PXD052734-1

PXD052734 is an original dataset announced via ProteomeXchange.

Title	Characterization of Stellar MS
Description	A set of plasma peptides were targeted with selected reaction monitoring (SRM) on an Altis Plus and also with parallel reaction monitoring (PRM) on a Stellar. The maximum concurrency of the assay was 624 transitions for the Altis, but only 128 precursors for the Stellar. The quantitative performance of the assays was characterized with a matrix-matched dilution curve of human into chicken plasma, where the Stellar had LOQs and LODs that were on average 12x and 2x better than the Altis. Targeted assays were created for absolute quantitation of the PQ500 light and heavy peptides for a 60 samples-per-day (SPD) and 100 SPD throughputs. The quantitative performance of these assays was characterized using dilution curves of the heavy standards spiked into 300 ng of human plasma with the Stellar mass spectrometer. Both assays gave good results, with the 60 SPD assay having LOQs about 1.6x better on average than the 100 SPD assay. Targeted assays were created for label-free quantitation of E. coli spiked into 200 ng of HeLa. Two 60 samples-per-day methods were created, one with 397 peptides, and another with 1302 peptides. These assays were based off of a gas-phase-fractionation (GPF) data independent acquisition (DIA) experiment using the Thermo Fisher Scientific Stellar mass spectrometer. The quantitative performance of these assays was characterized over the range of E. coli amounts from 100 ng to 0.78 ng. Both size assays gave good results, with the n=397 assay having LOQs about 1.2x better on average than the n=1302 assay.
HostingRepository	PanoramaPublic
AnnounceDate	2024-06-11
AnnouncementXML	Submission_2024-06-11_20:39:07.730.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Philip Remes
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; 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); Label:13C(6)15N(1)
Instrument	Stellar

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-30 19:12:30	ID requested
⏵ 1	2024-06-11 20:39:08	announced
2	2024-06-11 20:46:34	announced	: Updated citation

Remes, P. M.

Jacob, C. C.

Heil, L. R.

Shulman, N.

MacLean, B. X.

MacCoss, M. J. Hybrid Quadrupole Mass Filter Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics. bioRxiv June 1, 2024, p 2024.05.31.596848. https://doi.org/10.1101/2024.05.31.596848.

submitter keyword: Stellar, PRM, Targeted, matrix-matched, E. coli, HeLa, chicken, plasma, label-free, PQ500, absolute, quantitation

Philip Remes
contact affiliation	Thermo Fisher Scientific
contact email	philip.remes@thermofisher.com
lab head
Philip Remes
contact affiliation	Thermo Fisher Scientific
contact email	philip.remes@thermofisher.com
dataset submitter

Panorama Public dataset URI