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- Dr. Lennart Martens is Professor of Systems Biology at Ghent University, and Group Leader of the Computational Omics and Systems Biology (CompOmics) group at VIB, both in Ghent, Belgium. He has been working in proteomics bioinformatics since his Master’s degree, which focused on the computational interpretation of peptide mass spectra. He then worked as a software developer and framework architect for a software company for a few years, before returning to Ghent University to pursue a Ph.D. focused on proteomics and proteomics informatics. During this time, he worked on the development of high-throughput peptide centric proteomics techniques and on bioinformatics tools to support these new approaches. In 2003 he started the PRIDE proteomics database at the EBI as a Marie Curie fellow of the European Commission. After obtaining his Ph.D. in Sciences: Biotechnology from Ghent University, he rejoined the PRIDE group at EBI, which he coordinated for several years before moving back to Ghent University to take up his current position. Prof. Martens served as the chair of the ABRF iPRG in 2011, sits on the Boards of DELSA (http://www.delsaglobal.org), the Royal Flemish Society for Chemistry – Proteomics, and the Belgian Proteomics Association. He serves as Academic Editor for PLoS ONE, IEEE Journal of Biomedical and Health Informatics and Open Proteomics, and holds Editorial Board positions at PROTEOMICS, BBA Proteins and Proteomics and Molecular BioSystems. An author on more than 130 peer-reviewed papers in the field, he has also co-written two popular Wiley textbooks: Computational Methods for Mass Spectrometry Proteomics (ISBN: 978-0-470-51297-5), and Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (ISBN: 978-1-119-96400-1).
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Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model
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- Journal Article
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MS²Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0
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msqrob2PTM : differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level
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- Journal Article
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Ionmob: a Python package for prediction of peptide collisional cross-section values.
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- Journal Article
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The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions
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- Journal Article
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Updated MS²PIP web server supports cutting-edge proteomics applications
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- Miscellaneous
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Biodiversity analysis of metaproteomics samples with Unipept : a comprehensive tutorial
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Unipept Desktop 2.0 : construction of targeted reference protein databases for metaproteogenomics analyses
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- Journal Article
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lesSDRF is more : maximizing the value of proteomics data through streamlined metadata annotation
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- Journal Article
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Toward an integrated machine learning model of a proteomics experiment
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- Journal Article
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Quality control for the target decoy approach for peptide identification
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Machine learning on large-scale proteomics data identifies tissue and cell-type specific proteins
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- Miscellaneous
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FAVA : high-quality functional association networks inferred from scRNA-seq and proteomics data
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- Journal Article
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psm_utils : a high-level python API for parsing and handling peptide-spectrum matches and proteomics search results
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Cov²MS : an automated and quantitative matrix-independent assay for mass spectrometric measurement of SARS-CoV-2 nucleocapsid protein
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Machine learning on large-scale proteomics data identifies tissue- and cell type-specific proteins
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- Miscellaneous
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Psm_utils : a high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results
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- Journal Article
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An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia
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- Journal Article
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Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes
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Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator
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A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
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MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates
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Orthogonal proteomics methods to unravel the HOTAIR interactome
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Pout2Prot : an efficient tool to create protein (sub)groups from Percolator Output Files
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- Miscellaneous
- open access
Ionbot : a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification
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Orthogonal proteomics methods to unravel the HOTAIR interactome
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Unipept visualizations : an interactive visualization library for biological data
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- Journal Article
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Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit
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DeepLC can predict retention times for peptides that carry as-yet unseen modifications
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- Conference Paper
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MS²DIP : highly accurate MS2 spectrum prediction for modified peptides & MS²Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates
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Critical Assessment of MetaProteome Investigation (CAMPI) : a multi-laboratory comparison of established workflows
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- Miscellaneous
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Pout2Prot : an efficient tool to create protein (sub)groups from Percolator output files
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- Miscellaneous
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Critical assessment of metaproteome investigation (CAMPI) : a multi-lab comparison of established workflows
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Spectral prediction features as a solution for the search space size problem in proteogenomics
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- Journal Article
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Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients
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The RNA landscape of the human placenta in health and disease
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Personalized proteome : comparing proteogenomics and open variant search approaches for single amino acid variant detection
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MegaGO : a fast yet powerful approach to assess functional gene ontology similarity across meta-omics data sets
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- Journal Article
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Unipept Desktop : a faster, more powerful metaproteomics results analysis tool
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Precursor intensity-based label-free quantification software tools for proteomic and multi-omic analysis within the galaxy platform
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- Miscellaneous
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Pitfalls in re-analysis of observational omics studies: a post-mortem of the human pathology atlas
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MSqRob takes the missing hurdle : uniting intensity- and count-based proteomics
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Simple peptide quantification approach for MS-based proteomics quality control
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Robust summarization and inference in proteome-wide label-free quantification
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COSS : a fast and user-friendly tool for spectral library searching
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Scop3P : a comprehensive resource of human phosphosites within their full context
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Community standards for open cell migration data
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Generalized calibration across liquid chromatography setups for generic prediction of small-molecule retention times
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Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis
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Unipept CLI 2.0 : adding support for visualizations and functional annotations
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The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis
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The age of data-driven proteomics : how machine learning enables novel workflows
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Removing the hidden data dependency of DIA with predicted spectral libraries
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ThermoRawFileParser : modular, scalable and cross-platform RAW file conversion
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Anatomy and evolution of database search engines : a central component of mass spectrometry based proteomic workflows
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- Conference Paper
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- open access
MS²PIP : fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
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Rescoring peptide-to-spectrum-matches based on predicted fragment ion intensities leads to an increased identification rate in metaproteomics
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Prediction-based reduction of the search space in metaproteomics
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- Journal Article
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A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry : application to the characterisation of metabolites in rat urine
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Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions
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Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
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Challenges and promise at the interface of metaproteomics and genomics : an overview of recent progress in metaproteogenomic data analysis
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- Conference Paper
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Fast and accurate MS² peak intensity predictions for multiple fragmentation methods, instruments and labeling techniques
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- Conference Paper
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A time of enlightenment : straightforward identification of protein modifications
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- Conference Paper
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Robust summarisation and inference for Label-Free Quantification
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Comprehensive and empirical evaluation of machine learning algorithms for small molecule LC retention time prediction
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An update on the moFF algorithm for label-free quantitative proteomics
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- Journal Article
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DoRes within CellMissy : dose-response analysis on cell migration and related data
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Unipept 4.0 : functional analysis of metaproteome data
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- Journal Article
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LNCipedia 5 : towards a reference set of human long non-coding RNAs
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Prediction-based reduction of the search space in metaproteomics
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Prediction-based reduction of the search space in metaproteomics
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The study of degradation mechanisms of glyco-engineered plant produced anti-rabies monoclonal antibodies E559 and 62-71-3
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Cross-linked peptide identification : a computational forest of algorithms
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Data-driven rescoring of metabolite annotations significantly improves sensitivity
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- Journal Article
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Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins
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Surveillance of myelodysplastic syndrome via migration analyses of blood neutrophils : a potential prognostic tool
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- Journal Article
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SQANTI : extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
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Analysis of invasion dynamics of matrix-embedded cells in a multisample format
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- Journal Article
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The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease
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- Journal Article
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The online Tabloid Proteome : an annotated database of protein associations
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High-throughput metaproteomics data analysis with Unipept : a tutorial
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Quality control in mass spectrometry-based proteomics
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- Journal Article
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A community proposal to integrate proteomics activities in ELIXIR
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An accessible proteogenomics informatics resource for cancer researchers
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- Journal Article
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MPA Portable : a stand-alone software package for analyzing metaproteome samples on the go
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Mass spectrometrists should search for all peptides, but assess only the ones they care about
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Methods to calculate spectrum similarity
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Computational quality control tools for mass spectrometry proteomics
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- Journal Article
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A golden age for working with public proteomics data
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- Journal Article
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N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana
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- Journal Article
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Noncoding after all : biases in proteomics data do not explain observed absence of lncRNA translation products
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- Journal Article
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An end-to-end software solution for the analysis of high-throughput single-cell migration data
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- Journal Article
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Unbiased protein association study on the public human proteome reveals biological connections between co-occurring protein pairs
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- Journal Article
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MAPPI-DAT : data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform
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sfinx : an R package for the elimination of false positives from affinity purification-mass spectrometry datasets
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Protein complex analysis : from raw protein lists to protein interaction networks
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- Journal Article
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Identification of quantitative proteomic differences between Mycobacterium tuberculosis lineages with altered virulence
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- Journal Article
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Exploring the potential of public proteomics data
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Database search engines : paradigms, challenges and solutions
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Unsupervised quality assessment of mass spectrometry proteomics experiments by multivariate quality control metrics
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- Journal Article
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Designing biomedical proteomics experiments : state-of-the-art and future perspectives
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Metaproteomic data analysis at a glance : advances in computational microbial community proteomics
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Resolution of protein structure by mass spectrometry
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The Lyssavirus glycoprotein : a key to cross-immunity
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The impact of sequence database choice on metaproteomic results in gut microbiota studies
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Human proteome project mass spectrometry data interpretation guidelines 2.1
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moFF : a robust and automated approach to extract peptide ion intensities
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- Journal Article
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Up-to-date workflow for plant (phospho)proteomics identifies differential drought-responsive phosphorylation events in maize leaves
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Proteome-scale binary interactomics in human cells
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Xilmass: a new approach toward the identification of cross-linked peptides
