PXD052847-1

PXD052847 is an original dataset announced via ProteomeXchange.

Title	Linear Ion Trap Global to Targeted Proteomics: A workflow for targeted proteomics assay development using a versatile linear ion trap
Description	Advances in proteomics and mass spectrometry have enabled the study of limited cell populations, such as single-cell proteomics, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive nominal resolution measurements, these instruments are effectively limited to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. We demonstrate a workflow using a newly released, hybrid quadrupole-LIT instrument for developing targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Gas-phase fraction-based DIA enables rapid target library generation in the same background chemical matrix as each quantitative injection. Using a new software tool embedded within EncyclopDIA for scheduling parallel reaction monitoring assays, we show consistent quantification across three orders of magnitude of input material. Using this approach, we demonstrate measuring peptide quantitative linearity down to 25x dilution in a background of only a 1 ng proteome without requiring stable isotope labeled standards. At 1 ng total protein on column, we found clear consistency between immune cell populations measured using flow cytometry and immune markers measured using LIT-based proteomics. We believe hybrid quadrupole-LIT instruments represent an economic solution to democratizing mass spectrometry in a wide variety of laboratory settings.
HostingRepository	PanoramaPublic
AnnounceDate	2024-06-19
AnnouncementXML	Submission_2024-06-19_17:13:51.234.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Ariana Shannon
SpeciesList	scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationList	Carbamidomethyl
Instrument	Stellar

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-04 22:01:38	ID requested
⏵ 1	2024-06-19 17:13:51	announced

A workflow for targeted proteomics assay development using a versatile linear ion trap. Ariana E. Shannon, Rachael N. Teodorescu, Nojoon Soon, Lilian R. Heil, Cristina C. Jacob, Philip M. Remes, Mark P. Rubinstein, Brian C. Searle bioRxiv 2024.05.31.596891

doi: https://doi.org/10.1101/2024.05.31.596891

submitter keyword: Ion Trap, Stellar MS, DIA, Data-independent acquisition, DDA, High pH reverse phase fractionation, offline fractionation, global proteomics, targeted proteomics, parallel reaction monitoring, prm

Brian Searle
contact affiliation	The Ohio State University
contact email	searleb@gmail.com
lab head
Ariana Shannon
contact affiliation	The Ohio State University
contact email	ariana.shannon@osumc.edu
dataset submitter

Panorama Public dataset URI