QconCAT

What is a QconCAT?

A QconCAT (Quantification conCATamer) is an artificial protein, generated by concatenation of proteotypic peptides.

Advantages

  • Accurate quantification
  • Easy multiplexing (quantify a complete proteome using multiple QconCATs)
  • Scalable to 1000’s of samples/data points
  • Reproducible
  • Robust synthesis of large amounts
  • Easy integration into established quantitative protein analysis setup
  • Compatible with other methods
  • Internal sample preparation control

Application areas

QconCATs are valuable tools for research applications involving quantitative proteomics and have been used in numerous academic and industrial research projects.

Large scale quantification

A single custom-made QconCAT enables targeted measurement and quantification of several tens of proteins. Using multiple QconCATs facilitates quantification of hundreds of proteins in a single experiment.

QconCATs by PolyQuant were used for absolute quantification of complete proteomes, networks and pathways.

Selected publications

  • Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring.
    Lawless C, Holman SW, Brownridge P, Lanthaler K, Harman VM, Watkins R, Hammond DE, Miller RL, Sims PF, Grant CM, Eyers CE, Beynon RJ, Hubbard SJ.
    Mol Cell Proteomics. 2016 Apr;15(4):1309-22. [PubMed]
    Lawless et al. quantified over 1800 S. cerevisiae proteins by selected reaction monitoring (SRM) mass spectrometry using over 100 QconCATs.
  • Absolute protein quantification of the yeast chaperome under conditions of heat shock.
    Mackenzie RJ, Lawless C, Holman SW, Lanthaler K, Beynon RJ, Grant CM, Hubbard SJ, Eyers CE.
    Proteomics. 2016 Jun 2. [PubMed]
    Mackenzie et al determined copy per cell values for 49 key chaperones in S. cerevisiae under conditions of normal growth and heat shock, by selected reaction monitoring (SRM) mass spectrometry using QconCATs as reference peptides.
  • Quantitative Proteomics of Hepatic Drug-Metabolizing Enzymes and Transporters in Patients with Colorectal Cancer Metastasis
    Vasilogianni AM, Al-Majdoub ZM, Achour B, Peters SA, Barber J, Rostami-Hodjegan A.
    Clin Pharmacol Ther. 2022 May 3. [Pubmed]
    Vasilogianni et al. studied the impact of liver cancer metastasis on protein abundance of 22 drug-metabolizing enzymes (DMEs) and 25 transporters. They used targeted proteomics and QconCATs as reference standards for analysis of microsome preparations from individuals and cancer patients.
  • Full humanization of the glycolytic pathway in Saccharomyces cerevisiae
    Boonekamp FJ, Knibbe E, Vieira-Lara MA, Wijsman M, Luttik MAH, van Eunen K, Ridder MD, Bron R, Almonacid Suarez AM, van Rijn P, Wolters JC, Pabst M, Daran JM, Bakker BM, Daran-Lapujade P.
    Cell Rep. 2022 Jun 28;39(13):111010. [Pubmed]
    Boonekamp et al generated and characterized a yeast strain with a humanized glycolytic pathway, providing a new model to study human glycolysis in a simplified context. In their study they used 6 QconCATs to determine absolute concentrations of glycolytic targets by targeted proteomics.
  • A family of QconCATs (Quantification conCATemers) for the quantification of human pharmacological target proteins
    Vasilogianni AM, El-Khateeb E, Achour B, Alrubia S, Rostami-Hodjegan A, Barber J, Al-Majdoub ZM.
    J Proteomics. 2022 Jun 15;261:104572. [Pubmed]
    In this report, the authors describe the development and characterization of two QconCAT constructs for quantification of 24 enzymes and 21 receptor tyrosine kinases (RTKs), complementing two previously reported QconCATs for the quantification of key enzymes and drug transporters. The QconCATs were successfully applied in quantification of target proteins in human liver.

Complex stoichiometry and isoform specificity

QconCATs are perfectly suited for absolute quantification of components of protein complexes, either in whole cell lysates or after immunoprecipitation. By selecting isoform-specific tryptic peptides, QconCATs allow quantification of highly homologous proteins that can otherwise not be distinguished by antibodies.

