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Pre-print: Thunder-DDA-PASEF for identifying HLA class-I presented SARS-CoV-2 spike protein epitopes

The pre-print article “Thunder-DDA-PASEF enables high-coverage immunopeptidomics and identifies HLA class-I presented SarsCov-2 spike protein epitopes” describes a new method for identifying immunopeptides, which are a set of peptides presented by major histocompatibility complex (MHC) proteins. The researchers used liquid chromatography-ion mobility-tandem mass spectrometry (LC-IMS-MS/MS) and developed a method called Thunder-DDA-PASEF. This method selects immunopeptides based on the TIMS separation time and polygon isolation for semi-selectively fragmentation of potential immunopeptides including singly-charged peptides. Identification of singly charged peptides identifications contributed for more than 35% of the immunopeptidomic analysis. Additionally using MS²Rescore improved the the number of immunopeptides found by 150% compared to standard DDA-PASEF. The method enabled high coverage of the immunopeptidome, providing a valuable resource for the development of vaccines and immunotherapies.


This research utilised the IonOpticks Aurora Ultimate 25cm column for unmatched sensitivity and coverage.

Read the full paper here – Research Square – 2023

Authors – David Gomez-Zepeda, Danielle Arnold-Schild, Julian Beyrle, Elena Kumm, Ute Distler, Hansjörg Schild, Stefan Tenzer

Title – Thunder-DDA-PASEF enables high-coverage immunopeptidomics and identifies HLA class-I presented SarsCov-2 spike protein epitopes

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