Computational Proteomics Training European Innovative Network

Informazioni relative al progetto

PROTrEIN

ID dell’accordo di sovvenzione: 956148

DOI

10.3030/956148

Progetto chiuso

Data della firma CE 18 Agosto 2020

Data di avvio 1 Gennaio 2021

Data di completamento 31 Dicembre 2024

Finanziato da

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Costo totale

€ 3 917 904,12

Contributo UE

€ 3 917 904,12

Coordinato da

FUNDACIO CENTRE DE REGULACIO GENOMICA
Spain

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

Documents, reports (6)

Mid-term report on dissemination activities

Midterm report on dissemination activities

Report on Wikipedia editathon and blog site
Report on organised training activities year 1+2

Report on organised training activities year 12

Final report on dissemination activities
Report on Advertisement of vacancies in media

Report on Advertisement of vacancies in media.

Report on organised training activities year 3+4

Other (6)

Open-source tool for the real-time control of mass spectrometry experiments
Release of a new version of MaxQuant and Perseus software suites
Final PROTrEIN Symposium
New file format including ion mobility data to be incorporated into standard proteomics workflows
Web-interface to access the developed learning tools and re-scoring mechanism for crosslinked peptides
PROTrEIN (art) installation

Open Research Data Pilot (1)

Data Management Plan (DMP)

Data Management Plan DMP

Websites, patent fillings, videos etc. (1)

Project website and social media accounts

Pubblicazioni

Peer reviewed articles (11)

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

Autori: Mario Picciani, Wassim Gabriel, Victor‐George Giurcoiu, Omar Shouman, Firas Hamood, Ludwig Lautenbacher, Cecilia Bang Jensen, Julian Müller, Mostafa Kalhor, Armin Soleymaniniya, Bernhard Kuster, Matthew The, Mathias Wilhelm
Pubblicato in: PROTEOMICS, Numero 24, 2024, ISSN 1615-9853
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202300112

Proteomic Profiling Towards a Better Understanding of Genetic Based Muscular Diseases: The Current Picture and a Look to the Future

Autori: Marc Pauper, Andreas Hentschel, Malte Tiburcy, Sergi Beltran, Tobias Ruck, Ulrike Schara-Schmidt, Andreas Roos
Pubblicato in: Biomolecules, Numero 15, 2025, Pagina/e 130, ISSN 2218-273X
Editore: MDPI
DOI: 10.3390/biom15010130

Assessment and Prediction of Human Proteotypic Peptide Stability for Proteomics Quantification

Autori: Cristina Chiva, Zahra Elhamraoui, Amanda Solé, Marc Serret, Mathias Wilhelm, Eduard Sabidó
Pubblicato in: Analytical Chemistry, Numero 95, 2023, Pagina/e 13746-13749, ISSN 0003-2700
Editore: American Chemical Society
DOI: 10.1021/acs.analchem.3c02269

OpenMS WebApps: Building User-Friendly Solutions for MS Analysis

Autori: Tom David Müller, Arslan Siraj, Axel Walter, Jihyung Kim, Samuel Wein, Johannes von Kleist, Ayesha Feroz, Matteo Pilz, Kyowon Jeong, Justin Cyril Sing, Joshua Charkow, Hannes Luc Röst, Timo Sachsenberg
Pubblicato in: Journal of Proteome Research, Numero 24, 2025, Pagina/e 940-948, ISSN 1535-3893
Editore: American Chemical Society
DOI: 10.1021/acs.jproteome.4c00872

Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links

Autori: Arslan Siraj, Robbin Bouwmeester, Arthur Declercq, Luisa Welp, Aleksandar Chernev, Alexander Wulf, Henning Urlaub, Lennart Martens, Sven Degroeve, Oliver Kohlbacher, Timo Sachsenberg
Pubblicato in: PROTEOMICS, Numero 24, 2024, ISSN 1615-9853
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202300144

OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data

Autori: Julianus Pfeuffer, Chris Bielow, Samuel Wein, Kyowon Jeong, Eugen Netz, Axel Walter, Oliver Alka, Lars Nilse, Pasquale Domenico Colaianni, Douglas McCloskey, Jihyung Kim, George Rosenberger, Leon Bichmann, Mathias Walzer, Johannes Veit, Bertrand Boudaud, Matthias Bernt, Nikolaos Patikas, Matteo Pilz, Michał Piotr Startek, Svetlana Kutuzova, Lukas Heumos, Joshua Charkow, Justin Cyril Sing, Ayesha
Pubblicato in: Nature Methods, Numero 21, 2024, Pagina/e 365-367, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-024-02197-7

MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0

Autori: Louise Marie Buur, Arthur Declercq, Marina Strobl, Robbin Bouwmeester, Sven Degroeve, Lennart Martens, Viktoria Dorfer, Ralf Gabriels
Pubblicato in: Journal of Proteome Research, 2024, ISSN 1535-3893
Editore: American Chemical Society
DOI: 10.26434/chemrxiv-2023-rvr9n

Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification

Autori: Mostafa Kalhor, Joel Lapin, Mario Picciani, Mathias Wilhelm
Pubblicato in: Molecular & Cellular Proteomics, Numero 23, 2024, Pagina/e 100798, ISSN 1535-9476
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2024.100798

Theoretical Assessment of Indistinguishable Peptides in Mass Spectrometry-Based Proteomics

Autori: Zahra Elhamraoui, Eva Borràs, Mathias Wilhelm, Eduard Sabidó
Pubblicato in: Analytical Chemistry, Numero 96, 2024, Pagina/e 15829-15833, ISSN 0003-2700
Editore: American Chemical Society
DOI: 10.1021/acs.analchem.4c02803

How to deal with internal fragment ions?

Autori: Arthur Grimaud, Masa Babovic, Frederik Haugaard Holck, Ole N. Jensen, Veit Schwämmle
Pubblicato in: Molecular & Cellular Proteomics, 2025, Pagina/e 100896, ISSN 1535-9476
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2024.100896

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows

Autori: David Bouyssié, Pınar Altıner, Salvador Capella-Gutierrez, José M. Fernández, Yanick Paco Hagemeijer, Peter Horvatovich, Martin Hubálek, Fredrik Levander, Pierluigi Mauri, Magnus Palmblad, Wolfgang Raffelsberger, Laura Rodríguez-Navas, Dario Di Silvestre, Balázs Tibor Kunkli, Julian Uszkoreit, Yves Vandenbrouck, Juan Antonio Vizcaíno, Dirk Winkelhardt, Veit Schwämmle
Pubblicato in: Journal of Proteome Research, Numero 23, 2024, Pagina/e 418-429, ISSN 1535-3893
Editore: American Chemical Society
DOI: 10.1021/acs.jproteome.3c00636

Conference proceedings (1)

Extended Reality for Public Understanding of Science: A Systematic Literature Review

Autori: Prajwal DSouza, Nikoletta-Zampeta Legaki, Daniel Fernández Galeote, Juho Hamari
Pubblicato in: Proceedings of the 27th International Academic Mindtrek Conference, 2024, Pagina/e 168-175
Editore: ACM
DOI: 10.1145/3681716.3681734