PeptiQuant™ Plus Kits

Translation and Implementation of the PeptiQuant™ Plus Human Plasma BAK-270 (Application Note 50)

Translation and Implementation of the PeptiQuant™ Plus Human Plasma BAK-270 (Application Note 50)
Determination of the concentration range for 267 proteins from 21 lots of commercial human plasma using highly multiplexed multiple reaction monitoring mass spectrometry
Molecular phenotyping of laboratory mouse strains using 500 multiple reaction monitoring mass spectrometry plasma assays
ExSTA: External standard addition method for accurate high-throughput quantitation in targeted proteomics experiments

Researchers in academia and life-science industries continue to implement a bottom-up MS-based workflow for protein biomarker screening. Biomarker verification/validation requires absolute quantification of surrogate peptides in the sample matrix, a requirement that is best achieved using well-characterized standards. To ensure robust quantitative measurement, QC checks should be routinely performed.

CIL offers a collection of PeptiQuant™ Assay Kits (from MRM Proteomics Inc.) for QC and biomarker assessment using bottom-up LC-MS/MS methodologies. The QC kits are designed to evaluate the performance of an LC-MS platform, either alone or in combination with a human plasma proteomics workflow (see PeptiQuant Plus Quality Control Kits flyer for details). The biomarker assessment kits (BAKs) are intended to help researchers screen target panels of candidate protein disease biomarkers in human or mouse plasma samples (see PeptiQuant Plus Biomarkers Assessment Kits flyer for details).

Regarding the methodology, the PeptiQuant kits employ mixtures of synthetic stable isotope-labeled (SIS) and natural (NAT) peptides in the generation of of calibration curves and curve QCs. The SIS mixes are additionally used for matrix spike. Quantitation is achieved via forward curves in the Plus kits (approaches described in PMID: 27341553). The validated assays were rigorously characterized according to the complete set of CPTAC (Clinical Proteomic Tumor Analysis Consortium) guidelines and are available for viewing on the CPTAC Assay Portal.

Resources

PeptiQuant™ Plus Quality Control Kits

PeptiQuant™ Plus Biomarker Assessment Kits

Stable Isotope-Labeled Peptide and Protein Reagents/Kits

S ets, Mixes, and Kits for MS 'Omics and MS/MS Screening

Frequently Asked Questions

How many peptides/protein and MRM transitions do the PeptiQuant Plus kits monitor?

For each kit, one peptide/protein and three transitions per peptide.

How many calibration curves can be prepared with the PeptiQuant Plus BAKs?

The SIS and NAT mixes enable eight-point curves that span a 1000-fold concentration range. Each calibrant level is to be measured in singleton.

What are the contents of the PeptiQuant Plus kits?

Supplied with the kits are chemicals/reagents and a USB of product documents. Please see the QC kit and BAK flyers for details.

Are the PeptiQuant Plus kits platform dependent?

The kits have been optimized on specific LC-MS platforms (see QC kit and BAK flyers for details). The validated methods are provided with the kits in an instrument file, while the transition (in MRM analysis) or precursor ion (in PRM analysis) details are provided in a Skyline file for data analysis. These files are supplied, together with the user manual, on a USB along with the chemicals/reagents. Note that while the kits are optimized for specific LC-MS platforms, the kits are extendable to other platforms following minor parameter optimizations.

What types of disease association have the proteins in the human and mouse plasma PeptiQuant Plus BAKS been linked to?

The proteins have been linked to innumerable diseases (e.g., cancer, cardiovascular, neurodegenerative). Specific linkages can be provided upon request.

Are the 125 proteins in the human plasma BAK-125 contained in the human plasma BAK-270?

Yes. The BAK-270 is complemented by an additional 145 proteins of moderate-to-low abundance. Please see the PeptiQuant Plus Biomarker Assessment Kits flyer for panel details.

