wicha, Alexander Kensert, Zhigang Wang, João Sabino, Séverine Vermeire, Debby Thomas

    CPT: Pharmacometrics &amp; Systems Pharmacology, 11(8):1045-1059
17. Panoramic Perspective on Human PhosphositesPathmanaban Ramasamy, Elien Vandermarliere, Wim F. Vranken, Lennart Martens

    Journal of Proteome Research, 21(8):1894-1915
18. PepGM: A probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scoresTanja Holstein, Franziska Kistner, Lennart Martens, Thilo Muth

    Preprint
19. ProMetheusDB: An In-Depth Analysis of the High-Quality Human Methyl-proteomeEnrico Massignani, Roberto Giambruno, Marianna Maniaci, Luciano Nicosia, Avinash Yadav, Alessandro Cuomo, Francesco Raimondi, Tiziana Bonaldi

    Molecular &amp; Cellular Proteomics, 21(7):100243
20. Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and PeptidoformsRichard D. LeDuc, Eric W. Deutsch, Pierre-Alain Binz, Ryan T. Fellers, Anthony J. Cesnik, Joshua A. Klein, Tim Van Den Bossche, Ralf Gabriels

    Journal of Proteome Research, 21(4):1189-1195
21. Reboot surgery for chronic rhinosinusitis with nasal polyposis: recurrence and smell kineticsSara Costa Gomes, Carlo Cavaliere, Simonetta Masieri, Thibaut Van Zele, Philippe Gevaert, Gabriele Holtappels, Nan Zhang, Pathmanaban Ramasamy

    European Archives of Oto-Rhino-Laryngology, 279(12):5691-5699
22. Sensitive and Specific Spectral Library Searching with CompOmics Spectral Library Searching Tool and PercolatorGenet Abay Shiferaw, Ralf Gabriels, Robbin Bouwmeester, Tim Van Den Bossche, Elien Vandermarliere, Lennart Martens, Pieter-Jan Volders

    Journal of Proteome Research, 21(5):1365-1370
23. psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search ResultsRalf Gabriels, Arthur Declercq, Robbin Bouwmeester, Sven Degroeve, Lennart Martens

    Journal of Proteome Research, 22(2):557-560
24. psm_utils: A high level Python API for parsing and handling peptide-spectrum-matches and proteomics search resultsRalf Gabriels, Arthur Declercq, Robbin Bouwmeester, Sven Degroeve, Lennart Martens

    Preprint

2021

1. Antibiotic resistance in the environment: a critical insight on its occurrence, fate, and eco-toxicitySakina Bombaywala, Ashootosh Mandpe, Sonam Paliya, Sunil Kumar

   Environmental Science and Pollution Research, 28(20):24889-24916
2. Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 PatientsBart Van Puyvelde, Katleen Van Uytfanghe, Olivier Tytgat, Laurence Van Oudenhove, Ralf Gabriels, Robbin Bouwmeester, Simon Daled, Tim Van Den Bossche

   JACS Au, 1(6):750-765
3. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflowsTim Van Den Bossche, Benoit J. Kunath, Kay Schallert, Stephanie S. Schäpe, Paul E. Abraham, Jean Armengaud, Magnus Ø. Arntzen, Ariane Bassignani

   Nature Communications, 12(1)
4. Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the FutureNuno Bandeira, Eric W. Deutsch, Oliver Kohlbacher, Lennart Martens, Juan Antonio Vizcaíno

   Molecular &amp; Cellular Proteomics, 20:100071
5. Deep Q-learning for the selection of optimal isocratic scouting runs in liquid chromatographyAlexander Kensert, Gilles Collaerts, Kyriakos Efthymiadis, Gert Desmet, Deirdre Cabooter

   Journal of Chromatography A, 1638:461900
6. Deep convolutional autoencoder for the simultaneous removal of baseline noise and baseline drift in chromatogramsAlexander Kensert, Gilles Collaerts, Kyriakos Efthymiadis, Peter Van Broeck, Gert Desmet, Deirdre Cabooter

   Journal of Chromatography A, 1646:462093
7. DeepLC can predict retention times for peptides that carry as-yet unseen modificationsRobbin Bouwmeester, Ralf Gabriels, Niels Hulstaert, Lennart Martens, Sven Degroeve

   Nature Methods, 18(11):1363-1369
8. Determination of the urban rooftop photovoltaic potential: A state of the artElham Fakhraian, Marc Alier Forment, Francesc Valls Dalmau, Alireza Nameni, Maria José Casañ Guerrero

   Energy Reports, 7:176-185
9. Graph Convolutional Networks for Improved Prediction and Interpretability of Chromatographic Retention DataAlexander Kensert, Robbin Bouwmeester, Kyriakos Efthymiadis, Peter Van Broeck, Gert Desmet, Deirdre Cabooter

   Analytical Chemistry, 93(47):15633-15641
10. Ion Mobility Coupled to a Time-of-Flight Mass Analyzer Combined With Fragment Intensity Predictions Improves Identification of Classical Bioactive Peptides and Small Open Reading Frame-Encoded PeptidesMarlies K. R. Peeters, Geert Baggerman, Ralf Gabriels, Elise Pepermans, Gerben Menschaert, Kurt Boonen

    Frontiers in Cell and Developmental Biology, 9
11. MS ² Rescore: Data-driven rescoring dramatically boosts immunopeptide identification ratesArthur Declercq, Robbin Bouwmeester, Aurélie Hirschler, Christine Carapito, Sven Degroeve, Lennart Martens, Ralf Gabriels

    Preprint
12. Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transitMorgane Boone, Pathmanaban Ramasamy, Jasper Zuallaert, Robbin Bouwmeester, Berre Van Moer, Davy Maddelein, Demet Turan, Niels Hulstaert

    Nature Communications, 12(1)
13. MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data SetsPieter Verschaffelt, Tim Van Den Bossche, Wassim Gabriel, Michał Burdukiewicz, Alessio Soggiu, Lennart Martens, Bernhard Y. Renard, Henning Schiebenhoefer

    Journal of Proteome Research, 20(4):2083-2088
14. Mobility of antibiotic resistance and its co-occurrence with metal resistance in pathogens under oxidative stressSakina Bombaywala, Hemant J. Purohit, Nishant A. Dafale

    Journal of Environmental Management, 297:113315
15. Online biophysical predictions for SARS-CoV-2 proteinsLuciano Kagami, Joel Roca-Martínez, Jose Gavaldá-García, Pathmanaban Ramasamy, K. Anton Feenstra, Wim F. Vranken

    BMC Molecular and Cell Biology, 22(1)
16. PDBe-KB: collaboratively defining the biological context of structural dataMihaly Varadi, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S Nair

    Nucleic Acids Research, 50(D1):D534-D542
17. Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant DetectionRenee Salz, Robbin Bouwmeester, Ralf Gabriels, Sven Degroeve, Lennart Martens, Pieter-Jan Volders, Peter A.C. ’t Hoen

    Journal of Proteome Research, 20(6):3353-3364
18. Pharmacological inhibition of LSD1 triggers myeloid differentiation by targeting GSE1, a novel oncogene in AMLLuciano Nicosia, Francesca Ludovica Boffo, Elena Ceccacci, Isabella Pallavicini, Fabio Bedin, Enrico Massignani, Roberto Ravasio, Saverio Minucci

    Preprint
19. Polybrominated diphenyl ethers in the environment: a wake-up call for concerted action in IndiaSonam Paliya, Ashootosh Mandpe, Sakina Bombaywala, Manukonda Suresh Kumar, Sunil Kumar, Vivek Kumar Morya

