Absolute proteome quantification, without synthetic peptides.

How it works

Traditional targeted proteomics needs an expensive synthetic peptide standard for every protein you want to measure. SysQuan replaces that with whole mouse tissues that are metabolically labelled with heavy ¹³C₆-lysine (K6), so every protein in the tissue carries a uniform heavy label. We pre-quantify that mouse proteome once, using synthetic peptide standards.

To run your samples, the pre-quantified heavy mouse reference is mixed into your light (unlabelled) human or mouse tissue. Each peptide then has its own heavy internal standard at a known concentration, so the light/heavy ratio converts directly into an absolute amount, proteome-wide, in a single measurement.

Assays and data

Each protein in the database is backed by data from one or more acquisition modes:

• DDA (data-dependent acquisition): peptide identification and the reference spectral library.
• MRM (multiple reaction monitoring): optimized, high-throughput targeted assays on triple-quadrupole instruments.
• PRM-PASEF: parallel reaction monitoring with trapped ion mobility for added specificity on timsTOF instruments.
• DIA: large-scale data-independent acquisition for proteome-wide light/heavy ratios.

Every entry carries its quality metrics (heavy-label incorporation rate, missed cleavages, and reproducibility), so results transfer reliably between laboratories.

Publication

The methodology and validation are described in:

SysQuan: a comprehensive resource for systematic protein quantification across human tissues. Molecular & Cellular Proteomics, 2025.

Team

Built and maintained by a team of proteomics scientists, bioinformaticians, and software engineers at McGill University and the University of Manitoba.

Funding & partners

SysQuan is funded through the Canadian Biotechnology Innovation and Commercialization Initiative (CBIC), a $6.4M CAD program (2025-2029), administered by Génome Québec.

In collaboration with MRM Proteomics, Agilent Technologies, Bruker, and Evosep.

Built & funded with

Génome Québec Administers the CBIC funding program (2025-2029) behind SysQuan. Genome Canada National genomics funding organization, co-funding the CBIC program (2025-2029) behind SysQuan alongside Génome Québec. Lady Davis Institute Host research institute at the Jewish General Hospital, Montréal, where the K6-labeled reference proteome is produced, measured, and validated. Quantivum Builds the SysQuan software platform: the searchable database, data pipelines, and lab-automation that turn raw MS runs into absolute quantities. MRM Proteomics Commercial partner supplying standardized reagents and targeted-assay (MRM / PRM) expertise for the SysQuan kit.