Selected publications

  • CRAF dimerization with ARAF regulates KRAS-driven tumor growth.
    Venkatanarayan A, Liang J, Yen I, Shanahan F, Haley B, Phu L, Verschueren E, Hinkle TB, Kan D, Segal E, Long JE, Lima T, Liau NPD, Sudhamsu J, Li J, Klijn C, Piskol R, Junttila MR, Shaw AS, Merchant M, Chang MT, Kirkpatrick DS, Malek S.
    Cell Rep. 2022 Feb 8;38(6):110351. [PubMed]
    Venkatanarayan et al. used quantitative proteomics to demonstrate increased levels of CRAF:ARAF dimers in KRAS mutant cells and PRM analysis to quantify the stoichiometric relationships between wt and mutant MAPK components using a QconCAT incorporating wild type and mutant sequences for detection of disease associated mutations.
  • PIKES Analysis Reveals Response to Degraders and Key Regulatory Mechanisms of the CRL4 Network.
    Reichermeier KM, Straube R, Reitsma JM, Sweredoski MJ, Rose CM, Moradian A, den Besten W, Hinkle T, Verschueren E, Petzold G, Thomä NH, Wertz IE, Deshaies RJ, Kirkpatrick DS.
    Mol Cell. 2020 Jan 15. [Pubmed]
    Reichermeier et al. determined the stoichiometric relationships between approx. 30 proteins in cell lysates and immunoprecipitated samples using targeted proteomics and a QconCAT comprising of 67 peptides for 31 proteins.
  • Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach.
    Stelder SK, Benito de Moya C, Hoefsloot HCJ, de Koning LJ, Brul S, de Koster CG.
    J Proteome Res. 2018 Feb 2;17(2):903-917 [Pubmed]
    Stelder et al. quantified crucial spore proteins using a QconCAT reference standard, determining the absolute abundance of 21 proteins, covering approx. 5.66% of the total spore weight in wild type and approx. 4.13% in the ΔCotE mutant.
  • Rigorous determination of the stoichiometry of protein phosphorylation using mass spectrometry.
    Johnson H, Eyers CE, Eyers PA, Beynon RJ, Gaskell SJ.
    Journal of the American Society for Mass Spectrometry 2009 Dec;20(12):2211-20.
    [PubMed]
    Johnson et al. use QconCATs to determine absolute protein concentrations and the stoichiometry of phosphorylation at predefined sites.
  • COMMD Family Regulates Plasma LDL Levels and Attenuates Atherosclerosis Through Stabilizing the CCC Complex in Endosomal LDLR Trafficking.
    Fedoseienko A, Wijers M, Wolters JC, Dekker D, Smit M, Huijkman N, Kloosterhuis N, Klug H, Schepers A, Willems van Dijk K, Levels JH, Billadeau DD, Hofker MH, van Deursen J, Westerterp M, Burstein E, Kuivenhoven JA, van de Sluis B.
    Circ Res. 2018 Mar 15. [Pubmed]
    Fedoseienko et al. used QconCATs to quantify the protein concentrations of the COMMDs, components of retromer, the CCC and WASH complexes, etc in the samples of the different mouse models.
  • Characterization of CYP2B6 K262R allelic variants by quantitative allele-specific proteomics using a QconCAT standard
    Barber J, Russell MR, Rostami-Hodjegan A, Achour B.
    J Pharm Biomed Anal. 2020 Jan 30;178:112901. [Pubmed]
    Barber et al. used a QconCAT standard for targeted proteomics, simultaneously determining protein abundance and missense polymorphisms.
  • Loss of hepatic SMLR1 causes hepatosteatosis and protects against atherosclerosis due to decreased hepatic VLDL secretion
    van Zwol W, Rimbert A, Wolters JC, Smit M, Bloks VW, Kloosterhuis NJ, Huijkman N, Koster MH, Tharehalli U, de Neck SM, Bournez C, Fuh MM, Kuipers J, Rajan S, de Bruin A, Ginsberg HN, van Westen GJP, Hussain MM, Scheja L, Heeren J, Zimmerman P, van de Sluis B, Kuivenhoven JA.
     Hepatology. 2022 Sep 2. [Pubmed]
    Van Zwol et al. identified small leucine-rich protein 1 (SLMR1) as a player in the VLDL biogenesis pathway and assessed its role by generating a liver-specific knockout mouse. Due to absence of available antibodies, the downregulation of Smlr1 was determined by targeted proteomics.

Watch this video by Rob Beynon explaining how protein isoforms can be quantified using QconCAT technology:

show video

Biomarker discovery and validation, clinical research and diagnostics

QconCATs enhance data quality of targeted measurements in biomarker research projects. In clinical research, QconCATs can be also applied to pharmacological analyses, vaccine development and diagnostics.

