PXD017834-1

PXD017834 is an original dataset announced via ProteomeXchange.

Title	An Integrated Quantitative Proteomics Workflow for Biomarker Discovery and Validation in Plasma
Description	Blood plasma is one of the most widely used samples for biomarker discovery research as well as clinical investigations for diagnostic and therapeutic purposes. However, the plasma proteome is extremely complex due to its wide dynamic range of protein concentrations and the presence of high-abundance proteins. Here we are describing an optimized integrated quantitative proteomics pipeline combining the label-free and multiplexed-labeling-based (Isobaric tags for relative and absolute quantitation) proteome profiling methods for biomarker discovery, followed by the targeted approaches for validation of the identified potential marker proteins. In this workflow, the targeted quantitation of proteins is carried out by multiple-reaction monitoring (MRM) and parallel-reaction monitoring (PRM) mass spectrometry. Thus, our approach enables both unbiased screenings of biomarkers and their subsequent selective validation in human plasma. The overall procedure takes only 1–2 days to complete including the time for data acquisition (excluding database searching). This protocol is quick, flexible and eliminates the need for a separate immunoassay-based validation workflow in blood biomarker investigations.
HostingRepository	PRIDE
AnnounceDate	2020-09-07
AnnouncementXML	Submission_2020-09-06_23:32:58.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vipin Kumar
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-02 23:30:42	ID requested
⏵ 1	2020-09-06 23:32:59	announced
2	2024-10-22 05:11:48	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project, Plasma (B/D-HPP)

submitter keyword: label-free quantitation, Label-based quantitation, Targeted proteomics

Prof. Sanjeeva Srivastava
contact affiliation	Proteomics Lab, Department of Biosciences and Bioengineering, IIT Bombay.
contact email	sanjeeva@iitb.ac.in
lab head
Vipin Kumar
contact affiliation	Research Scholar
contact email	vipin5@iitb.ac.in
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/2020/09/PXD017834

PRIDE project URI

• PRIDE
  1. PXD017834
     1. Label: PRIDE project
     2. Name: An Integrated Quantitative Proteomics Workflow for Biomarker Discovery and Validation in Plasma