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

Mohammed, Y.; Richard, V. R.; Madlangsakay, I. R.; Lao, Y.; Spicer, V.; Popp, R.; Gaither, C.; Hennecken, L.; Kleinekofort, W.; Zahedi, R. P.; Borchers, C. H.

doi:10.1101/2024.11.05.622109

bioRxiv · 10.1101/2024.11.05.622109

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

Mohammed, Y.·Richard, V. R.·Madlangsakay, I. R.·Lao, Y.·Spicer, V.·Popp, R.·Gaither, C.·Hennecken, L.·Kleinekofort, W.·Zahedi, R. P.·Borchers, C. H.

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Abstract

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. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/622109v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@c7a58org.highwire.dtl.DTLVardef@1344320org.highwire.dtl.DTLVardef@2321e3org.highwire.dtl.DTLVardef@85bf2d_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Mohammed, Y., Richard, V. R., Madlangsakay, I. R., Lao, Y., Spicer, V., Popp, R., Gaither, C., Hennecken, L., Kleinekofort, W., Zahedi, R. P., Borchers, C. H.. 2024-11-08. SysQuan: repurposing SILAC mice for the affordable absolute quantitation of the human proteome. https://doi.org/10.1101/2024.11.05.622109

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