Selected publications

  • Cov2MS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid Protein.
    Van Puyvelde B, Van Uytfanghe K, Van Oudenhove L, Gabriels R, Van Royen T, Matthys A, Razavi M, Yip R, Pearson T, Drouin N, Claereboudt J, Foley D, Wardle R, Wyndham K, Hankemeier T, Jones D, Saelens X, Martens G, Stove CP, Deforce D, Martens L, Vissers JPC, Anderson NL, Dhaenens M.
    Anal Chem. 2022 Dec 20;94(50):17379-17387. [Pubmed]
    Van Puyvelde et al improved Cov-MS by adding SISCAPA technology to enrich proteotypic peptides of the SARS-CoV-2 nucleocapsid (N) protein from trypsin-digested patient samples. The Cov2MS assay is compatible with most matrices including nasopharyngeal swabs, saliva, and plasma, has increased sensitivity and a strong positive correlation with qPCR detection beyond a quantification cycle of 30-31.
  • A fast and sensitive absolute quantification assay for the detection of SARS-CoV-2 peptides using parallel reaction monitoring mass spectrometry
    Gajbhiye A, Nalbanta A, Heunisa T, Sidgwick F, Porter A, Tahab Y, Trost M
    Journal of Proteomics. Vol. 265, 15 August 2022. [Pubmed]
    Gajbhiyea et al. developed a high-throughput PRM-MS assay to directly detect viral peptides in nasopharyngeal swab samples. The assay enables sensitive detection and absolute quantification of SARS-CoV-2 nucleocapsid peptides with short turn-around times by using the Cov-MS isotopically labelled synthetic polypeptide as reference standard.
  • Proteomics of colorectal cancer liver metastasis: A quantitative focus on drug elimination and pharmacodynamics effects
    Vasilogianni AM, Al-Majdoub ZM, Achour B, Peters SA, Rostami-Hodjegan A, Barber J.
    Br J Clin Pharmacol. 2022 Feb;88(4):1811-1823. [Pubmed]
    Vasilogianni et al. used QconCATs to quantify drug-metabolising enzymes, transporters, receptor tyrosine kinases (RTK) and protein markers in samples from colorectal cancer liver metastasis (CLRM) patients. The detected alterations in protein abundance may provide valuable information for diagnosis and therapeutic intervention.
  • Targeted LC-MS/MS for the evaluation of proteomics biomarkers in the blood of neonates with necrotizing enterocolitis and late-onset sepsis.
    Chatziioannou AC, Wolters JC, Sarafidis K, Thomaidou A, Agakidis C, Govorukhina N, Kuivenhoven JA, Bischoff R, Theodoridis G.
    Anal Bioanal Chem. 2018 Nov;410(27):7163-7175. [Pubmed]
    Chatziioannou et al. used QconCATs and synthetic peptides belonging to 47 protein markers for a prospective case-control study evaluating serum proteomics profiles. They were able to define two panels of three proteins each that allow highly sensitive diagnosis of late-onset sepsis (LOS) and differential diagnosis between LOS and necrotizing enterocolitis.
  • Non-uniformity of Changes in Drug-Metabolizing Enzymes and Transporters in Liver Cirrhosis: Implications for Drug Dosage Adjustment.
    El-Khateeb E, Achour B, Al-Majdoub ZM, Barber J, Rostami-Hodjegan A.
    Mol Pharm. 2021 Sep 6;18(9):3563-3577.[Pubmed]
    El-Katheeb et al. used QconCAT-based targeted proteomics to determine the absolute abundance of 51 drug-metabolizing enzymes and transporters in human liver microsomes across the three degrees for cirrhosis severity to determine their impact on the predictive performance of PBPK (physiologically based pharmacokinetic) models. Their work demonstrates the utility of proteomics-informed PBPK modeling for drug-specific dose adjustments in liver cirrhosis.
  • Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients
    Bart Van Puyvelde, Katleen Van Uytfanghe, Olivier Tytgat, Laurence Van Oudenhove, Ralf Gabriels, Robbin Bouwmeester, Simon Daled, Tim Van Den Bossche, Pathmanaban Ramasamy, Sigrid Verhelst, Laura De Clerck, Laura Corveleyn, Sander Willems, Nathan Debunne, Evelien Wynendaele, Bart De Spiegeleer, Peter Judak, Kris Roels, Laurie De Wilde, Peter Van Eenoo, Tim Reyns, Marc Cherlet, Emmie Dumont, Griet Debyser, Ruben t’Kindt, Koen Sandra, Surya Gupta, Nicolas Drouin, Amy Harms, Thomas Hankemeier, Donald J. L. Jones, Pankaj Gupta, Dan Lane, Catherine S. Lane, Said El Ouadi, Jean-Baptiste Vincendet, Nick Morrice, Stuart Oehrle, Nikunj Tanna, Steve Silvester, Sally Hannam, Florian C. Sigloch, Andrea Bhangu-Uhlmann, Jan Claereboudt, N. Leigh Anderson, Morteza Razavi, Sven Degroeve, Lize Cuypers, Christophe Stove, Katrien Lagrou, Geert A. Martens, Dieter Deforce, Lennart Martens, Johannes P. C. Vissers, and Maarten Dhaenens.
    JACS Au 2021, 1, 6, 750–765.[Pubmed]
    The authors established a consortium consisting of 15 academic laboratories and several industrial partners to identify peptides for MS-based detection of SARS-CoV-2 infection. They describe the full pipeline for developing a fast and sensitive MS-based assay for detection of viral presence directly in clinical samples using conventional instrumentation.