References

Percy, A.J.; Borchers, C.H. 2021. Detailed method for performing the ExSTA approach in quantitative bottom-up plasma proteomics. Methods Mol Biol, 2228, 353-384. PMID: 33950503

Mohammed, Y.; Bhowmick, P.; Michaud, S.A.; et al. 2021. Mouse Quantitative Proteomics Knowledgebase: reference protein concentration ranges in 20 mouse tissues using 5000 quantitative proteomics assays. Bioinformatics, in press. PMID: 33483739

Ayton, S.; Janelidze, S.; Roberts, B.; et al. 2021. Acute phase markers in CSF reveal inflammatory changes in Alzheimer’s disease that intersect with pathology, APOE ε4, sex and age. Prog Neurobiol, 101904. PMID: 32882319

Gaither, C.; Popp, R.; Mohammed, Y.; et al. 2020. Determination of the concentration range for 267 proteins from 21 lots of commercial human plasma using highly multiplexed multiple reaction monitoring mass spectrometry. Analyst, 145(10), 3634-3644. PMID: 32255452

Tilburg, J.; Michaud, S.A.; Maracle, C.X.; et al. 2020. Plasma protein signatures of a murine venous thrombosis model and Slc44a2 knockout mice using quantitative-targeted proteomics. Thromb Haemost, 120(3), 423-436. PMID: 32135563

Bhardwaj, M.; Weigl, K.; Tikk, K.; et al. 2020. Multiplex quantitation of 270 plasma protein markers to identify a signature for early detection of colorectal cancer. Eur J Cancer, 127, 30-40. PMID: 31972396

Michaud, S.A.; Sinclair, N.J.; Pětrošovå, H.; et al. 2018. Molecular phenotyping of laboratory mouse strains using 500 multiple reaction monitoring mass spectrometry plasma assays. Commun Biol, 1(78). PMID: 30271959

Orti, V.; Mertens, B.; Vialaret, J.; et al. 2018. Data from a targeted proteomics approach to discover biomarkers in saliva for the clinical diagnosis of perioddontitis. Data Brief, 18, 294-299. PMID: 29900194

Mohammed, Y.; Pan, J.; Zhang, S.; et al. 2018. ExSTA: external standard addition method for accurate high-throughput quantitation in targeted proteomics experiments. Proteomics Clin Appl, 12(2). PMID: 28895300

LeBlanc, A.; Michaud, S.A.; Percy, A.J.; et al. 2017. Multiplexed MRM-based protein quantitation using two different stable isotope-labeled peptide isotopologues for calibration. J Proteome Res, 16(7), 2527-2536. PMID: 28516774

Percy, A.J.; Michaud, S.A.; Jardim, A.; et al. 2016. Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue. Proteomics, 17(7). PMID: 27688154

Hirtz,C.; Vialaret, J.; Nowak, N.; et al. 2016. Absolute quantification of 35 plasma biomarkers in human saliva using targeted MS. Bioanalysis, 8(1), 43-53. PMID: 26647646

Percy, A.J.; Mohammed, Y.; Yang, J.; et al. 2015. A standard kit for automated quantitative assessment of candidate protein biomakers in human plasma. Bioanalysis, 7(23), 2991-3004. PMID: 26626236

Mohammed, Y.; Percy, A.J.; Chambers, A.G.; et al. 2015. Qualis-SIS: automated standard curve generation and quality assessment for multiplexed targeted quantitative proteomic experiments with labeled standards. J Proteome Res, 14(2), 1137-1146. PMID: 25546269

Percy, A.J.; Tamura-Wells, J.; Albarb, J.P.; et al. 2015. Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment. EuPA Open Proteomics, 8, 6-15. doi.org/10.1016/j.euprot.2015.06.001

Percy, A.J.; Simon, R.; Chambers, A.G.; et al. 2014. Enhanced sensitivity and mulitplexing with 2D LC/MRM-MS and labeled standards for deeper and more comprehensive protein quantitation. J Proteomics, 106, 113-124. PMID: 24769237

Percy, A.J.; Chambers, A.G.; Yang, J.; et al. 2013. Method and platform standardization in MRM-based quantitative plasma proteomics. J Proteomics, 95, 66-76. PMID: 23933160

Percy, A.J.; Chambers, A.G.; Smith, D.S.; et al. 2013. Standardized protocols for quality control of MRM-based plasma proteomic workflows. J Proteome Res, 12(1), 222-233. PMID: 23245390

Andrew Percy, PhD

Senior Applications Chemist – Mass Spectrometry

Dr. Andrew Percy is the Senior Applications Chemist for Mass Spectrometry and the MS ‘Omics Product Manager at CIL. His responsibilities minimally involve providing technical support, overseeing product development, identifying new product market opportunities, assisting in the analysis of product-related applications, and writing/reviewing marketing literature.

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