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PSM rescoring boosts immunopeptide identification on timsTOF compared to Orbitrap

ABSTRACT: 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.

INSTRUMENT(S): timsTOF Pro, Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Kurt Boonen Wout Bittremieux

PROVIDER: MSV000092461 | MassIVE | Mon Jul 17 13:08:00 BST 2023

REPOSITORIES: MassIVE

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