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A pipeline for differential proteomics in unsequenced species
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- Journal Article
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An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics
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- Journal Article
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Taking aim at moving targets in computational cell migration
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SFINX : straightforward filtering index for affinity purification mass spectrometry data analysis
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- Journal Article
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Phospho-iTRAQ data article : assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry
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JSparklines : making tabular proteomics data come alive
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Open-source, platform-independent library and online scripting environment for accessing thermo scientific RAW files
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- Journal Article
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Pladipus enables universal distributed computing in proteomics bioinformatics
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- Journal Article
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MS²PIP prediction server : compute and visualize MS² peak intensity predictions for CID and HCD fragmentation
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Ariadne's thread : a robust software solution leading to automated absolute and relative quantification of SRM data
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Colonic metaproteomic signatures of active bacteria and the host in obesity
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Navigating through metaproteomics data : a logbook of database searching
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- Journal Article
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The iceLogo web server and SOAP service for determining protein consensus sequences
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Limited proteolysis combined with stable isotope labeling reveals conformational changes in protein (pseudo)kinases upon binding small molecules
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- Journal Article
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- open access
sORFs.org : a repository of small ORFs identified by ribosome profiling
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The MetaProteomeAnalyzer : a powerful open-source software suite for metaproteomics data analysis and interpretation
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Scop3D : three-dimensional visualization of sequence conservation
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Viewing the proteome : how to visualize proteomics data?
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A decoy-free approach to the identification of peptides
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iMonDB : mass spectrometry quality control through instrument monitoring
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- Miscellaneous
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Managing expectations when publishing tools and methods for computational proteomics
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- Journal Article
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Ryanodine receptors are targeted by anti-apoptotic Bcl-X-L involving its BH4 domain and Lys87 from its BH3 domain
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PepShell : visualization of conformational proteomics data
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Structural investigation of B-Raf paradox breaker and inducer inhibitors
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PeptideShaker enables reanalysis of MS-derived proteomics data sets
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An open data ecosystem for cell migration research
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Summarization vs. peptide-based models in label-free quantitative proteomics : performance, pitfalls, and data analysis guidelines
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- Journal Article
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An update on LNCipedia : a database for annotated human lncRNA sequences
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An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes
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Phospho-iTRAQ : assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry
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- Miscellaneous
- open access
Informaticawetenschappen in het leerplichtonderwijs
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Unraveling the specificities of the different human methionine sulfoxide reductases
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qcML: an exchange format for quality control metrics from mass spectrometry experiments
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jqcML: an open-source Java API for mass spectrometry quality control data in the qcML format
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Shedding light on black boxes in protein identification
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ProteomeXchange provides globally coordinated proteomics data submission and dissemination
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Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory
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Machine learning applications in proteomics research: how the past can boost the future
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Toward more transparent and reproducible omics studies through a common metadata checklist and data publications
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Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways
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DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra
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- Journal Article
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Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics
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Delsa workshop IV : launching the Quantified Human Initiative
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LNCipedia 2.0: a database for annotated human lncRNA transcript sequences and structures
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LNCipedia: a database for annotated human lncRNA transcript sequences and structures
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LNCipedia 2.0: a database for annotated human lncRNA transcript sequences and structures
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Pride-asap: automatic fragment ion annotation of identified PRIDE spectra
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- Journal Article
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About dice, bouldering, and team empowerment: running the CompOmics group at VIB and Ghent University, Belgium
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In praise of open research measures
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D-score: a search engine independent MD-score
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Proteome-derived peptide libraries to study the substrate specificity profiles of carboxypeptidases
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Early targets of MIR-34A in neuroblastoma
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Getting intimate with trypsin, the leading protease in proteomics
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Asn₃, a reliable, robust, and universal lock mass for improved accuracy in LC-MS and LC-MS/MS
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- Journal Article
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MS²PIP: a tool for MS/MS peak intensity prediction
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CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays
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- Journal Article
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Resilience in the proteomics data ecosystem: how the field cares for its data
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Bringing proteomics into the clinic: the need for the field to finally take itself seriously
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Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report
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ProteoCloud: a full-featured open source proteomics cloud computing pipeline
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- Conference Paper
- C3
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PiTRAQ, a strategy to simultaneously correlate protein expression and phosphorylation stoichiometry between different samples: evaluation on different mass spectrometers
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Predicting tryptic cleavage from proteomics data using decision tree ensembles
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Crowdsourcing in proteomics: public resources lead to better experiments
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Protein structure as a means to triage proposed PTM sites
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Searching for a needle in a stack of needles: challenges in metaproteomics data analysis
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- Journal Article
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The Online Protein Processing Resource (TOPPR) : a database and analysis platform for protein processing events
