| Year |
Citation |
Score |
| 2025 |
Declercq A, Devreese R, Scheid J, Jachmann C, Van Den Bossche T, Preikschat A, Gomez-Zepeda D, Rijal JB, Hirschler A, Krieger JR, Srikumar T, Rosenberger G, Martelli C, Trede D, Carapito C, et al. TIMSRescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MSRescore. Journal of Proteome Research. PMID 39915959 DOI: 10.1021/acs.jproteome.4c00609 |
0.628 |
|
| 2025 |
Van Den Bossche T, Beslic D, van Puyenbroeck S, Suomi T, Holstein T, Martens L, Elo LL, Muth T. Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing. Proteomics. e202400321. PMID 39888246 DOI: 10.1002/pmic.202400321 |
0.755 |
|
| 2025 |
Moortele TV, Verschaffelt P, Huang Q, Doncheva NT, Holstein T, Jachmann C, Dawyndt P, Martens L, Mesuere B, Van Den Bossche T. PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways. Molecular & Cellular Proteomics : McP. 100918. PMID 39880083 DOI: 10.1016/j.mcpro.2025.100918 |
0.613 |
|
| 2025 |
Vande Moortele T, Devlaminck B, Van de Vyver S, Van Den Bossche T, Martens L, Dawyndt P, Mesuere B, Verschaffelt P. Unipept in 2024: Expanding Metaproteomics Analysis with Support for Missed Cleavages and Semitryptic and Nontryptic Peptides. Journal of Proteome Research. 24: 949-954. PMID 39792626 DOI: 10.1021/acs.jproteome.4c00848 |
0.54 |
|
| 2024 |
Klein J, Lam H, Mak TD, Bittremieux W, Perez-Riverol Y, Gabriels R, Shofstahl J, Hecht H, Binz PA, Kawano S, Van Den Bossche T, Carver J, Neely BA, Mendoza L, Suomi T, et al. The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF. Analytical Chemistry. 96: 18491-18501. PMID 39514576 DOI: 10.1021/acs.analchem.4c04091 |
0.353 |
|
| 2024 |
Rajczewski AT, Blakeley-Ruiz JA, Meyer A, Vintila S, McIlvin MR, Van Den Bossche T, Searle BC, Griffin TJ, Saito MA, Kleiner M, Jagtap PD. Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome. Biorxiv : the Preprint Server For Biology. PMID 39345414 DOI: 10.1101/2024.09.18.613707 |
0.383 |
|
| 2024 |
Van Den Bossche T, Verschaffelt P, Vande Moortele T, Dawyndt P, Martens L, Mesuere B. Biodiversity Analysis of Metaproteomics Samples with Unipept: A Comprehensive Tutorial. Methods in Molecular Biology (Clifton, N.J.). 2836: 183-215. PMID 38995542 DOI: 10.1007/978-1-0716-4007-4_11 |
0.561 |
|
| 2024 |
Beltrao P, Van Den Bossche T, Gabriels R, Holstein T, Kockmann T, Nameni A, Panse C, Schlapbach R, Lautenbacher L, Mattanovich M, Nesvizhskii A, Van Puyvelde B, Scheid J, Schwämmle V, Strauss M, et al. Proceedings of the EuBIC-MS developers meeting 2023. Journal of Proteomics. 105246. PMID 38964537 DOI: 10.1016/j.jprot.2024.105246 |
0.323 |
|
| 2024 |
Bielow C, Hoffmann N, Jimenez-Morales D, Van Den Bossche T, Vizcaíno JA, Tabb DL, Bittremieux W, Walzer M. Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java. Journal of the American Society For Mass Spectrometry. PMID 38918936 DOI: 10.1021/jasms.4c00174 |
0.386 |
|
| 2023 |
Sakarika M, Kerckhof FM, Van Peteghem L, Pereira A, Van Den Bossche T, Bouwmeester R, Gabriels R, Van Haver D, Ulčar B, Martens L, Impens F, Boon N, Ganigué R, Rabaey K. The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions. Microbial Cell Factories. 22: 254. PMID 38072930 DOI: 10.1186/s12934-023-02265-1 |
0.692 |
|
| 2023 |
Claeys T, Van Den Bossche T, Perez-Riverol Y, Gevaert K, Vizcaíno JA, Martens L. lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation. Nature Communications. 14: 6743. PMID 37875519 DOI: 10.1038/s41467-023-42543-5 |
0.55 |
|
| 2023 |
Verschaffelt P, Tanca A, Abbondio M, Van Den Bossche T, Moortele TV, Dawyndt P, Martens L, Mesuere B. Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics Analyses. Journal of Proteome Research. PMID 37459443 DOI: 10.1021/acs.jproteome.3c00091 |
0.594 |
|
| 2022 |
Shiferaw GA, Gabriels R, Bouwmeester R, Van Den Bossche T, Vandermarliere E, Martens L, Volders PJ. Sensitive and Specific Spectral Library Searching with CompOmics Spectral Library Searching Tool and Percolator. Journal of Proteome Research. 21: 1365-1370. PMID 35446579 DOI: 10.1021/acs.jproteome.2c00075 |
0.615 |
|
| 2022 |