    Environmental Science and Pollution Research, 28(33):44693-44715
20. Research culture: science from bench to societyLorenzo Canti, Anna Chrzanowska, M. Giulia Doglio, Lia Martina, Tim Van Den Bossche

    Biology Open, 10(8)
21. Sensitive and specific spectral library searching with COSS and PercolatorGenet Abay Shiferaw, Ralf Gabriels, Robbin Bouwmeester, Tim Van Den Bossche, Elien Vandermarliere, Lennart Martens, Pieter-Jan Volders

    Preprint
22. Solid Waste Treatment: Technological Advancements and ChallengesVinay Pratap, Sakina Bombaywala, Ashootosh Mandpe, Saif Ullah Khan

    Soft Computing Techniques in Solid Waste and Wastewater Management, 215-231
23. Spectral Prediction Features as a Solution for the Search Space Size Problem in ProteogenomicsSteven Verbruggen, Siegfried Gessulat, Ralf Gabriels, Anna Matsaroki, Hendrik Van de Voorde, Bernhard Kuster, Sven Degroeve, Lennart Martens

    Molecular &amp; Cellular Proteomics, 20:100076
24. Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic ApproachMarianna Maniaci, Francesca Ludovica Boffo, Enrico Massignani, Tiziana Bonaldi

    Frontiers in Molecular Biosciences, 8
25. The European Bioinformatics Community for Mass Spectrometry (EuBIC‐MS): an open community for bioinformatics training and researchWout Bittremieux, David Bouyssié, Viktoria Dorfer, Marie Locard‐Paulet, Yasset Perez‐Riverol, Veit Schwämmle, Julian Uszkoreit, Tim Van Den Bossche

    Rapid Communications in Mass Spectrometry, 39(S1)
26. The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomesTim Van Den Bossche, Magnus Ø. Arntzen, Dörte Becher, Dirk Benndorf, Vincent G. H. Eijsink, Céline Henry, Pratik D. Jagtap, Nico Jehmlich

    Microbiome, 9(1)
27. The Urban Rooftop Photovoltaic Potential DeterminationElham Fakhraian, Marc Alier, Francesc Valls Dalmau, Alireza Nameni, Maria José Casañ Guerrero

    Sustainability, 13(13):7447
28. UMGAP: the Unipept MetaGenomics Analysis PipelineFelix Van der Jeugt, Rien Maertens, Aranka Steyaert, Pieter Verschaffelt, Caroline De Tender, Peter Dawyndt, Bart Mesuere

    Preprint
29. Understanding the Role of Genetic and Protein Networking Involved in Microbial BioremediationUpasana Jhariya, Shweta Srivastava, Sanchita Das, Sakina Bombaywala, Sejal Mahallea, Nishant A. Dafale

    Bioremediation of Environmental Pollutants, 187-219
30. Unipept Desktop: A Faster, More Powerful Metaproteomics Results Analysis ToolPieter Verschaffelt, Tim Van Den Bossche, Lennart Martens, Peter Dawyndt, Bart Mesuere

    Journal of Proteome Research, 20(4):2005-2009
31. Unipept Visualizations: an interactive visualization library for biological dataPieter Verschaffelt, James Collier, Alexander Botzki, Lennart Martens, Peter Dawyndt, Bart Mesuere

    Bioinformatics, 38(2):562-563
32. Universal Spectrum Identifier for mass spectraEric W. Deutsch, Yasset Perez-Riverol, Jeremy Carver, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Pierre-Alain Binz

    Nature Methods, 18(7):768-770
33. b2bTools: online predictions for protein biophysical features and their conservationLuciano Porto Kagami, Gabriele Orlando, Daniele Raimondi, Francois Ancien, Bhawna Dixit, Jose Gavaldá-García, Pathmanaban Ramasamy, Joel Roca-Martínez

    Nucleic Acids Research, 49(W1):W52-W59
34. ionbot: a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identificationSven Degroeve, Ralf Gabriels, Kevin Velghe, Robbin Bouwmeester, Natalia Tichshenko, Lennart Martens

    Preprint

2020

1. Biochemical and Computational Approaches for the Large-Scale Analysis of Protein Arginine Methylation by Mass SpectrometryDaniele Musiani, Enrico Massignani, Alessandro Cuomo, Avinash Yadav, Tiziana Bonaldi

   Current Protein &amp; Peptide Science, 21(7):725-739
2. COSS: A Fast and User-Friendly Tool for Spectral Library SearchingGenet Abay Shiferaw, Elien Vandermarliere, Niels Hulstaert, Ralf Gabriels, Lennart Martens, Pieter-Jan Volders

   Journal of Proteome Research, 19(7):2786-2793
3. Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data AnalysisTim Van Den Bossche, Pieter Verschaffelt, Kay Schallert, Harald Barsnes, Peter Dawyndt, Dirk Benndorf, Bernhard Y. Renard, Bart Mesuere

   Journal of Proteome Research, 19(8):3562-3566
4. Cov-MS: a community-based template assay for clinical MS-based protein detection in SARS-CoV-2 patientsB. Van Puyvelde, K. Van Uytfanghe, O. Tytgat, L. Van Oudenhove, R. Gabriels, R. Bouwmeester, S. Daled, T. Van Den Bossche

   Preprint
5. Extracellular vesicles in patients in the acute phase of psychosis and after clinical improvement: an explorative studyMette Elise Tunset, Hanne Haslene-Hox, Tim Van Den Bossche, Arne Einar Vaaler, Einar Sulheim, Daniel Kondziella

   PeerJ, 8:e9714
6. Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention TimesRobbin Bouwmeester, Lennart Martens, Sven Degroeve

   Analytical Chemistry, 92(9):6571-6578
7. Generalized calibration across LC-setups for generic prediction of small molecule retention timesRobbin Bouwmeester, Lennart Martens, Sven Degroeve

   Preprint
8. MSqRob Takes the Missing Hurdle: Uniting Intensity- and Count-Based ProteomicsLudger J. E. Goeminne, Adriaan Sticker, Lennart Martens, Kris Gevaert, Lieven Clement

   Analytical Chemistry, 92(9):6278-6287
9. MobiDB: intrinsically disordered proteins in 2021Damiano Piovesan, Marco Necci, Nahuel Escobedo, Alexander Miguel Monzon, András Hatos, Ivan Mičetić, Federica Quaglia, Lisanna Paladin

   Nucleic Acids Research, 49(D1):D361-D367
10. PRMT1 Is Recruited via DNA-PK to Chromatin Where It Sustains the Senescence-Associated Secretory Phenotype in Response to CisplatinDaniele Musiani, Roberto Giambruno, Enrico Massignani, Marica Rosaria Ippolito, Marianna Maniaci, Sriganesh Jammula, Daria Manganaro, Alessandro Cuomo

    Cell Reports, 30(4):1208-1222.e9
11. Pitfalls in re-analysis of observational omics studies: a post-mortem of the human pathology atlasJeroen Gilis, Steff Taelman, Lucas Davey, Lennart Martens, Lieven Clement

    Preprint
12. Precursor intensity-based label-free quantification software tools for proteomic and multiomic analysis within the Galaxy PlatformSubina Mehta, Caleb Easterly, Ray Sajulga, Robert J. Millikin, Andrea Argentini, Ignacio Eguinoa, Lennart Martens, Michael R. Shortreed

    Preprint
13. Proceedings of the EuBIC-MS 2020 Developers’ MeetingChristopher Ashwood, Wout Bittremieux, Eric W. Deutsch, Nadezhda T. Doncheva, Viktoria Dorfer, Ralf Gabriels, Vladimir Gorshkov, Surya Gupta

