PXD049004

PXD049004 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	PSM rescoring boosts identification of trypsin, AspN, and GluC peptides on timsTOF
Description	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.
HostingRepository	MassIVE
AnnounceDate	2024-01-30
AnnouncementXML	Submission_2024-01-30_05:49:13.646.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Charlotte Adams
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; scientific name: Mycobacterium tuberculosis; NCBI TaxID: 1773;
ModificationList	Acetyl; Oxidation; Carbamidomethyl
Instrument	timsTOF Pro

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-30 05:12:10	ID requested
⏵ 1	2024-01-30 05:49:14	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: timsTOF, Prosit, Multiple proteases

submitter keyword: timsTOF, Prosit, Multiple proteases

Contact List

Kurt Boonen
contact affiliation	University of Antwerp
contact email	kurt.boonen@uantwerpen.be
lab head
Charlotte Adams
contact affiliation	University of Antwerp
contact email	charlotte.adams@uantwerpen.be
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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MassIVE dataset URI

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/MSV000093954/