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PSM rescoring boosts identification of trypsin, AspN, and GluC peptides on timsTOF

ABSTRACT: To investigate whether samples digested with trypsin, GluC, or AspN benefit from PSM rescoring, we rescored a timsTOF Pro dataset that was digested using different proteases. For detailed information on data acquisition, please refer to the original publication by Fossati et al. (PXD025671). In brief, for spectral library generation 500 ng for each fraction were acquired using DDA PASEF on the timsTOF Pro (Bruker Daltonik, Germany). Individual spectrum peak files were searched against a combined human-Mtb database encompassing the *Mycobacterium Tuberculosis* proteome (4,081 entries, downloaded from Uniprot on 12/02/2021) and Homo Sapiens proteome (20,397 entries, downloaded on 07/01/2021). The number of missed cleavages was fixed to 2, using cysteine carbamidomethylation as fixed modification, and N-terminal acetylation and methionine oxidation as variable modifications. The search results were rescored by integrating Prosit's fragment ion intensity predictions, using Oktoberfest version 0.5.3 (https://github.com/wilhelm-lab/oktoberfest). PSM rescoring of the samples cleaved with AspN, GluC, and trypsin resulted in 1.5-fold, 1.7-fold, and 1.4-fold increases in unique identified peptides, respectively.

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Mycobacterium Tuberculosis (ncbitaxon:1773) Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Kurt Boonen

PROVIDER: MSV000093954 | MassIVE | Tue Jan 30 05:12:00 GMT 2024

SECONDARY ACCESSION(S): PXD049004

REPOSITORIES: MassIVE

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PSM rescoring boosts immunopeptide identification on timsTOF compared to Orbitrap

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