PXD057580-1

PXD057580 is an original dataset announced via ProteomeXchange.

Title	SysQuan: repurposing SILAC mice for the affordable absolute quantitation of the human proteome
Description	Relative quantitation, used by most MS-based proteomics laboratories to determine protein fold-changes, requires samples being processed and analyzed together for best comparability through minimizing batch differences. This limits the adoption of MS-based proteomics in population-wide studies, and the detection of subtle but relevant changes in heterogeneous samples. Absolute quantitation circumvents these limitations and enables comparison of results across laboratories, studies, and longitudinally. However, high costs of the essential stable isotope labeled (SIL) standards prevents widespread access and limits the number of quantifiable proteins. Our new approach, called “SysQuan”, repurposes SILAC mouse tissues/biofluids as system-wide internal standards for matched human samples to enable absolute quantitation of, theoretically, two-thirds of the human proteome using 157,086 shared tryptic peptides. We demonstrate that SysQuan enables quantification of 70% and 31% of the liver and plasma proteomes, respectively. We demonstrate for 14 metabolic proteins that abundant SIL mouse tissues enable cost-effective reverse absolute quantitation in, theoretically, 1000s of human samples. Moreover, 10,000s of light/heavy doublets in untargeted SysQuan datasets enable unique post-acquisition absolute quantitation. SysQuan empowers researchers to replace relative quantitation with affordable absolute quantitation at scale, making data comparable across laboratories, diseases and tissues, enabling completely novel study designs and increasing reusability of data in repositories.
HostingRepository	PanoramaPublic
AnnounceDate	2025-01-07
AnnouncementXML	Submission_2025-01-07_08:27:37.245.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Vincent Richard
SpeciesList	scientific name: Mus musculus; NCBI TaxID: 10090; scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Label:13C(6)
Instrument	6495C Triple Quadrupole LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-06 10:33:46	ID requested
⏵ 1	2025-01-07 08:27:37	announced

doi: https://doi.org/10.1101/2024.11.05.622109

submitter keyword: absolute quantitation, targeted and untargeted quantitation, stable isotope labeling, SILAC mice, multiplexing

Dr. Christoph Borchers
contact affiliation	Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
contact email	christoph.borchers@mcgill.ca
lab head
Vincent Richard
contact affiliation	Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
contact email	vincentroyrichard@gmail.com
dataset submitter

Panorama Public dataset URI