    EuPA Open Proteomics, 24:1-6
14. Robust Summarization and Inference in Proteome-wide Label-free QuantificationAdriaan Sticker, Ludger Goeminne, Lennart Martens, Lieven Clement

    Molecular &amp; Cellular Proteomics, 19(7):1209-1219
15. Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full ContextPathmanaban Ramasamy, Demet Turan, Natalia Tichshenko, Niels Hulstaert, Elien Vandermarliere, Wim Vranken, Lennart Martens

    Journal of Proteome Research, 19(8):3478-3486
16. Study of indiscriminate distribution of restrained antimicrobial resistome of different environmental nichesSakina Bombaywala, Nishant A. Dafale, Varsha Jha, Abhay Bajaj, Hemant J. Purohit

    Environmental Science and Pollution Research, 28(9):10780-10790
17. The Age of Data‐Driven Proteomics: How Machine Learning Enables Novel WorkflowsRobbin Bouwmeester, Ralf Gabriels, Tim Van Den Bossche, Lennart Martens, Sven Degroeve

    PROTEOMICS, 20(21-22)
18. Unipept CLI 2.0: adding support for visualizations and functional annotationsPieter Verschaffelt, Philippe Van Thienen, Tim Van Den Bossche, Felix Van der Jeugt, Caroline De Tender, Lennart Martens, Peter Dawyndt, Bart Mesuere

    Bioinformatics, 36(14):4220-4221
19. gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organismsMaria Muñoz-Benavent, Felix Hartkopf, Tim Van Den Bossche, Vitor C Piro, Carlos García-Ferris, Amparo Latorre, Bernhard Y Renard, Thilo Muth

    NAR Genomics and Bioinformatics, 2(3)

2019

1. 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 urineLeanne C. Nye, Jonathan P. Williams, Nyasha C. Munjoma, Marine P.M. Letertre, Muireann Coen, Robbin Bouwmeester, Lennart Martens, Jonathan R. Swann

   Journal of Chromatography A, 1602:386-396
2. A simple approach for accurate peptide quantification in MS-based proteomicsTeresa Mendes Maia, An Staes, Kim Plasman, Jarne Pauwels, Katie Boucher, Andrea Argentini, Lennart Martens, Tony Montoye

   Preprint
3. Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functionsAna S C. Silva, Robbin Bouwmeester, Lennart Martens, Sven Degroeve

   Bioinformatics, 35(24):5243-5248
4. Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysisHenning Schiebenhoefer, Tim Van Den Bossche, Stephan Fuchs, Bernhard Y. Renard, Thilo Muth, Lennart Martens

   Expert Review of Proteomics, 16(5):375-390
5. Comprehensive and Empirical Evaluation of Machine Learning Algorithms for Small Molecule LC Retention Time PredictionRobbin Bouwmeester, Lennart Martens, Sven Degroeve

   Analytical Chemistry, 91(5):3694-3703
6. PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesisValeria Spadotto, Roberto Giambruno, Enrico Massignani, Marija Mihailovich, Marianna Maniaci, Francesca Patuzzo, Francesco Ghini, Francesco Nicassio

   Nucleic Acids Research, 48(1):96-115
7. Proteomics Standards Initiative Extended FASTA FormatPierre-Alain Binz, Jim Shofstahl, Juan Antonio Vizcaíno, Harald Barsnes, Robert J. Chalkley, Gerben Menschaert, Emanuele Alpi, Karl Clauser

   Journal of Proteome Research, 18(6):2686-2692
8. Proteomics profiling of arginine methylation defines PRMT5 substrate specificityDaniele Musiani, Jabez Bok, Enrico Massignani, Liling Wu, Tommaso Tabaglio, Marica Rosaria Ippolito, Alessandro Cuomo, Umut Ozbek

   Science Signaling, 12(575)
9. Removing the hidden data dependency of DIA with predicted spectral librariesB. Van Puyvelde, S. Willems, R. Gabriels, S. Daled, L. De Clerck, S. Vande Casteele, A. Staes, F. Impens

   Preprint
10. Stress-induced phospho-ubiquitin formation causes parkin degradationLyudmila Kovalchuke, Eugene V. Mosharov, Oren A. Levy, Lloyd A. Greene

    Scientific Reports, 9(1)
11. Therapeutic Targeting of RNA Splicing Catalysis through Inhibition of Protein Arginine MethylationJia Yi Fong, Luca Pignata, Pierre-Alexis Goy, Kimihito Cojin Kawabata, Stanley Chun-Wei Lee, Cheryl M. Koh, Daniele Musiani, Enrico Massignani

    Cancer Cell, 36(2):194-209.e9
12. ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File ConversionNiels Hulstaert, Jim Shofstahl, Timo Sachsenberg, Mathias Walzer, Harald Barsnes, Lennart Martens, Yasset Perez-Riverol

    Journal of Proteome Research, 19(1):537-542
13. Transfer Learning with Deep Convolutional Neural Networks for Classifying Cellular Morphological ChangesAlexander Kensert, Philip J. Harrison, Ola Spjuth

    SLAS Discovery, 24(4):466-475
14. Updated MS ² PIP web server delivers fast and accurate MS ² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniquesRalf Gabriels, Lennart Martens, Sven Degroeve

    Preprint
15. Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniquesRalf Gabriels, Lennart Martens, Sven Degroeve

    Nucleic Acids Research, 47(W1):W295-W299
16. hmSEEKER: Identification of hmSILAC Doublets in MaxQuant Output DataEnrico Massignani, Alessandro Cuomo, Daniele Musiani, SriGanesh Jammula, Giulio Pavesi, Tiziana Bonaldi

    PROTEOMICS, 19(5)

2018

1. A well-ordered nanoflow LC-MS/MS approach for proteome profiling using 200 cm long micro pillar array columnsJeff Op De Beeck, Jarne Pauwels, Natalie Van Landuyt, Paul Jacobs, Wim De Malsche, Gert Desmet, Andrea Argentini, An Staes

   Preprint
2. Data-Driven Rescoring of Metabolite Annotations Significantly Improves SensitivityAna S. C. Silva, Andrew Palmer, Vitaly Kovalev, Artem Tarasov, Theodore Alexandrov, Lennart Martens, Sven Degroeve

   Analytical Chemistry, 90(19):11636-11642
3. Evaluating parameters for ligand-based modeling with random forest on sparse data setsAlexander Kensert, Jonathan Alvarsson, Ulf Norinder, Ola Spjuth

   Journal of Cheminformatics, 10(1)
4. LNCipedia 5: towards a reference set of human long non-coding RNAsPieter-Jan Volders, Jasper Anckaert, Kenneth Verheggen, Justine Nuytens, Lennart Martens, Pieter Mestdagh, Jo Vandesompele

   Nucleic Acids Research, 47(D1):D135-D139
5. More than the “Killer Trait”: Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium HostKatrin Grosser, Pathmanaban Ramasamy, Azim Dehghani Amirabad, Marcel H Schulz, Gilles Gasparoni, Martin Simon, Martina Schrallhammer

   Genome Biology and Evolution, 10(2):646-656
6. Scop3D: Online Visualization of Mutation Rates on Protein StructureLukasz Kreft, Demet Turan, Niels Hulstaert, Alexander Botzki, Lennart Martens, Elien Vandermarliere

   Journal of Proteome Research, 18(2):765-769
7. Transgenic expression of the RNA binding protein IMP2 stabilizes miRNA targets in murine microsteatosisAzim Dehghani Amirabad, Pathmanaban Ramasamy, Marina Wierz, Karl Nordström, Sonja M. Kessler, Marcel H. Schulz, Martin Simon

   Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1864(10):3099-3108
8. Unipept 4.0: Functional Analysis of Metaproteome DataRobbert Gurdeep Singh, Alessandro Tanca, Antonio Palomba, Felix Van der Jeugt, Pieter Verschaffelt, Sergio Uzzau, Lennart Martens, Peter Dawyndt

   Journal of Proteome Research, 18(2):606-615
9. Update on the moFF Algorithm for Label-Free Quantitative ProteomicsAndrea Argentini, An Staes, Björn Grüning, Subina Mehta, Caleb Easterly, Timothy J. Griffin, Pratik Jagtap, Francis Impens

   Journal of Proteome Research, 18(2):728-731

2017

1. Do you speak open science? Resources and tips to learn the languagePaola Masuzzo, Lennart Martens
2. MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the GoThilo Muth, Fabian Kohrs, Robert Heyer, Dirk Benndorf, Erdmann Rapp, Udo Reichl, Lennart Martens, Bernhard Y. Renard

   Analytical Chemistry, 90(1):685-689
3. Mass spectrometrists should search for all peptides, but assess only the ones they care aboutAdriaan Sticker, Lennart Martens, Lieven Clement

   Nature Methods, 14(7):643-644
4. N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thalianaPatrick Willems, Elvis Ndah, Veronique Jonckheere, Simon Stael, Adriaan Sticker, Lennart Martens, Frank Van Breusegem, Kris Gevaert

   Molecular &amp; Cellular Proteomics, 16(6):1064-1080
5. Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation ProductsKenneth Verheggen, Pieter-Jan Volders, Pieter Mestdagh, Gerben Menschaert, Petra Van Damme, Kris Gevaert, Lennart Martens, Jo Vandesompele

   Journal of Proteome Research, 16(7):2508-2515
6. Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein PairsSurya Gupta, Kenneth Verheggen, Jan Tavernier, Lennart Martens

   Journal of Proteome Research, 16(6):2204-2212

2016

1. Differential subcellular distribution of four phospholipase C isoforms and secretion of GPI-PLC activityEmanuel Staudt, Pathmanaban Ramasamy, Helmut Plattner, Martin Simon

   Biochimica et Biophysica Acta (BBA) - Biomembranes, 1858(12):3157-3168
2. moFF: a robust and automated approach to extract peptide ion intensitiesAndrea Argentini, Ludger J E Goeminne, Kenneth Verheggen, Niels Hulstaert, An Staes, Lieven Clement, Lennart Martens

   Nature Methods, 13(12):964-966

2014

1. DeNovoGUI: An Open Source Graphical User Interface for <i>de Novo</i> Sequencing of Tandem Mass SpectraThilo Muth, Lisa Weilnböck, Erdmann Rapp, Christian G. Huber, Lennart Martens, Marc Vaudel, Harald Barsnes

   Journal of Proteome Research, 13(2):1143-1146
2. Introduction to opportunities and pitfalls in functional mass spectrometry based proteomicsMarc Vaudel, Albert Sickmann, Lennart Martens

   Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1844(1):12-20
3. Machine learning applications in proteomics research: How the past can boost the futurePieter Kelchtermans, Wout Bittremieux, Kurt De Grave, Sven Degroeve, Jan Ramon, Kris Laukens, Dirk Valkenborg, Harald Barsnes

   PROTEOMICS, 14(4-5):353-366
4. Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathwaysFlorian Beck, Jörg Geiger, Stepan Gambaryan, Johannes Veit, Marc Vaudel, Peter Nollau, Oliver Kohlbacher, Lennart Martens

   Blood, 123(5):e1-e10
5. Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data PublicationsEugene Kolker, Vural Özdemir, Lennart Martens, William Hancock, Gordon Anderson, Nathaniel Anderson, Sukru Aynacioglu, Ancha Baranova

   OMICS: A Journal of Integrative Biology, 18(1):10-14

2013

1. <scp>D</scp>‐score: A search engine independent <scp>MD</scp>‐scoreMarc Vaudel, Daniela Breiter, Florian Beck, Jörg Rahnenführer, Lennart Martens, René P. Zahedi

   PROTEOMICS, 13(6):1036-1041
2. About Dice, Bouldering, and Team Empowerment: Running the CompOmics Group at VIB and Ghent University, BelgiumLennart Martens

   PLoS Computational Biology, 9(11):e1003332
3. Asn₃, a Reliable, Robust, and Universal Lock Mass for Improved Accuracy in LC–MS and LC–MS/MSAn Staes, Jonathan Vandenbussche, Hans Demol, Marc Goethals, Şule Yilmaz, Niels Hulstaert, Sven Degroeve, Pieter Kelchtermans

   Analytical Chemistry, 85(22):11054-11060
4. Bringing proteomics into the clinic: The need for the field to finally take itself seriouslyLennart Martens

   PROTEOMICS – Clinical Applications, 7(5-6):388-391
5. CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assaysPaola Masuzzo, Niels Hulstaert, Lynn Huyck, Christophe Ampe, Marleen Van Troys, Lennart Martens

   Bioinformatics, 29(20):2661-2663
6. Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop reportYasset Perez-Riverol, Henning Hermjakob, Oliver Kohlbacher, Lennart Martens, David Creasy, Jürgen Cox, Felipe Leprevost, Baozhen Paul Shan

   Journal of Proteomics, 87:134-138
7. Crowdsourcing in proteomics: public resources lead to better experimentsHarald Barsnes, Lennart Martens

   Amino Acids, 44(4):1129-1137
8. Distributed computing and data storage in proteomics: Many hands make light work, and a stronger memoryKenneth Verheggen, Harald Barsnes, Lennart Martens

   PROTEOMICS, 14(4-5):367-377
9. Getting intimate with trypsin, the leading protease in proteomicsElien Vandermarliere, Michael Mueller, Lennart Martens

   Mass Spectrometry Reviews, 32(6):453-465
10. MS2PIP: a tool for MS/MS peak intensity predictionSven Degroeve, Lennart Martens

    Bioinformatics, 29(24):3199-3203
11. Predicting Tryptic Cleavage from Proteomics Data Using Decision Tree EnsemblesThomas Fannes, Elien Vandermarliere, Leander Schietgat, Sven Degroeve, Lennart Martens, Jan Ramon

    Journal of Proteome Research, 12(5):2253-2259
12. Pride-asap: Automatic fragment ion annotation of identified PRIDE spectraNiels Hulstaert, Florian Reisinger, Jonathan Rameseder, Harald Barsnes, Juan Antonio Vizcaíno, Lennart Martens

    Journal of Proteomics, 95:89-92
13. Protein structure as a means to triage proposed <scp>PTM</scp> sitesElien Vandermarliere, Lennart Martens

    PROTEOMICS, 13(6):1028-1035
14. ProteoCloud: A full-featured open source proteomics cloud computing pipelineThilo Muth, Julian Peters, Jonathan Blackburn, Erdmann Rapp, Lennart Martens

    Journal of Proteomics, 88:104-108
15. Proteome-derived Peptide Libraries to Study the Substrate Specificity Profiles of CarboxypeptidasesSebastian Tanco, Julia Lorenzo, Javier Garcia-Pardo, Sven Degroeve, Lennart Martens, Francesc Xavier Aviles, Kris Gevaert, Petra Van Damme

    Molecular &amp; Cellular Proteomics, 12(8):2096-2110
16. Resilience in the proteomics data ecosystem: How the field cares for its dataLennart Martens

    PROTEOMICS, 13(10-11):1548-1550

2012

1. A Complex Standard for Protein Identification, Designed by EvolutionMarc Vaudel, Julia M. Burkhart, Daniela Breiter, René P. Zahedi, Albert Sickmann, Lennart Martens

