SysQuan Database: A Community Resource for System-Wide Absolute Quantitation of the Human Proteome

Abstract Absolute protein quantitation is essential for cross-study comparability and clinical translation of mass spectrometry-based proteomics, yet relative quantitation remains the norm and suffers from batch effects in large-scale and longitudinal studies. SysQuan repurposes SILAM mouse tissues as system-wide internal standards for cost-effective absolute quantitation of the human proteome, but a community resource operationalizing this approach has been lacking. Here we present the SysQuan Database (sysquan.com), a freely accessible web resource covering four human tissues and biofluids: kidney, liver, lung and plasma. It contains 780,583 peptide entries representing nearly 10,000 quantifiable proteins with characterized light/heavy doublets spanning approximately 7 orders of magnitude. Peptides were evaluated for targeted quantitation by proteotypicity, amino acid composition, missed cleavages and incorporation efficiency, yielding 3,899 optimized MRM and 1,046 PRM-PASEF peptide methods exportable in.csv, Agilent MassHunter and Bruker formats. Absolute reference concentrations for 64 liver and lung proteins were determined with synthetic light peptide calibration curves spanning 0.1 to 139 fmol/μg tissue (median R2 0.986; 97% of peptides with R2 ≥ 0.95), with established lower limits of quantitation and coefficients of variation. Three independent validation projects achieved CV ≤ 15% for 94% of measurements (median CV 5.2%), with 79% above the LLOQ.