Dataset Information

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

ABSTRACT: 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.

INSTRUMENT(S): timsTOF HT

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Liver

SUBMITTER: Vincent Richard

LAB HEAD: Christoph H. Borchers

PROVIDER: PXD057266 | Pride | 2025-06-16

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	EV002667_VR_SynQuan_Human-K6Mouse_mix_liver_HpH_DDA_F1_S2-a1_1_3366.d.zip	Other
	EV002668_VR_SynQuan_Human-K6Mouse_mix_liver_HpH_DDA_F2_S2-a2_1_3367.d.zip	Other
	EV002669_VR_SynQuan_Human-K6Mouse_mix_liver_HpH_DDA_F3_S2-a3_1_3368.d.zip	Other
	EV002670_VR_SynQuan_Human-K6Mouse_mix_liver_HpH_DDA_F4_S2-a4_1_3369.d.zip	Other
	EV002671_VR_SynQuan_Human-K6Mouse_mix_liver_HpH_DDA_F5_S2-a5_1_3370.d.zip	Other

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Publications

SysQuan: Repurposing SILAC Mice for the Cost-Effective Absolute Quantitation of the Human Proteome.

Mohammed Yassene Y Richard Vincent R VR Reyes Madlangsakay M Immanuel MI Lao Ying Y Spicer Victor V Popp Robert R Gaither Claudia C Hennecken Laura L Kleinekofort Wolfgang W Zahedi René P RP Borchers Christoph H CH

Molecular & cellular proteomics : MCP 20250418 6

Relative quantitation, used by most mass spectrometry-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 mass spectrometry-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 laborat ...[more]

PMID: 40254065

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Project description:Targeted mass spectrometry (MS) approaches, which are powerful methods for uniquely and confidently quantifying a specific panel of proteins in complex biological samples, play a crucial role in validation and clinical translation of protein biomarkers discovered by global proteomic profiling. Common targeted MS methods, such as multiple reaction monitoring (MRM) and parallel-reaction monitoring (PRM), employ specific mass spectrometric technologies to quantify protein levels by comparing the transitions of specific endogenous (Endo) peptides with those of stable isotope labeled (SIL) peptide counterparts. These methods utilizing amino acid analyzed (AAA) SIL peptides warrants sensitive and precise measurements required for targeted MS assays. Compared to MRM, PRM provides higher experimental throughput by simultaneously acquiring all transitions of the target peptides and thereby compensate for different ion suppression among transitions of a target peptide. However, PRM still suffers different ion suppressions between Endo and SIL peptides due to poor spray stability as the Endo and SIL peptides were monitored at different liquid chromatography (LC) retention times. Here we introduce a new targeted MS method, termed as wideband PRM (WBPRM), designed for high-throughput targeted MS approach. WBPRM employs a wide isolation window for simultaneous fragmentations of both Endo and SIL peptides along with multiplexed single ion monitoring (SIM) scans for enhanced MS sensitivity of target peptides. Compared to PRM, WBPRM was demonstrated to provide increased sensitivity, precision, and accuracy of quantitative measurements of target peptides with increased throughput, allowing more target peptide measurements in a short experiment time. Its adaptability to a MS method provided by the manufacture makes it a facile method to implement for MS based assays, particularly in complex biological samples, where the needs for higher accuracy, sensitivity and efficiency are paramount.