   Journal of Proteome Research, 11(10):5065-5071
2. Chromatographic retention time prediction for posttranslationally modified peptidesLuminita Moruz, An Staes, Joseph M. Foster, Maria Hatzou, Evy Timmerman, Lennart Martens, Lukas Käll

   PROTEOMICS, 12(8):1151-1159
3. Current methods for global proteome identificationMarc Vaudel, Albert Sickmann, Lennart Martens

   Expert Review of Proteomics, 9(5):519-532
4. Enabling Computational Proteomics by Public and Local Data Management SystemsKenny Helsens, Lennart Martens

   Circulation: Cardiovascular Genetics, 5(2):266-266
5. Integral Quantification Accuracy Estimation for Reporter Ion-based Quantitative Proteomics (iQuARI)Marc Vaudel, Julia M. Burkhart, Sonja Radau, René P. Zahedi, Lennart Martens, Albert Sickmann

   Journal of Proteome Research, 11(10):5072-5080
6. LNCipedia: a database for annotated human lncRNA transcript sequences and structuresPieter-Jan Volders, Kenny Helsens, Xiaowei Wang, Björn Menten, Lennart Martens, Kris Gevaert, Jo Vandesompele, Pieter Mestdagh

   Nucleic Acids Research, 41(D1):D246-D251
7. PRIDE Inspector: a tool to visualize and validate MS proteomics dataRui Wang, Antonio Fabregat, Daniel Ríos, David Ovelleiro, Joseph M Foster, Richard G Côté, Johannes Griss, Attila Csordas

   Nature Biotechnology, 30(2):135-137
8. Searching for a needle in a stack of needles: challenges in metaproteomics data analysisThilo Muth, Dirk Benndorf, Udo Reichl, Erdmann Rapp, Lennart Martens

   Molecular BioSystems, 9(4):578-585
9. Sigpep: Calculating unique peptide signature transition sets in a complete proteome backgroundKenny Helsens, Michael Mueller, Niels Hulstaert, Lennart Martens

   PROTEOMICS, 12(8):1142-1146
10. The Effect of Peptide Identification Search Algorithms on MS2-Based Label-Free Protein QuantificationSven Degroeve, An Staes, Pieter-Jan De Bock, Lennart Martens

    OMICS: A Journal of Integrative Biology, 16(9):443-448
11. The HUPO initiative on Model Organism Proteomes, iMOPAlexandra M. E. Jones, Ruedi Aebersold, Christian H. Ahrens, Rolf Apweiler, Katja Baerenfaller, Mark Baker, Emøke Bendixen, Steve Briggs

    PROTEOMICS, 12(3):340-345
12. The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing eventsNiklaas Colaert, Davy Maddelein, Francis Impens, Petra Van Damme, Kim Plasman, Kenny Helsens, Niels Hulstaert, Joël Vandekerckhove

    Nucleic Acids Research, 41(D1):D333-D337
13. The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange ConsortiumRichard G. Côté, Johannes Griss, José A. Dianes, Rui Wang, James C. Wright, Henk W.P. van den Toorn, Bas van Breukelen, Albert J.R. Heck

    Molecular &amp; Cellular Proteomics, 11(12):1682-1689
14. The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathwaysJulia M. Burkhart, Marc Vaudel, Stepan Gambaryan, Sonja Radau, Ulrich Walter, Lennart Martens, Jörg Geiger, Albert Sickmann

    Blood, 120(15):e73-e82
15. Towards a human proteomics atlasGiulia Gonnelli, Niels Hulstaert, Sven Degroeve, Lennart Martens

    Analytical and Bioanalytical Chemistry, 404(4):1069-1077
16. TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition ListsEric W. Deutsch, Matthew Chambers, Steffen Neumann, Fredrik Levander, Pierre-Alain Binz, Jim Shofstahl, David S. Campbell, Luis Mendoza

    Molecular &amp; Cellular Proteomics, 11(4):R111.015040
17. iTRAQ Data InterpretationMarc Vaudel, Julia Maria Burkhart, René Peiman Zahedi, Lennart Martens, Albert Sickmann

    Methods in Molecular Biology, 501-509

2011

1. A Case Study on the Comparison of Different Software Tools for Automated Quantification of PeptidesNiklaas Colaert, Joël Vandekerckhove, Lennart Martens, Kris Gevaert

   Methods in Molecular Biology, 373-398
2. A comparison of MS2‐based label‐free quantitative proteomic techniques with regards to accuracy and precisionNiklaas Colaert, Joël Vandekerckhove, Kris Gevaert, Lennart Martens

   PROTEOMICS, 11(6):1110-1113
3. A global analysis of peptide fragmentation variabilityHarald Barsnes, Ingvar Eidhammer, Lennart Martens

   PROTEOMICS, 11(6):1181-1188
4. A posteriori quality control for the curation and reuse of public proteomics dataJoseph M. Foster, Sven Degroeve, Laurent Gatto, Matthieu Visser, Rui Wang, Johannes Griss, Rolf Apweiler, Lennart Martens

   PROTEOMICS, 11(11):2182-2194
5. A reproducibility‐based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methodsSven Degroeve, Niklaas Colaert, Joël Vandekerckhove, Kris Gevaert, Lennart Martens

   PROTEOMICS, 11(6):1172-1180
6. Analysis of the Resolution Limitations of Peptide Identification AlgorithmsNiklaas Colaert, Sven Degroeve, Kenny Helsens, Lennart Martens

   Journal of Proteome Research, 10(12):5555-5561
7. Bioinformatics Analysis of a <i>Saccharomyces cerevisiae</i> N-Terminal Proteome Provides Evidence of Alternative Translation Initiation and Post-Translational N-Terminal AcetylationKenny Helsens, Petra Van Damme, Sven Degroeve, Lennart Martens, Thomas Arnesen, Joël Vandekerckhove, Kris Gevaert

   Journal of Proteome Research, 10(8):3578-3589
8. Bioinformatics Challenges in Mass Spectrometry-Driven ProteomicsLennart Martens

   Methods in Molecular Biology, 359-371
9. Bioinformatics Challenges in the Proteomic Analysis of Human PlasmaJoseph M. Foster, Lennart Martens

   Methods in Molecular Biology, 333-347
10. Combining quantitative proteomics data processing workflows for greater sensitivityNiklaas Colaert, Christophe Van Huele, Sven Degroeve, An Staes, Joël Vandekerckhove, Kris Gevaert, Lennart Martens

    Nature Methods, 8(6):481-483
11. Data Management in Mass Spectrometry-Based ProteomicsLennart Martens

    Methods in Molecular Biology, 321-332
12. Mass Spectrometry-Driven Proteomics: An IntroductionKenny Helsens, Lennart Martens, Joël Vandekerckhove, Kris Gevaert

    Methods in Molecular Biology, 1-27
13. Peptide identification quality controlMarc Vaudel, Julia M. Burkhart, Albert Sickmann, Lennart Martens, René P. Zahedi

    PROTEOMICS, 11(10):2105-2114
14. Quality Control in Proteomics

    PROTEOMICS, 11(6):1015-1016
15. RIBAR and xRIBAR: Methods for Reproducible Relative MS/MS-based Label-Free Protein QuantificationNiklaas Colaert, Kris Gevaert, Lennart Martens

    Journal of Proteome Research, 10(7):3183-3189
16. SearchGUI: An open‐source graphical user interface for simultaneous OMSSA and X!Tandem searchesMarc Vaudel, Harald Barsnes, Frode S. Berven, Albert Sickmann, Lennart Martens

