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 .
Deliverables
Report on the creation of the initial version of the project's data management plan, describing the intended data to be generated, the storage and handling of this data with an eye to IP and ethics constraints, and it's long-term archival and/or (where appropriate and possible) public dissemination approach.
Report on epitopes and antigens identified for MTB and BCG (opens in new window)Description of the performance of a miniaturized and automated procedure for immunopeptidomics sample preparation, including MHC Class I and II peptide complex immunoprecipitation in 96-wells using a positive pressure liquid handling device.
Report on the application of SaaS on immunopeptidomics results (opens in new window)Description of the utility of applying the Search All, Select Subset statistical approach for false discovery rate estimation on (small) subsets of identifications coming from mass spectrometry based proteomics approaches, on immunopeptidomics data sets.
Report on a miniaturized and (semi-)automated pipeline for immunopeptidomics sample preparation (opens in new window)Description of the performance of a miniaturized and automated procedure for immunopeptidomics sample preparation, including MHC Class I and II peptide complex immunoprecipitation in 96-wells using a positive pressure liquid handling device.
Dissemination and exploitation plan (opens in new window)The plan describes the planned measures to maximize the impact of the project, including the dissemination and exploitation measures that are planned, and the target group(s) addressed. Regarding communication measures and public engagement strategy, the aim is to inform and reach out to society and show the activities performed, and the use and the benefits the project will have for citizens.
Report on improved immunopeptide separation ionization and fragmentation (opens in new window)Assessment of peptide TMT derivatization to improve ionization and fragmentation of MHC Class I and II immunopeptides along with EThcD fragmentation. Evaluation of peptide pre-fractionation to reduce sample complexity, and novel nanoLC columns that should increase the number of identified immunopeptides.
Policy briefing 1 (opens in new window)At the end of the 1st reporting period, a report (policy briefing) will be shared with the policy makers.
Report on a new version of MS²Rescore with an EThcD-TMT model and DeepLC (opens in new window)Description of a new version of the MSRescore immunopeptidomics mass spectrometry data analysis algorithm, implementing DeepLC retention time prediction, and an updated prediction algorithm for the prediction of fragmentation spectra for peptides carrying TMT tags, and fragmented using the EThcD method.
Setup of a project website and logo (opens in new window)Report on the availability of a project website and a logo for the project.
Report on immuno-ionbot, a version of ionbot capable of performing open modification searches on immunopeptidomics data (opens in new window)Description of an updated verison of the ionbot algorithm, which will be fitted with the capability to handle non-tryptic peptides (including immunopeptides), alongside the use of immunopeptide fragmentation and retention time predictions coming from the MS²PIP and DeepLC predictors, respectively.
IP management plan in place (opens in new window)Report on the IP management plan as described in the project's Grant Agreement, including conflict resolution approaches.
Publications
Author(s):
David Gomez-Zepeda, Danielle Arnold-Schild, Julian Beyrle, Arthur Declercq, Ralf Gabriels, Elena Kumm, Annica Preikschat, Mateusz Krzysztof Łącki, Aurélie Hirschler, Jeewan Babu Rijal, Christine Carapito, Lennart Martens, Ute Distler, Hansjörg Schild, Stefan Tenzer
Published in:
Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher:
Springer Science and Business Media LLC
DOI:
10.1038/S41467-024-46380-Y
Author(s):
