Levin, Nikita;Saylan, Cemil Can;Lapin, Joel;Demyanenko, Yana;Yang, Kevin L.;Sidda, John;Nesvizhskii, Alexey I.;Wilhelm, Mathias;Mohammed, Shabaz
Integration of alternative fragmentation techniques into standard LC-MS workflows using a single deep learning model enhances proteome coverage
Nature Methods
2026

Klaproth-Andrade, Daniela;Bruns, Yanik;Gabriel, Wassim;Nix, Christian;Bergant, Valter;Pichlmair, Andreas;Wilhelm, Mathias;Gagneur, Julien
Modanovo: A Unified Model for Post-translational Modification-Aware De Novo Sequencing Using Experimental Spectra From In Vivo and Synthetic Peptides
Molecular & Cellular Proteomics
2026
25
2
101501

Gholizadeh, Elham;Zangene, Ehsan;Vadadokhau, Uladzislau;Ritz, Danilo;Miettinen, Juho J.;Soliymani, Rabah;Baumann, Marc;Wilhelm, Mathias;Kankuri, Esko;Haynes, Paul A.;Heckman, Caroline A.;Saei, Amir A.;Jafari, Mohieddin
Solubility based mechanistic profiling of combinatorial drug therapy
Nature Communications
2026
17
1

Meelker González, Rebecca;Laposchan, Sophia;Riedel, Erik;Fürst, Anna;O’Sullivan, Naomi;Gabriel, Wassim;Wilhelm, Mathias;Knolle, Percy A.;Médard, Guillaume;Kuster, Bernhard;Lee, Chien-Yun
High-throughput chemical proteomics workflow for profiling protein citrullination dynamics
Nature Communications
2026
17
1

Picciani, Mario;Soleymaniniya, Armin;Müller, Julian;Sakhteman, Amirhossein;Tzanakis, Konstantinos;Bernett, Judith;Kahl, Elias;Hamood, Firas;Kersting, Johannes;Pourjam, Mohsen;Nagai, Luis Augusto Eijy;List, Markus;Kuster, Bernhard;The, Matthew;Wilhelm, Mathias
Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale
Nucleic Acids Research
2025

Lautenbacher, Ludwig;Yang, Kevin L.;Kockmann, Tobias;Panse, Christian;Gabriel, Wassim;Bold, Dulguun;Kahl, Elias;Chambers, Matthew;MacLean, Brendan X.;Li, Kai;Yu, Fengchao;Searle, Brian C.;Wilburn, Damien Beau;Shahneh, Mohammad Reza Zare;Hong, Yuhui;Tang, Haixu;Wang, Mingxun;Gabriels, Ralf;Bouwmeester, Robbin;Devreese, Robbe;Angelis, Jesse;Sabidó, Eduard;Schmidt, Tobias K.;Nesvizhskii, Alexey I.;Wilhelm, Mathias
Koina: Democratizing machine learning for proteomics research
Nature Communications
2025
16
1

Rajczewski, Andrew T.;Mehta, Subina;Wagner, Reid;Gabriel, Wassim;Johnson, James;Do, Katherine;Vintila, Simina;Wilhelm, Mathias;Kleiner, Manuel;Searle, Brian C.;Griffin, Timothy J.;Jagtap, Pratik D.
Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset
Journal of Proteomics
2026
322
105549

Kalhor, Mostafa;Saylan, Cemil Can;Picciani, Mario;Fischer, Lutz;Schimweg, Falk Boudewijn;Lapin, Joel;Rappsilber, Juri;Wilhelm, Mathias
Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures
Nature Communications
2025
16
1

Elhamraoui, Zahra;Borràs, Eva;Wilhelm, Mathias;Sabidó, Eduard
MSCI: an open-source Python package for information content assessment of peptide fragmentation spectra
Bioinformatics Advances
2024
5
1

Lapin, Joel;Nilsson, Alfred;Wilhelm, Mathias;Käll, Lukas
Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra
Journal of Proteome Research
2025