    PROTEOMICS, 11(5):996-999
17. compomics-utilities: an open-source Java library for computational proteomicsHarald Barsnes, Marc Vaudel, Niklaas Colaert, Kenny Helsens, Albert Sickmann, Frode S Berven, Lennart Martens

    BMC Bioinformatics, 12(1)
18. iTRAQ protein quantification: A quality‐controlled workflowJulia M. Burkhart, Marc Vaudel, René P. Zahedi, Lennart Martens, Albert Sickmann

    PROTEOMICS, 11(6):1125-1134
19. jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM TransitionsKenny Helsens, Mi-Youn Brusniak, Eric Deutsch, Robert L. Moritz, Lennart Martens

    Journal of Proteome Research, 10(11):5260-5263
20. mzML—a Community Standard for Mass Spectrometry DataLennart Martens, Matthew Chambers, Marc Sturm, Darren Kessner, Fredrik Levander, Jim Shofstahl, Wilfred H. Tang, Andreas Römpp

    Molecular &amp; Cellular Proteomics, 10(1):R110.000133
21. thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome Discoverer <i>msf</i> FilesNiklaas Colaert, Harald Barsnes, Marc Vaudel, Kenny Helsens, Evy Timmerman, Albert Sickmann, Kris Gevaert, Lennart Martens

    Journal of Proteome Research, 10(8):3840-3843
22. “4D Biology for health and disease” workshop reportJan-Pieter Abrahams, Rolf Apweiler, Rudi Balling, Michela G. Bertero, Janusz M. Bujnicki, Naomi E. Chayen, Patrick Chène, Gary L. Corthals

    New Biotechnology, 28(4):291-293

2010

1. A report on the ESF workshop on quality control in proteomicsLennart Martens

   Molecular BioSystems, 6(6):935-938
2. FragmentationAnalyzer: An open‐source tool to analyze MS/MS fragmentation dataHarald Barsnes, Ingvar Eidhammer, Lennart Martens

   PROTEOMICS, 10(5):1087-1090
3. Nucleophilic Acyl Substitution via Aromatic Cation Activation of Carboxylic Acids: Rapid Generation of Acid Chlorides under Mild ConditionsDavid J. Hardee, Lyudmila Kovalchuke, Tristan H. Lambert

   Journal of the American Chemical Society, 132(14):5002-5003
4. OLS Dialog: An open-source front end to the Ontology Lookup ServiceHarald Barsnes, Richard G Côté, Ingvar Eidhammer, Lennart Martens

   BMC Bioinformatics, 11(1)
5. PRIDE and “Database on Demand” as Valuable Tools for Computational ProteomicsJuan Antonio Vizcaíno, Florian Reisinger, Richard Côté, Lennart Martens

   Methods in Molecular Biology, 93-105
6. PRIDE: Data Submission and AnalysisJuan Antonio Vizcaíno, Florian Reisinger, Richard Côté, Lennart Martens

   Current Protocols in Protein Science, 60(1)
7. Peptide and protein quantification: A map of the minefieldMarc Vaudel, Albert Sickmann, Lennart Martens

   PROTEOMICS, 10(4):650-670
8. Proteomics Databases and RepositoriesLennart Martens

   Methods in Molecular Biology, 213-227
9. Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further researchJuan Antonio Vizcaíno, Joseph M. Foster, Lennart Martens

   Journal of Proteomics, 73(11):2136-2146
10. Submitting Proteomics Data to PRIDE Using PRIDE ConverterHarald Barsnes, Juan Antonio Vizcaíno, Florian Reisinger, Ingvar Eidhammer, Lennart Martens

    Methods in Molecular Biology, 237-253
11. The Ontology Lookup Service: bigger and betterR. Cote, F. Reisinger, L. Martens, H. Barsnes, J. A. Vizcaino, H. Hermjakob

    Nucleic Acids Research, 38(Web Server):W155-W160
12. XTandem Parser: An open‐source library to parse and analyse X!Tandem MS/MS search resultsThilo Muth, Marc Vaudel, Harald Barsnes, Lennart Martens, Albert Sickmann

    PROTEOMICS, 10(7):1522-1524
13. jTraqX: A free, platform independent tool for isobaric tag quantitation at the protein levelThilo Muth, Daniela Keller, Stephanie Michaela Puetz, Lennart Martens, Albert Sickmann, Andreas M. Boehm

    PROTEOMICS, 10(6):1223-1225
14. jmzML, an open‐source Java API for mzML, the PSI standard for MS dataRichard G. Côté, Florian Reisinger, Lennart Martens

    PROTEOMICS, 10(7):1332-1335
15. ms_lims, a simple yet powerful open source laboratory information management system for MS‐driven proteomicsKenny Helsens, Niklaas Colaert, Harald Barsnes, Thilo Muth, Kristian Flikka, An Staes, Evy Timmerman, Steffi Wortelkamp

    PROTEOMICS, 10(6):1261-1264

2009

1. A HUPO test sample study reveals common problems in mass spectrometry–based proteomicsAlexander W Bell, Eric W Deutsch, Catherine E Au, Robert E Kearney, Ron Beavis, Salvatore Sechi, Tommy Nilsson, John J M Bergeron

   Nature Methods, 6(6):423-430
2. A guide to the Proteomics Identifications Database proteomics data repositoryJuan Antonio Vizcaíno, Richard Côté, Florian Reisinger, Joseph M. Foster, Michael Mueller, Jonathan Rameseder, Henning Hermjakob, Lennart Martens

   PROTEOMICS, 9(18):4276-4283
3. Algorithms and DatabasesLennart Martens, Rolf Apweiler

   Methods in Molecular Biology™, 245-259
4. Charting online OMICS resources: A navigational chart for clinical researchersJuan Antonio Vizcaíno, Michael Mueller, Henning Hermjakob, Lennart Martens

   PROTEOMICS – Clinical Applications, 3(1):18-29
5. Database on Demand – An online tool for the custom generation of FASTA‐formatted sequence databasesFlorian Reisinger, Lennart Martens

   PROTEOMICS, 9(18):4421-4424
6. Getting a grip on proteomics data – Proteomics Data Collection (ProDaC)Martin Eisenacher, Lennart Martens, Tanja Hardt, Michael Kohl, Harald Barsnes, Kenny Helsens, Jari Häkkinen, Fredrik Levander

   PROTEOMICS, 9(15):3928-3933
7. Improved visualization of protein consensus sequences by iceLogoNiklaas Colaert, Kenny Helsens, Lennart Martens, Joël Vandekerckhove, Kris Gevaert

   Nature Methods, 6(11):786-787
8. OMSSA Parser: An open‐source library to parse and extract data from OMSSA MS/MS search resultsHarald Barsnes, Steffen Huber, Albert Sickmann, Ingvar Eidhammer, Lennart Martens

   PROTEOMICS, 9(14):3772-3774
9. PRIDE Converter: making proteomics data-sharing easyHarald Barsnes, Juan Antonio Vizcaíno, Ingvar Eidhammer, Lennart Martens

   Nature Biotechnology, 27(7):598-599
10. Proteomics Data Collection – 4^th ProDaC Workshop 15 August 2008, Amsterdam, The NetherlandsMartin Eisenacher, Michael Kohl, Lennart Martens, Harald Barsnes, Tanja Hardt, Fredrik Levander, Jari Häkkinen, Rolf Apweiler

    PROTEOMICS, 9(2):218-222
11. Proteomics Data Collection – 5th ProDaC Workshop 4 March 2009, Kolympari, Crete, GreeceMartin Eisenacher, Lennart Martens, Harald Barsnes, Tanja Hardt, Michael Kohl, Jari Häkkinen, Rolf Apweiler, Helmut E. Meyer