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- Journal Article
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LNCipedia : a database for annotated human lncRNA transcript sequences and structures
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Lncipedia: a novel database for annotated lncRNA sequences and structures
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- Conference Paper
- C3
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Evaluation of a strategy for parallel protein phosphorylation and expression analysis
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iTRAQ data interpretation
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The PRoteomics IDEntification (PRIDE) converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium
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Current methods for global proteome identification
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Enabling computational proteomics by public and local data management systems
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The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways
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A complex standard for protein identification, designed by evolution
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Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI)
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Towards a human proteomics atlas
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The effect of peptide identification search algorithms on MS2-based label-free protein quantification
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Chromatographic retention time prediction for posttranslationally modified peptides
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Sigpep: calculating unique peptide signature transition sets in a complete proteome background
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The HUPO initiative on Model Organism Proteomes, iMOP
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TraML: a standard format for exchange of selected reaction monitoring transition lists
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PRIDE Inspector: a tool to visualize and validate MS proteomics data
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A case study on the comparison of different software tools for automated quantification of peptides
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N-Terminal combined fractional diagonal chromatographic (COFRADIC) analysis of the human platelet proteome
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'4D Biology for health and disease' workshop report
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Analysis of the resolution limitations of peptide identification algorithms
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Quality control in proteomics
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jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions
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thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files
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Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation
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A posteriori quality control for the curation and reuse of public proteomics data
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Combining quantitative proteomics data processing workflows for greater sensitivity
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Peptide identification quality control
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- Journal Article
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RIBAR and xRIBAR: methods for reproducible relative MS/MS-based label-free protein quantification
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- Journal Article
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compomics-utilities: an open-source Java library for computational proteomics
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SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches
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mzML: a community standard for mass spectrometry data
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A global analysis of peptide fragmentation variability
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iTRAQ protein quantification: a quality-controlled workflow
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A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision
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A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods
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- Journal Article
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The Proteomics Identifications database : 2010 update
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- Journal Article
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The Ontology Lookup Service : bigger and better
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Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research
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jTraqX: a free, platform independent tool for isobaric tag quantitation at the protein level
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XTandem parser: an open-source library to parse and analyse X!Tandem MS/MS search results
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jmzML, an open-source Java API for mzML, the PSI standard for MS data
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A report on the ESF workshop on quality control in proteomics
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High-throughput proteomics and bioinformatics : joined at the hip
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FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data
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ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics
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- Journal Article
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- open access
OLS Dialog : an open-source front end to the Ontology Lookup Service
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Peptide and protein quantification: A map of the minefield
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PRIDE Converter: making proteomics data-sharing easy
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A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
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Proteomics data collection: 5th ProDaC workshop: 4 March 2009, Kolympari, Crete, Greece
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Proteomics data collection : 4th ProDaC workshop: 15 August 2008, Amsterdam, The Netherlands
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The PSI semantic validator: a framework to check MIAPE compliance of proteomics data
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Database on Demand: an online tool for the custom generation of FASTA-formatted sequence databases
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Charting online OMICS resources: a navigational chart for clinical researchers
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OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results
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Toward a successful clinical neuroproteomics : the 11th HUPO Brain Proteome Project Workshop 3 March, 2009, Kolymbari, Greece
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A guide to the Proteomics Identifications Database proteomics data repository
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Improved visualization of protein consensus sequences by iceLogo
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Getting a grip on proteomics data: Proteomics Data Collection (ProDaC)
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- Journal Article
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The Ontology Lookup Service : more data and better tools for controlled vocabulary queries
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Proteomics data collection: 3rd ProDaC workshop April 22nd 2008, Toledo, Spain
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The HUPO Brain Proteome project wish list : summary of the 9th HUPO BPP Workshop 9-10 January 2008, Barbados
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- Journal Article
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PRIDE : new developments and new datasets
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Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
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OMSSAGUI: an open-source user interface component to configure and run the OMSSA search engine
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6th HUPO Annual World Congress : Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea
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Proteomics data collection : 2nd ProDaC workshop : 5 October 2007, Seoul, Korea
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Analyzing large-scale proteomics projects with latent semantic indexing
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Peptizer: a tool for assessing false positive peptide identifications and manually validating selected results
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Human Proteinpedia enables sharing of human protein data
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- Journal Article
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The Protein Identifier Cross-Referencing (PICR) service : reconciling protein identifiers across multiple source databases
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High performance proteomics : 7th HUPO Brain Proteome project workshop, March 7-9, 2007, Wellcome Trust Conference Centre, Hinxton, UK