PXD057266-1

PXD057266 is an original dataset announced via ProteomeXchange.

Title	SysQuan: repurposing SILAC mice for affordable absolute quantitation of the human proteome
Description	Relative quantitation, used by most MS-based proteomics laboratories to determine protein fold-changes, requires that samples are processed and analyzed together to enable best comparability through minimizing batch differences. This limits the detection of subtle but relevant changes in heterogeneous samples and the adoption of MS-based proteomics in population-wide studies. Absolute quantitation (AbsQuan) of protein concentrations circumvents these limitations and enables comparison of data across laboratories, studies, and over time. However, the high cost of the essential stable isotope labeled (SIL) standards prevents widespread access and limits the number of quantifiable proteins. SysQuan repurposes SILAC mouse tissues/biofluids as system-wide internal standards for matched human samples to enable AbsQuan of theoretically >2/3 of the human proteome using 132k shared tryptic peptides. We demonstrate that SysQuan enables quantifying 70% and 31% of the largest liver and plasma reference proteomes, respectively. We exemplify for 14 metabolic proteins that abundant SIL mouse tissues enable cost-effective reverse AbsQuan in – theoretically 1000s of – human samples. Moreover, 10,000s of light/heavy doublets in untargeted SysQuan datasets enable unique post-acquisition AbsQuan. SysQuan empowers researchers to replace relative quantitation with affordable AbsQuan at scale, making data comparable across labs, diseases and tissues, thus enabling completely novel study designs, and transforming the use of data repositories.
HostingRepository	PRIDE
AnnounceDate	2025-06-16
AnnouncementXML	Submission_2025-06-15_16:16:21.987.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vincent Richard
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	6x(13)C labeled residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-28 13:37:49	ID requested
⏵ 1	2025-06-15 16:16:22	announced

10.1016/j.mcpro.2025.100974;

Mohammed Y, Richard VR, Reyes Madlangsakay MI, Lao Y, Spicer V, Popp R, Gaither C, Hennecken L, Kleinekofort W, Zahedi RP, Borchers CH, SysQuan: Repurposing SILAC Mice for the Cost-Effective Absolute Quantitation of the Human Proteome. Mol Cell Proteomics, 24(6):100974(2025) [pubmed]

submitter keyword: proteomics, SILAC, stable isotope, targeted proteomics, absolute quantitation

Christoph H. Borchers
contact affiliation	Segal Cancer Proteomics Centre, Jewish General Hospital, Montreal, QC, Canada Gerald Bronfman Department of Oncology, Jewish GeneraHospital, Montreal, QC, Canada Division of Experimental Medicine, McGill University, Montreal, QC, Canada Department of Pathology, McGill University, Montreal, QC, Canada
contact email	christoph.borchers@mcgill.ca
lab head
Vincent Richard
contact affiliation	Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University
contact email	vincentroyrichard@gmail.com
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/2025/06/PXD057266

PRIDE project URI

• PRIDE
  1. PXD057266
     1. Label: PRIDE project
     2. Name: SysQuan: repurposing SILAC mice for affordable absolute quantitation of the human proteome