    PROTEOMICS, 9(14):3626-3629
12. The PSI semantic validator: A framework to check MIAPE compliance of proteomics dataLuisa Montecchi‐Palazzi, Samuel Kerrien, Florian Reisinger, Bruno Aranda, Andrew R. Jones, Lennart Martens, Henning Hermjakob

    PROTEOMICS, 9(22):5112-5119
13. The Proteomics Identifications database: 2010 updateJuan Antonio Vizcaíno, Richard Côté, Florian Reisinger, Harald Barsnes, Joseph M. Foster, Jonathan Rameseder, Henning Hermjakob, Lennart Martens

    Nucleic Acids Research, 38(suppl_1):D736-D742
14. Toward a Successful Clinical Neuroproteomics The 11th HUPO Brain Proteome Project Workshop 3 March, 2009, Kolymbari, GreeceYoung Hye Kim, Katrin Marcus, Lea Tenenholz Grinberg, Heike Goehler, Jens Wiltfang, Christian Stephan, Martin Eisenacher, Tanja Hardt

    PROTEOMICS – Clinical Applications, 3(9):1012-1016
15. Using the PRIDE Proteomics Identifications Database for Knowledge Discovery and Data AnalysisPhilip Jones, Lennart Martens

    Methods in Molecular Biology, 297-307

2008

1. 6^th HUPO Annual World Congress – Proteomics Standards Initiative Workshop 6–10 October 2007, Seoul, KoreaSandra Orchard, Lennart Martens, Joshua Tasman, Pierre‐Alain Binz, Juan Pablo Albar, Henning Hermjakob

   PROTEOMICS, 8(7):1331-1333
2. Analysis of the experimental detection of central nervous system‐related genes in human brain and cerebrospinal fluid datasetsMichael Mueller, Juan Antonio Vizcaíno, Philip Jones, Richard Côté, David Thorneycroft, Rolf Apweiler, Henning Hermjakob, Lennart Martens

   PROTEOMICS, 8(6):1138-1148
3. Data Standards and Controlled Vocabularies for ProteomicsLennart Martens, Luisa Montecchi Palazzi, Henning Hermjakob

   Methods in Molecular Biology, 279-286
4. Human Proteinpedia enables sharing of human protein dataSuresh Mathivanan, Mukhtar Ahmed, Natalie G Ahn, Hainard Alexandre, Ramars Amanchy, Philip C Andrews, Joel S Bader, Brian M Balgley

   Nature Biotechnology, 26(2):164-167
5. OMSSAGUI: An open‐source user interface component to configure and run the OMSSA search engineRavi Tharakan, Lennart Martens, Jennifer E. Van Eyk, David R. Graham

   PROTEOMICS, 8(12):2376-2378
6. Peptizer, a Tool for Assessing False Positive Peptide Identifications and Manually Validating Selected ResultsKenny Helsens, Evy Timmerman, Joeül Vandekerckhove, Kris Gevaert, Lennart Martens

   Molecular &amp; Cellular Proteomics, 7(12):2364-2372
7. Proteomics Data Collection – 2^nd ProDaC Workshop 5 October 2007, Seoul, KoreaMartin Eisenacher, Tanja Hardt, Michael Hamacher, Lennart Martens, Jari Häkkinen, Fredrik Levander, Rolf Apweiler, Helmut E. Meyer

   PROTEOMICS, 8(7):1326-1330
8. Proteomics Data Collection – 3^rd ProDaC Workshop April 22^nd 2008, Toledo, SpainMartin Eisenacher, Tanja Hardt, Lennart Martens, Jari Häkkinen, Rolf Apweiler, Michael Hamacher, Helmut E. Meyer, Christian Stephan

   PROTEOMICS, 8(20):4163-4167
9. The HUPO Brain Proteome Project Wish List – Summary of the 9^th HUPO BPP Workshop 9–10 January 2008, BarbadosMichael Hamacher, Martin Eisenacher, Florian Tribl, Christian Stephan, Katrin Marcus, Tanja Hardt, Jens Wiltfang, Lennart Martens

   PROTEOMICS, 8(11):2160-2164
10. The Ontology Lookup Service: more data and better tools for controlled vocabulary queriesR. G. Cote, P. Jones, L. Martens, R. Apweiler, H. Hermjakob

    Nucleic Acids Research, 36(Web Server):W372-W376
11. Using the Proteomics Identifications Database (PRIDE)Lennart Martens, Phil Jones, Richard Côté

    Current Protocols in Bioinformatics, 21(1)

2007

1. A la carte proteomics with an emphasis on gel‐free techniquesKris Gevaert, Petra Van Damme, Bart Ghesquière, Francis Impens, Lennart Martens, Kenny Helsens, Joël Vandekerckhove

   PROTEOMICS, 7(16):2698-2718
2. Analyzing Large-Scale Proteomics Projects with Latent Semantic IndexingSebastian Klie, Lennart Martens, Juan Antonio Vizcaíno, Richard Côté, Phil Jones, Rolf Apweiler, Alexander Hinneburg, Henning Hermjakob

   Journal of Proteome Research, 7(1):182-191
3. Annotating the human proteome: Beyond establishing a parts listMichael Mueller, Lennart Martens, Rolf Apweiler

   Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1774(2):175-191
4. High Performance Proteomics: 7 ^th HUPO Brain Proteome Project Workshop March 7–9, 2007 Wellcome Trust Conference Centre, Hinxton, UKMichael Hamacher, Christian Stephan, Martin Eisenacher, Piotr Lewczuk, Jens Wiltfang, Lennart Martens, Juan Antonio Vizcaíno, Kyung‐Hoon Kwon

   PROTEOMICS, 7(15):2490-2496
5. Implementation and application of a versatile clustering tool for tandem mass spectrometry dataKristian Flikka, Jeroen Meukens, Kenny Helsens, Joël Vandekerckhove, Ingvar Eidhammer, Kris Gevaert, Lennart Martens

   PROTEOMICS, 7(18):3245-3258
6. Large-Scale Identification of N-Terminal Peptides in the Halophilic Archaea <i>Halobacterium </i><i>salinarum</i> and <i>Natronomonas </i><i>pharaonis</i>Michalis Aivaliotis, Kris Gevaert, Michaela Falb, Andreas Tebbe, Kosta Konstantinidis, Birgit Bisle, Christian Klein, Lennart Martens

   Journal of Proteome Research, 6(6):2195-2204
7. MascotDatfile: An open‐source library to fully parse and analyse MASCOT MS/MS search resultsKenny Helsens, Lennart Martens, Joël Vandekerckhove, Kris Gevaert

   PROTEOMICS, 7(3):364-366
8. PRIDE: new developments and new datasetsP. Jones, R. G. Cote, S. Y. Cho, S. Klie, L. Martens, A. F. Quinn, D. Thorneycroft, H. Hermjakob

   Nucleic Acids Research, 36(Database):D878-D883
9. Proteomics Data Collection – The 1^st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, FranceMartin Eisenacher, Tanja Hardt, Michael Hamacher, Lennart Martens, Jari Häkkinen, Fredrik Levander, Rolf Apweiler, Helmut E. Meyer

   PROTEOMICS, 7(17):3034-3037
10. Proteomics data validation: why all must provide dataLennart Martens, Henning Hermjakob

    Molecular BioSystems, 3(8):518-522
11. Proteomics for everyday use: Activities of the HUPO Brain Proteome Project during the 5^th HUPO World CongressMichael Hamacher, Christian Stephan, Martin Eisenacher, Andre van Hall, Katrin Marcus, Lennart Martens, Young Mok Park, Howard B. Gutstein