LeDuc RD, Deutsch EW, Binz PA, Fellers RT, Cesnik AJ, Klein JA, Van Den Bossche T, Gabriels R, Yalavarthi A, Perez-Riverol Y, Carver J, Bittremieux W, Kawano S, Pullman B, Bandeira N, et al. Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. Journal of Proteome Research. PMID 35290070 DOI: 10.1021/acs.jproteome.1c00771 |
0.36 |
|
| 2022 |
Schallert K, Verschaffelt P, Mesuere B, Benndorf D, Martens L, Van Den Bossche T. : An Efficient Tool to Create Protein (Sub)groups from Percolator Output Files. Journal of Proteome Research. 21: 1175-1180. PMID 35143215 DOI: 10.1021/acs.jproteome.1c00685 |
0.541 |
|
| 2021 |
Van Den Bossche T, Arntzen MØ, Becher D, Benndorf D, Eijsink VGH, Henry C, Jagtap PD, Jehmlich N, Juste C, Kunath BJ, Mesuere B, Muth T, Pope PB, Seifert J, Tanca A, et al. The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. Microbiome. 9: 243. PMID 34930457 DOI: 10.1186/s40168-021-01176-w |
0.661 |
|
| 2021 |
Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, et al. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications. 12: 7305. PMID 34911965 DOI: 10.1038/s41467-021-27542-8 |
0.734 |
|
| 2021 |
Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, ... ... Van Den Bossche T, et al. A proteomics sample metadata representation for multiomics integration and big data analysis. Nature Communications. 12: 5854. PMID 34615866 DOI: 10.1038/s41467-021-26111-3 |
0.639 |
|
| 2021 |
Van Puyvelde B, Van Uytfanghe K, Tytgat O, Van Oudenhove L, Gabriels R, Bouwmeester R, Daled S, Van Den Bossche T, Ramasamy P, Verhelst S, De Clerck L, Corveleyn L, Willems S, Debunne N, Wynendaele E, et al. Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients. Jacs Au. 1: 750-765. PMID 34254058 DOI: 10.1021/jacsau.1c00048 |
0.659 |
|
| 2021 |
Bittremieux W, Bouyssié D, Dorfer V, Locard-Paulet M, Perez-Riverol Y, Schwämmle V, Uszkoreit J, Van Den Bossche T. The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS): an open community for bioinformatics training and research. Rapid Communications in Mass Spectrometry : Rcm. e9087. PMID 33861485 DOI: 10.1002/rcm.9087 |
0.306 |
|
| 2021 |
Verschaffelt P, Van Den Bossche T, Gabriel W, Burdukiewicz M, Soggiu A, Martens L, Renard BY, Schiebenhoefer H, Mesuere B. MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets. Journal of Proteome Research. PMID 33661648 DOI: 10.1021/acs.jproteome.0c00926 |
0.564 |
|
| 2021 |
Verschaffelt P, Van Den Bossche T, Martens L, Dawyndt P, Mesuere B. Unipept Desktop: A Faster, More Powerful Metaproteomics Results Analysis Tool. Journal of Proteome Research. PMID 33401902 DOI: 10.1021/acs.jproteome.0c00855 |
0.586 |
|
| 2020 |
Muñoz-Benavent M, Hartkopf F, Van Den Bossche T, Piro VC, García-Ferris C, Latorre A, Renard BY, Muth T. Erratum: gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms. Nar Genomics and Bioinformatics. 2: lqaa083. PMID 33577626 DOI: 10.1093/nargab/lqaa083 |
0.626 |
|
| 2020 |
Muñoz-Benavent M, Hartkopf F, Van Den Bossche T, Piro VC, García-Ferris C, Latorre A, Renard BY, Muth T. gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms. Nar Genomics and Bioinformatics. 2: lqaa058. PMID 33575609 DOI: 10.1093/nargab/lqaa058 |
0.687 |
|
| 2020 |
Verschaffelt P, Van Thienen P, Van Den Bossche T, Van der Jeugt F, De Tender C, Martens L, Dawyndt P, Mesuere B. Unipept CLI 2.0: adding support for visualisations and functional annotations. Bioinformatics (Oxford, England). PMID 32492134 DOI: 10.1093/Bioinformatics/Btaa553 |
0.592 |
|
| 2020 |
Van Den Bossche T, Verschaffelt P, Schallert K, Barsnes H, Dawyndt P, Benndorf D, Renard BY, Mesuere B, Martens L, Muth T. Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis. Journal of Proteome Research. PMID 32431147 DOI: 10.1021/Acs.Jproteome.0C00136 |
0.768 |
|
| 2019 |
Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, ... ... Van Den Bossche T, et al. Proteomics Standards Initiative Extended FASTA Format (PEFF). Journal of Proteome Research. PMID 31081335 DOI: 10.1021/Acs.Jproteome.9B00064 |
0.692 |
|
| 2019 |
Schiebenhoefer H, Van Den Bossche T, Fuchs S, Renard BY, Muth T, Martens L. Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis. Expert Review of Proteomics. PMID 31002542 DOI: 10.1080/14789450.2019.1609944 |
0.767 |
|
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