PXD065471

PXD065471 is an original dataset announced via ProteomeXchange.

Title	Development of highly multiplex targeted proteomics assays in biofluids using a nominal mass ion trap mass spectrometer
Description	The development of targeted assays that monitor biomedically relevant proteins is an important step in bridging discovery experiments to large scale clinical studies. Targeted assays are currently unable to scale to hundreds or thousands of targets. We demonstrate the generation of large-scale assays using a novel hybrid nominal mass instrument. The scale of these assays is achievable with the StellarTM mass spectrometer through the accommodation of shifting retention times by real-time alignment, while being sensitive and fast enough to handle many concurrent targets. Assays were constructed using precursor information from gas-phase fractionated (GPF) data-independent acquisition (DIA). We demonstrate the ability to schedule methods from an orbitrap and linear ion trap acquired GPF DIA library and compare the quantification of a matrix-matched calibration curve from orbitrap DIA and linear ion trap parallel reaction monitoring (PRM). Two applications of these proposed workflows are shown with a cerebrospinal fluid (CSF) neurodegenerative disease protein PRM assay and with a Mag-Net enriched plasma extracellular vesicle (EV) protein survey PRM assay.
HostingRepository	PanoramaPublic
AnnounceDate	2025-06-25
AnnouncementXML	Submission_2025-06-25_19:49:15.888.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Deanna Plubell
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Gallus gallus; NCBI TaxID: 9031;
ModificationList	Carbamidomethyl; Oxidation; Label:13C(6)15N(2); Label:13C(6)15N(4)
Instrument	Orbitrap Exploris 480; Stellar

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-25 18:18:21	ID requested
⏵ 1	2025-06-25 19:49:16	announced

Dataset with its publication pending

submitter keyword: PRM, targeted proteomics, Alzheimer's disease, Parkinson's disease, assay development

Michael MacCoss
contact affiliation	University of Washington
contact email	maccoss@uw.edu
lab head
Deanna Plubell
contact affiliation	University of Washington
contact email	plubell@uw.edu
dataset submitter

Panorama Public dataset URI