PXD028306

PXD028306 is an original dataset announced via ProteomeXchange.

Title	Highly multiplexed quantification by targeted mass spectrometry to triage protein candidate biomarkers in plasma
Description	Despite improvements in capabilities of proteomics technologies, the introduction of new plasma-based protein biomarkers for clinical use remains low. One reason is the cumbersome requirement to test thousands of protein candidates in follow-up quantitative verification studies. We sought to evaluate internal standard triggered parallel reaction monitoring (IS-PRM) in the context of biomarker verification by developing a method to quantify 5,176 peptides (1,314 proteins) as candidate biomarkers for early detection of breast cancer. Method performance was characterized in a response curve showing large linear range (4 orders of magnitude) and good repeatability (median CV 7.7%). The method was applied to pools of cancer and control human plasma, detecting 893 proteins and qualifying 164 candidates to advance for further evaluation. The method shows good quantitative performance, greatly expanding the capabilities for quantification of large numbers of proteins, and is well suited for large scale relative quantification of protein sets.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:53:52.881.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jacob Kennedy
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-09 08:20:40	ID requested
1	2022-06-29 17:28:44	announced
⏵ 2	2023-11-14 08:53:53	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Human, Breast cancer, plasma, IS-PRM, protein, LC-MS/MS

Amanda G Paulovich
contact affiliation	Clinical Research Division, Fred Hutchinson Cancer Reseaarch Center
contact email	apaulovi@fredhutch.org
lab head
Jacob Kennedy
contact affiliation	Fred Hutchinson Cancer Research Center
contact email	jkennedy@fhcrc.org
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/2022/06/PXD028306

PRIDE project URI

• PRIDE
  1. PXD028306
     1. Label: PRIDE project
     2. Name: Highly multiplexed quantification by targeted mass spectrometry to triage protein candidate biomarkers in plasma