MassIVE MSV000092461

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PSM rescoring boosts immunopeptide identification on timsTOF compared to Orbitrap

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Description

To compare the rescoring performance on Orbitrap versus timsTOF data, we utilized a comparison dataset comprising both HLA-I and HLA-II peptides measured on an Orbitrap and on a timsTOF. For detailed information on data acquisition, please refer to the original publication by Gravel et al. (PXD038782). In brief, 10 samples were measured in technical triplicate (two technical replicates for the HNSCC sample) on the Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientic, Waltham, USA) and on the timsTOF Pro (Bruker Daltonik, Germany). Individual spectrum peak files were searched against a database containing 20,598 human UniProt entries downloaded from https://www.ebi.ac.uk/reference_proteomes/ with MaxQuant version 2.0.3.1 and rescored by integrating Prosit's fragment ion intensity predictions, using Oktoberfest (https://github.com/wilhelm-lab/oktoberfest). To perform rescoring on the Orbitrap data we employed the 2020 CID Prosit model with a CE set to 35 for HLA-I peptides, and the 2020 HCD Prosit model with CE set to 30 for the HLA-II peptides. For timsTOF data, rescoring was performed using the TOF Prosit 2023 model with the reported CEs for each PSM. Rescoring the Orbitrap data resulted in on average 2.5-fold more unique HLA-I peptides and 1.4-fold more unique HLA-II peptides. In contrast, rescoring timsTOF data resulted in a higher increase, with on average 2.8-fold more unique HLA-I peptides and 1.7-fold more unique HLA-II peptides. [doi:10.25345/C54Q7R125] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: timsTOF ; immunopeptidomics ; Orbitrap ; Prosit

Contact

Principal Investigators:
(in alphabetical order) 		Kurt Boonen, University of Antwerp, Belgium
Wout Bittremieux, University of Antwerp, Belgium
Submitting User: CAdams
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