PXD049004-1
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 |
Keyword List
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 |
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/ |