PXD025671

PXD025671 is an original dataset announced via ProteomeXchange.

Title	Towards comprehensive plasma proteomics by orthogonal protease digestion
Description	Rapid and consistent protein identification across large clinical cohorts is an important goal for clinical proteomics. With the development of data-independent technologies (DIA/SWATH-MS), it is now possible to analyze hundreds of samples with great reproducibility and quantitative accuracy. However, this technology benefits from empirically derived spectral libraries that define the detectable set of peptides and proteins. Here we apply a simple and accessible tip-based workflow for the generation of spectral libraries to provide a comprehensive overview on the plasma proteome in individuals with and without active tuberculosis (TB). To boost protein coverage, we utilized non-conventional proteases such as GluC and AspN together with the gold standard trypsin, identifying more than 30,000 peptides mapping to 3,309 proteins. Application of this library to quantify plasma proteome differences in TB infection recovered more than 400 proteins in 50 minutes of MS-acquisition, including diagnostic Mycobacterium Tuberculosis(Mtb) proteins that have previously been detectable primarily by antibody-based assays and intracellular proteins not previously described to be in plasma.
HostingRepository	PRIDE
AnnounceDate	2021-07-29
AnnouncementXML	Submission_2021-07-28_23:39:30.483.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrea Fossati
SpeciesList	scientific name: Mycobacterium tuberculosis TKK-01-0032; NCBI TaxID: 1267361; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-27 22:13:03	ID requested
⏵ 1	2021-07-28 23:39:30	announced

Dataset with its publication pending

submitter keyword: DIA-MS, Clinical proteomics, TB, Human

Danielle Swaney
contact affiliation	University of California San Francisco, Quantitative Biosciences Institute (QBI), SanFrancisco, CA, 94158, USA, J. David Gladstone Institutes, San Francisco, CA 94158, USA
contact email	danielle.swaney@ucsf.edu
lab head
Andrea Fossati
contact affiliation	UCSF
contact email	andrea.fossati@ucsf.edu
dataset submitter

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://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD025671

PRIDE project URI

• PRIDE
  1. PXD025671
     1. Label: PRIDE project
     2. Name: Towards comprehensive plasma proteomics by orthogonal protease digestion