PXD025671 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-04-27 22:13:03 | ID requested | |
⏵ 1 | 2021-07-28 23:39:30 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: DIA-MS, Clinical proteomics, TB, Human |
Contact List
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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD025671
- Label: PRIDE project
- Name: Towards comprehensive plasma proteomics by orthogonal protease digestion