SysQuan: repurposing SILAC mice for affordable absolute quantitation of the human proteome

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.