Integrative mechanistic and multi-omics Modelling of Antigen Presentation to predict epitope dynamics

Project Information

IMAP

Grant agreement ID: 945528

DOI

10.3030/945528

EC signature date 13 October 2020

Start date 1 April 2021

End date 31 March 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 495 000,00

EU contribution

€ 1 495 000,00

Coordinated by

MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
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 (14)

The maintenance of oocytes in the mammalian ovary involves extreme protein longevity

Author(s): Katarina Harasimov, Rebecca L. Gorry, Luisa M. Welp, Sarah Mae Penir, Yehor Horokhovskyi, Shiya Cheng, Katsuyoshi Takaoka, Alexandra Stützer, Ann-Sophie Frombach, Ana Lisa Taylor Tavares, Monika Raabe, Sara Haag, Debojit Saha, Katharina Grewe, Vera Schipper, Silvio O. Rizzoli, Henning Urlaub, Juliane Liepe, Melina Schuh
Published in: Nature Cell Biology, Issue 26, 2024, Page(s) 1124-1138, ISSN 1465-7392
Publisher: Nature Publishing Group
DOI: 10.1038/s41556-024-01442-7

iBench: A ground truth approach for advanced validation of mass spectrometry identification method

Author(s): John A. Cormican, Wai Tuck Soh, Michele Mishto, Juliane Liepe
Published in: Proteomics, Issue 16159853, 2022, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202200271

Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing

Author(s): Wai Tuck Soh, Hanna P. Roetschke, John A. Cormican, Bei Fang Teo, Nyet Cheng Chiam, Monika Raabe, Ralf Pflanz, Fabian Henneberg, Stefan Becker, Ashwin Chari, Haiyan Liu, Henning Urlaub, Juliane Liepe, Michele Mishto
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-45339-3

Database search engines and target database features impinge upon the identification of post-translationally cis-spliced peptides in HLA class I immunopeptidomes

Author(s): Michele Mishto, Yehor Horokhovskyi, John A. Cormican, Xiaoping Yang, Steven Lynham, Henning Urlaub, Juliane Liepe
Published in: Proteomics, Issue 16159853, 2022, Page(s) 2100226, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202100226

Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid–protein interaction sites by mass spectrometry

Author(s): Luisa M Welp, Alexander Wulf, Aleksandar Chernev, Yehor Horokhovskyi, Sergei Moshkovskii, Olexandr Dybkov, Piotr Neumann, Martin Pašen, Arslan Siraj, Monika Raabe, Henri Göthert, James L Walshe, Deliana A Infante, Ana C de A.P. Schwarzer, Achim Dickmanns, Sven Johannsson, Jana Schmitzová, Ingo Wohlgemuth, Eugen Netz, Yi He, Kai Fritzemeier, Bernard Delanghe, Rosa Viner, Seychelle M Vos,
Published in: Nucleic Acids Research, Issue 53, 2025, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaf727

An Automated Workflow to Address Proteome Complexity and the Large Search Space Problem in Proteomics and HLA-I Immunopeptidomics

Author(s): Yehor Horokhovskyi, Hanna P. Roetschke, John A. Cormican, Martin Pašen, Sina Garazhian, Michele Mishto, Juliane Liepe
Published in: Molecular & Cellular Proteomics, Issue 24, 2025, Page(s) 101039, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2025.101039

Predicting the success of Fmoc-based peptide synthesis.

Author(s): Ilanit Gutman; Ron Gutman; John Sidney; Leila Chihab; Michele Mishto; Juliane Liepe; Anthony Chiem; Jason Greenbaum; Zhen Yan; Alessandro Sette; Zeynep Koşaloğlu-Yalçın; Bjoern Peters
Published in: ACS Omega, Issue 24701343, 2022, ISSN 2470-1343
Publisher: American Chemical Society
DOI: 10.25418/crick.20376597.v1

A roadmap for ribosome assembly in human mitochondria

Author(s): Elena Lavdovskaia, Elisa Hanitsch, Andreas Linden, Martin Pašen, Venkatapathi Challa, Yehor Horokhovskyi, Hanna P. Roetschke, Franziska Nadler, Luisa Welp, Emely Steube, Marleen Heinrichs, Mandy Mong-Quyen Mai, Henning Urlaub, Juliane Liepe, Ricarda Richter-Dennerlein
Published in: Nature Structural & Molecular Biology, Issue 31, 2024, Page(s) 1898-1908, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-024-01356-w

Response: Commentary: An In Silico–In Vitro Pipeline Identifying an HLA-A*02:01+ KRAS G12V+ Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients

Author(s): Michele Mishto, Guillermo Rodriguez-Hernandez, Jacques Neefjes, Henning Urlaub, Juliane Liepe4*
Published in: Frontiers in Immunology, Issue 12, 2021, ISSN 1664-3224
Publisher: Lausanne: Frontiers Media S.A., 2010-
DOI: 10.3389/fimmu.2021.679836

Proteasome isoforms in human thymi and mouse models

Author(s): Michele Mishto, Iina Takala, Paola Bonfanti, Juliane Liepe
Published in: Immunology Letters, Issue 269, 2025, Page(s) 106899, ISSN 0165-2478
Publisher: Elsevier BV
DOI: 10.1016/j.imlet.2024.106899

PEPSeek-Mediated Identification of Novel Epitopes From Viral and Bacterial Pathogens and the Impact on Host Cell Immunopeptidomes

Author(s): John A. Cormican, Lobna Medfai, Magdalena Wawrzyniuk, Martin Pašen, Hassnae Afrache, Constance Fourny, Sahil Khan, Pascal Gneiße, Wai Tuck Soh, Arianna Timelli, Emanuele Nolfi, Yvonne Pannekoek, Andrew Cope, Henning Urlaub, Alice J.A.M. Sijts, Michele Mishto, Juliane Liepe
Published in: Molecular & Cellular Proteomics, Issue 24, 2025, Page(s) 100937, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2025.100937

Potential Mimicry of Viral and Pancreatic β Cell Antigens Through Non-Spliced and cis-Spliced Zwitter Epitope Candidates in Type 1 Diabetes

Author(s): Michele Mishto, Artem Mansurkhodzhaev, Teresa Rodriguez-Calvo, Juliane Liepe
Published in: Front. Immunol., Issue 16643224, 2021, ISSN 1664-3224
Publisher: Lausanne: Frontiers Media S.A., 2010-
DOI: 10.3389/fimmu.2021.656451

InvitroSPI and a large database of proteasome-generated spliced and non-spliced peptides

Author(s): Hanna P. Roetschke; Guillermo Rodriguez-Hernandez; John A. Cormican; Xiaoping Yang; Steven Lynham; Michele Mishto; Juliane Liepe
Published in: Scientific Data, Issue 1, 2023, ISSN 2052-4463
Publisher: Nature Publishing Group, 2014-
DOI: 10.1038/s41597-022-01890-6

inSPIRE: An open-source tool for increased mass spectrometry identification rates using Prosit spectral prediction

Author(s): John A. Cormican, Yehor Horokhovskyi, Wai Tuck Soh, Michele Mishto, Juliane Liepe
Published in: Molecular & Cellular Proteomics, Issue 15359476, 2022, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2022.100432