Arthur Declercq, Robbe Devreese, Jonas Scheid, Caroline Jachmann, Tim Van Den Bossche, Annica Preikschat, David Gomez-Zepeda, Jeewan Babu Rijal, Aurélie Hirschler, Jonathan R Krieger, Tharan Srikumar, George Rosenberger, Claudia Martelli, Dennis Trede, Christine Carapito, Stefan Tenzer, Juliane S Walz, Sven Degroeve, Robbin Bouwmeester, Lennart Martens, Ralf Gabriels
Published in:
Journal of Proteome Research, 2025, ISSN 1535-3893
Publisher:
American Chemical Society (ACS)
DOI:
10.1021/ACS.JPROTEOME.4C00609
Author(s):
Sofie Meulewaeter, Ilke Aernout, Joke Deprez, Yanou Engelen, Margo De Velder, Lorenzo Franceschini, Karine Breckpot, Serge Van Calenbergh, Caroline Asselman, Katie Boucher, Francis Impens, Stefaan C. De Smedt, Rein Verbeke, Ine Lentacker
Published in:
Journal of Controlled Release, Issue 370, 2025, ISSN 0168-3659
Publisher:
Elsevier BV
DOI:
10.1016/j.jconrel.2024.04.052
Author(s):
Simon Hackl, Caroline Jachmann, Mathias Witte Paz, Theresa Anisja Harbig, Lennart Martens, Kay Nieselt
Published in:
Journal of Proteome Research, Issue 24, 2025, ISSN 1535-3893
Publisher:
American Chemical Society (ACS)
DOI:
10.1021/acs.jproteome.4c00679
Author(s):
Adillah Gul, Lecia L. Pewe, Patrick Willems, Rupert Mayer, Fabien Thery, Caroline Asselman, Ilke Aernout, Rein Verbeke, Denzel Eggermont, Laura Van Moortel, Ellen Upton, Yifeng Zhang, Katie Boucher, Laia Miret-Casals, Hans Demol, Stefaan C. De Smedt, Ine Lentacker, Lilliana Radoshevich, John T. Harty, Francis Impens
Published in:
Molecular & Cellular Proteomics, Issue 23, 2024, ISSN 1535-9476
Publisher:
Elsevier BV
DOI:
10.1016/j.mcpro.2024.100829
Author(s):
Louise M. Buur, Arthur Declercq, Marina Strobl, Robbin Bouwmeester, Sven Degroeve, Lennart Martens, Viktoria Dorfer, Ralf Gabriels
Published in:
Journal of Proteome Research, Issue 23, 2024, ISSN 1535-3893
Publisher:
American Chemical Society (ACS)
DOI:
10.1021/acs.jproteome.3c00785
Author(s):
Charlotte Wallaeys, Natalia Garcia-Gonzalez, Steven Timmermans, Jolien Vandewalle, Tineke Vanderhaeghen, Somara De Beul, Hester Dufoor, Melanie Eggermont, Elise Moens, Victor Bosteels, Riet De Rycke, Fabien Thery, Francis Impens, Serge Verbanck, Stefan Lienenklaus, Sophie Janssens, Richard S. Blumberg, Takao Iwawaki, Claude Libert
Published in:
Cell Host & Microbe, Issue 32, 2024, ISSN 1931-3128
Publisher:
Elsevier BV
DOI:
10.1016/j.chom.2024.08.007
Author(s):
Patrick Willems, Fabien Thery, Laura Van Moortel, Margaux De Meyer, An Staes, Adillah Gul, Lyudmila Kovalchuke, Arthur Declercq, Robbe Devreese, Robbin Bouwmeester, Ralf Gabriels, Lennart Martens, Francis Impens
Published in:
2024
Publisher:
Cold Spring Harbor Laboratory
DOI:
10.1101/2024.11.22.624860
Author(s):
Robbe Devreese, Alireza Nameni, Arthur Declercq, Emmy Terryn, Ralf Gabriels, Francis Impens, Kris Gevaert, Lennart Martens, Robbin Bouwmeester
Published in:
2025
Publisher:
Cold Spring Harbor Laboratory
DOI:
10.1101/2025.02.18.638865
Author(s):
Jonas Scheid, Steffen Lemke, Naomi Hoenisch-Gravel, Anna Dengler, Timo Sachsenberg, Arthur Declerq, Ralf Gabriels, Jens Bauer, Marcel Wacker, Leon Bichmann, Lennart Martens, Marissa L. Dubbelaar, Sven Nahnsen, Juliane S. Walz
Published in:
2024
Publisher:
Springer Science and Business Media LLC
DOI:
10.21203/rs.3.rs-5560023/v1
Author(s):
Yasset Perez-Riverol, Wout Bittremieux, William S. Noble, Lennart Martens, Aivett Bilbao, Michael R. Lazear, Bjorn Grüning, Daniel S. Katz, Michael J. MacCoss, Chengxin Dai, Jimmy K. Eng, Robbin Bouwmeester, Michael Robert Shortreed, Enrique Audain, Timo Sachsenberg, Jeroen Van Goey, Georg Wallmann, Bo Wen, Lukas Käll, William E. Fondrie
Published in:
2024
Publisher:
American Chemical Society (ACS)
DOI:
10.26434/CHEMRXIV-2024-WF6DW
Author(s):
Arthur Declercq, Nina Demeulemeester, Ralf Gabriels, Robbin Bouwmeester, Sven Degroeve, Lennart Martens
Published in:
Methods in Molecular Biology, Mass Spectrometry Based Single Cell Proteomics, 2024
Publisher:
Springer US
DOI:
10.1007/978-1-0716-3934-4_15
Author(s):
Ilke Aernout, Rein Verbeke, Stefaan C. De Smedt, Francis Impens, Ine Lentacker
Published in:
Trends in mRNA Vaccine Research, 2024
Publisher:
Wiley
DOI:
10.1002/9783527838394.ch12
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