Immunopeptidomics Platform
Dr. David Gomez-Zepeda
Aim
The High-throughput immunopeptidomics (HTIP) platform aims to identify cancer-specific immunopeptides (MHC-ligands), antigens that can trigger the immune response, and potential targets for immunotherapy. MHC ligand peptides are valuable targets for vaccines or personalized immunotherapies since tumor antigens can elicit the immune response and the elimination of cancer cells. Moreover, neoantigens resulting directly or indirectly from tumor-derived mutations constitute highly-specific targets. However, specific changes in the immunopeptidome in cancer and tumors are unique to each patient and can vary during disease progression and as a response to treatments. Liquid chromatography-mass spectrometry (LC-MS)-based immunopeptidomics is the gold standard for directly identifying MHC ligands in biological samples. However, most workflows are not adapted to the throughput and response times required for clinical studies or patient monitoring. To meet these needs, we are developing high-throughput immunopeptidomics workflows by optimizing parallelized sample preparation, high-sensitivity LC-MS methods, and streamlined data analysis pipelines.
Immunopeptidomics Platform
Dr. David Gomez-Zepeda
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[since 2023] Head of the lmmunopeptidomics Platform (HI-TRON), Germany
[2021 - 2023] Junior team leader, Immunoproteomics Unit, Helmholtz Institute for Translational Oncology Mainz (HI-TRON), Germany
[2020 - 2021] Senior postdoctoral research scientist, Mass Spectrometry Facility, Institute of Immunology, University Medical Center Mainz, Germany
[2017 - 2019] Postdoctoral fellow research scientist, Mass Spectrometry Facility, National Laboratory of Genomics for Biodiversity (LANGEBIO – CINVESTAV), Mexico
[2013 - 2016] Doctoral scientist, Ph.D. student, INSERM UMR-S 1144, Paris Descartes University, Response Variability to Psychotropics, France
[2018 - 2022] Member of the National System of Researchers (SNI), Mexico
[2017 - 2019] Postdoctoral fellowship, National Council for Science and Technology (CONACYT), Mexico
HI-TRON Mainz DKFZ
Immunopeptidomics Platform
Obere Zahlbacherstr. 63
Building 911
55131 Mainz
Collaborations
In addition to assisting scientists at HI-TRON, we have strong collaborations with scientists from the German Cancer Research Center (DKFZ), the Johannes Gutenberg University Mainz (JGU), the University Medical Center Mainz (UMC) , the Research Institute for Translational Oncology (TRON, gGmbH) at the UMC, and the Charité University Medicine Berlin.
Selected publications of D. Gomez-Zepeda
- Gomez-Zepeda D, Arnold-Schild D, Beyrle J, Declercq A, Gabriels R, Kumm E, Preikschat A, Łącki MK, Hirschler A, Rijal JB, Carapito C, Martens L, Distler U, Schild H, Tenzer S. Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model. Nature Communications. 2024; 15(1), 2288.
- Gomez-Zepeda D, Beyrle J, Preikschat A, Declercq A, Chen Y, Gabriels R, Martens L, Distler U, Tenzer S. High-coverage immunopeptidomics using timsTOF mass spectrometers with Thunder-DDA-PASEF boosted by MS2Rescore. Preprint available at Research Square. 2024.
- Declercq A, Devreese R, Scheid J, Jachmann C, Van Den Bossche T, Preikschat A, Gomez-Zepeda D, Rijal JB, Hirschler A, Krieger JR, Srikumar T, Rosenberger G, Trede D, Carapito C, Tenzer S, Walz JS, Degroeve S, Bouwmeester R, Martens L, Gabriels R. TIMS2Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS2Rescore. Preprint available at bioRxiv. 2024.
- Gomez-Zepeda D, Perrière N, Glacial F, Taghi M, Chhuon C, Scherrmann J, Sergen tP, Moreau A, Denizot C, Parmentier Y, Cisternino S, Decleves X, Menet M. Functional and targeted proteomics characterization of a human primary endothelial cell model of the blood-brain barrier (BBB) for drug permeability studies. Toxicol. Appl. Pharmacol. 2023; 465 (116456)
- Gomez-Zepeda D, Taghi M, Scherrmann J, Decleves X, Menet MC. ABC Transporters at the Blood–Brain Interfaces, Their Study Models, and Drug Delivery Implications in Gliomas. Pharmaceutics. 2019;12 20
- Gomez-Zepeda D, Taghi M, Smirnova M, Sergent P, Liu W, Chhuon C, Vidal M, Picard M, Thioulouse E, Broutin I, Guerrera I, Scherrmann J, Parmentier Y, Decleves X, Menet M. LC–MS/MS-based quantification of efflux transporter proteins at the BBB. J. Pharm. Biomedical Analysis. 2019; 164: 496–508.
Platform News
12/2024: The Opentron (OT2) pipetting robot is being upgraded to the latest version, the OT Flex
11/2024: David gave an invited talk at the Symposium of the Mexican Society for Proteomics
10/2024: Megan and David attended the HUPO Congress in Dresden, Germany, and both earned travel awards (A big thanks to HUPO!)
08/2024: Megan and David attended the HUPO-HIPP Summer School in Montreal, Canada; where David gave a course about optimizing immunopeptidomics LC-MS methods
07/2024: Lucas passed the IHK-trainer examination (AEVO).04/2024: A new member joins the platform: Lucas Kleinort
02/2023: A new member joins the platform: Megan Ford
12/2023: The Bruker timsTOF Ultra mass spectrometer arrived.
