Learning Isoform Fingerprints to Discover the Molecular Diversity of Life

Project Information

ORIGIN

Grant agreement ID: 101077037

DOI

10.3030/101077037

EC signature date 15 December 2022

Start date 1 June 2023

End date 31 May 2028

Funded under

• European Research Council (ERC)

Total cost

€ 1 498 939,00

EU contribution

€ 1 498 939,00

Coordinated by

TECHNISCHE UNIVERSITAET MUENCHEN
Germany

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (8)

Unifying the analysis of bottom-up proteomics data with CHIMERYS

Author(s): Martin Frejno; Michelle T. Berger; Johanna Tüshaus; Alexander Hogrebe; Florian Seefried; Michael Graber; Patroklos Samaras; Samia Ben Fredj; Vishal Sukumar; Layla Eljagh; Igor Brohnshtein; Lizi Mamisashvili; Markus Schneider; Siegfried Gessulat; Tobias Schmidt; Bernhard Kuster; Daniel P. Zolg; Mathias Wilhelm
Published in: Nature Methods, 2024, ISSN 1548-7105
Publisher: Nature Publishing Group
DOI: 10.1038/S41592-025-02663-W

SWAPS: A Modular Deep-Learning Empowered Peptide Identity Propagation Framework Beyond Match-Between-Run

Author(s): Zixuan Xiao, Johanna Tüshaus, Bernhard Kuster, Matthew The, Mathias Wilhelm
Published in: Journal of Proteome Research, 2025, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/ACS.JPROTEOME.4C00972

Peptide Property Prediction for Mass Spectrometry Using AI: An Introduction to State of the Art Models

Author(s): Jesse Angelis; Eva Ayla Schröder; Zixuan Xiao; Wassim Gabriel; Mathias Wilhelm
Published in: PROTEOMICS, 2025, ISSN 1615-9861
Publisher: Wiley
DOI: 10.1002/PMIC.202400398

Deep Learning Enhances Precision of Citrullination Identification in Human and Plant Tissue Proteomes

Author(s): Wassim Gabriel; Rebecca Meelker González; Sophia Laposchan; Erik Riedel; Gönül Dündar; Brigitte Poppenberger; Mathias Wilhelm; Chien-Yun Lee
Published in: Molecular&Cellular Proteomics, 2024, ISSN 1535-9484
Publisher: Elsevier Inc
DOI: 10.1101/2024.10.11.617769

Oktoberfest: Open‐source spectral library generation and rescoring pipeline based on Prosit

Author(s): Picciani, Mario; Gabriel, Wassim; Giurcoiu, Victor‐George; Shouman, Omar; Hamood, Firas; Lautenbacher, Ludwig; Jensen, Cecilia Bang; Müller, Julian; Kalhor, Mostafa; Soleymaniniya, Armin; Kuster, Bernhard; The, Matthew; Wilhelm, Mathias
Published in: PROTEOMICS, 2023, ISSN 1615-9861
Publisher: Wiley
DOI: 10.1002/PMIC.202300112

ProSIMSIt: The Best of Both Worlds in Data-Driven Rescoring and Identification Transfer

Author(s): Firas Hamood, Wassim Gabriel, Pia Pfeiffer, Bernhard Kuster, Mathias Wilhelm, Matthew The
Published in: Journal of Proteome Research, 2025, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/ACS.JPROTEOME.4C00967

To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry

Author(s): Naim Abdul-Khalek, Mario Picciani, Omar Shouman, Reinhard Wimmer, Michael Toft Overgaard, Mathias Wilhelm, Simon Gregersen Echers
Published in: Journal of Proteome Research, 2025, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/ACS.JPROTEOME.4C00973

Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra

Author(s): Joel Lapin, Alfred Nilsson, Mathias Wilhelm, Lukas Käll
Published in: Journal of Proteome Research, 2025, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/ACS.JPROTEOME.5C00063

Conference proceedings (1)

PROSPECT PTMs: Rich Labeled Tandem Mass Spectrometry Dataset of Modified Peptides for Machine Learning in Proteomics

Author(s): Wassim Gabriel, Omar Shouman, Eva Ayla Schröder, Florian Bößl, Mathias Wilhelm
Published in: Advances in Neural Information Processing Systems 37 (NeurIPS 2024), 2024
Publisher: NeurIPS 2024