    PROTEOMICS, 7(7):1012-1015
12. The PSI formal document process and its implementation on the PSI websiteJuan Antonio Vizcaíno, Lennart Martens, Henning Hermjakob, Randall K. Julian, Norman W. Paton

    PROTEOMICS, 7(14):2355-2357
13. The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databasesRichard G Côté, Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler

    BMC Bioinformatics, 8(1)
14. The minimum information about a proteomics experiment (MIAPE)Chris F Taylor, Norman W Paton, Kathryn S Lilley, Pierre-Alain Binz, Randall K Julian, Andrew R Jones, Weimin Zhu, Rolf Apweiler

    Nature Biotechnology, 25(8):887-893

2006

1. A New Functional, Chemical Proteomics Technology To Identify Purine Nucleotide Binding Sites in Complex ProteomesXavier Hanoulle, Jozef Van Damme, An Staes, Lennart Martens, Marc Goethals, Joël Vandekerckhove, Kris Gevaert

   Journal of Proteome Research, 5(12):3438-3445
2. A comparison of the HUPO Brain Proteome Project pilot with other proteomics studiesLennart Martens, Michael Müller, Christian Stephan, Michael Hamacher, Kai A. Reidegeld, Helmut E. Meyer, Martin Blüggel, Joël Vandekerckhove

   PROTEOMICS, 6(18):5076-5086
3. Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phaseChristian Stephan, Kai A. Reidegeld, Michael Hamacher, André van Hall, Katrin Marcus, Chris Taylor, Philip Jones, Michael Müller

   PROTEOMICS, 6(18):5015-5029
4. Cell_motility: a cross-platform, open source application for the study of cell motion pathsLennart Martens, Geert Monsieur, Christophe Ampe, Kris Gevaert, Joël Vandekerckhove

   BMC Bioinformatics, 7(1)
5. Four Stage Liquid Chromatographic Selection of Methionyl Peptides for Peptide-Centric Proteome Analysis:  The Proteome of Human Multipotent Adult Progenitor CellsKris Gevaert, Jef Pinxteren, Hans Demol, Koen Hugelier, An Staes, Jozef Van Damme, Lennart Martens, Joël Vandekerckhove

   Journal of Proteome Research, 5(6):1415-1428
6. Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot studyMichael Mueller, Lennart Martens, Kai A. Reidegeld, Michael Hamacher, Christian Stephan, Martin Blüggel, Gerhard Körting, Daniel Chamrad

   PROTEOMICS, 6(18):5059-5075
7. HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategyMichael Hamacher, Rolf Apweiler, Georg Arnold, Albert Becker, Martin Blüggel, Odile Carrette, Christine Colvis, Michael J. Dunn

   PROTEOMICS, 6(18):4890-4898
8. Improving the reliability and throughput of mass spectrometry‐based proteomics by spectrum quality filteringKristian Flikka, Lennart Martens, Joël Vandekerckhove, Kris Gevaert, Ingvar Eidhammer

   PROTEOMICS, 6(7):2086-2094
9. PRIDE: a public repository of protein and peptide identifications for the proteomics communityP. Jones

   Nucleic Acids Research, 34(90001):D659-D663
10. Proteome-wide Characterization of N-Glycosylation Events by Diagonal ChromatographyBart Ghesquière, Jozef Van Damme, Lennart Martens, Joël Vandekerckhove, Kris Gevaert

    Journal of Proteome Research, 5(9):2438-2447
11. The HUPO Brain Proteome Project Jamboree: Centralised summary of the pilot studiesMichael Hamacher, Christian Stephan, Martin Blüggel, Daniel Chamrad, Gerhard Körting, Lennart Martens, Michael Müller, Henning Hermjakob

    PROTEOMICS, 6(6):1719-1721
12. The power of cooperative investigation: Summary and comparison of the HUPO Brain Proteome Project pilot study resultsKai A. Reidegeld, Michael Müller, Christian Stephan, Martin Blüggel, Michael Hamacher, Lennart Martens, Gerhard Körting, Daniel C. Chamrad

    PROTEOMICS, 6(18):4997-5014

2005

1. 5 ^th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK – Setting the Analysis FrameChristian Stephan, Michael Hamacher, Martin Blüggel, Gerhard Körting, Daniel Chamrad, Christian Scheer, Katrin Marcus, Kai A. Reidegeld

   PROTEOMICS, 5(14):3560-3562
2. Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosisPetra Van Damme, Lennart Martens, Jozef Van Damme, Koen Hugelier, An Staes, Joël Vandekerckhove, Kris Gevaert

   Nature Methods, 2(10):771-777
3. DBToolkit: processing protein databases for peptide-centric proteomicsL. Martens, J. Vandekerckhove, K. Gevaert

   Bioinformatics, 21(17):3584-3585
4. Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome ProjectMarcin Adamski, Thomas Blackwell, Rajasree Menon, Lennart Martens, Henning Hermjakob, Chris Taylor, Gilbert S. Omenn, David J. States

   PROTEOMICS, 5(13):3246-3261
5. Diagonal reverse-phase chromatography applications in peptide-centric proteomics: Ahead of catalogue-omics?Kris Gevaert, Petra Van Damme, Lennart Martens, Joël Vandekerckhove

   Analytical Biochemistry, 345(1):18-29
6. Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositoriesLennart Martens, Alexey I. Nesvizhskii, Henning Hermjakob, Marcin Adamski, Gilbert S. Omenn, Joël Vandekerckhove, Kris Gevaert

   PROTEOMICS, 5(13):3501-3505
7. Global phosphoproteome analysis on human HepG2 hepatocytes using reversed‐phase diagonal LCKris Gevaert, An Staes, Jozef Van Damme, Sara De Groot, Koen Hugelier, Hans Demol, Lennart Martens, Marc Goethals

   PROTEOMICS, 5(14):3589-3599
8. PRIDE: The proteomics identifications databaseLennart Martens, Henning Hermjakob, Philip Jones, Marcin Adamski, Chris Taylor, David States, Kris Gevaert, Joël Vandekerckhove

   PROTEOMICS, 5(13):3537-3545
9. The human platelet proteome mapped by peptide‐centric proteomics: A functional protein profileLennart Martens, Petra Van Damme, Jozef Van Damme, An Staes, Evy Timmerman, Bart Ghesquière, Grégoire R. Thomas, Joël Vandekerckhove

   PROTEOMICS, 5(12):3193-3204

2004

1. Global Differential Non-Gel Proteomics by Quantitative and Stable Labeling of Tryptic Peptides with Oxygen-18An Staes, Hans Demol, Jozef Van Damme, Lennart Martens, Joël Vandekerckhove, Kris Gevaert

   Journal of Proteome Research, 3(4):786-791
2. Reversible labeling of cysteine‐containing peptides allows their specific chromatographic isolation for non‐gel proteome studiesKris Gevaert, Bart Ghesquière, An Staes, Lennart Martens, Jozef Van Damme, Grégoire R. Thomas, Joël Vandekerckhove

   PROTEOMICS, 4(4):897-908

2003

1. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptidesKris Gevaert, Marc Goethals, Lennart Martens, Jozef Van Damme, An Staes, Grégoire R. Thomas, Joël Vandekerckhove

   Nature Biotechnology, 21(5):566-569

2002

1. Chromatographic Isolation of Methionine-containing Peptides for Gel-free Proteome AnalysisKris Gevaert, Jozef Van Damme, Marc Goethals, Grégoire R. Thomas, Bart Hoorelbeke, Hans Demol, Lennart Martens, Magda Puype

   Molecular &amp; Cellular Proteomics, 1(11):896-903