Quality control

Production of therapeutic proteins in biological systems demands for sophisticated quality control as even low levels of process-related impurities (host cell proteins, HCP) negatively impact stability and efficacy of the biopharmaceutical products and may cause a potential risk for patient health. Determination and monitoring of the levels of HCPs using custom-made QconCATs, developed for a biopharmaceutical product, provides critical information for determination of protein quality and process evaluation.

more…

Most recent publications employing QconCAT technology
  • Proteomic quantification of receptor tyrosine kinases involved in the development and progression of colorectal cancer liver metastasis.
    Vasilogianni AM, Al-Majdoub ZM, Achour B, Peters SA, Rostami-Hodjegan A, Barber J.
    Front Oncol. 2023 Feb 20;13:1010563. [Pubmed]
    Vasilogianni et al., assessed protein abundance of 21 RTKs in 15 healthy and 18 cancerous liver samples. They used a QconCAT to validate protein abundance, identifying proteins with reduced protein levels in cancerous liver samples, but also proteins whose protein levels were increased.
  • Targeting Ligand Independent Tropism of siRNA-LNP by Small Molecules for Directed Therapy of Liver or Myeloid Immune Cells
    Lin C, Mostafa A, Jans A, Wolters JC, Mohamed MR, Van der Vorst EPC, Trautwein C, Bartneck M.
    Adv. Healthcare Mater. 2023 Jan 8 [Pubmed]
    During the SARS-CoV-2 pandemic, mRNA vaccines were developed. These vaccines require lipid nanoparticles (LNPs) for stability and to ensure intracellular delivery. To study the mechanism of LNP distribution in the body, Lin et al performed proteomics analysis of liver tissue and serum. They performed untargeted proteomics to detect alterations of protein abundance in serum upon siRNA-LNP administration and targeted proteomics for more in-depth analysis of selected proteins using QconCATs.
  • Pharmacological inhibition of MEK1/2 signaling disrupts bile acid metabolism through loss of Shp and enhanced Cyp7a1 expression.
    Verzijl CRC, van de Peppel IP, Eilers RE, Bloks VW, Wolters JC, Koehorst M, Kloosterhuis NJ, Havinga R, Jalving M, Struik D, Jonker JW.
    Biomed Pharmacother. 2023 Mar;159:114270. [Pubmed]
    In their study, Verzijl et al. quantified 13 proteins involved in hepatic bile acid metabolism using targeted proteomics. The 20 reference peptides were derived from 13C-labelled QconCATs from previous studies.
  • Cargo-Specific Role for Retriever Subunit VPS26C in Hepatocyte Lipoprotein Receptor Recycling to Control Postprandial Triglyceride-Rich Lipoproteins.
    Vos DY, Wijers M, Smit M, Huijkman N, Kloosterhuis NJ, Wolters JC, Tissink JJ, Pronk ACM, Kooijman S, Rensen PCN, Kuivenhoven JA, van de Sluis B.
    Arterioscler Thromb Vasc Biol. 2023 Jan;43(1):e29-e45. [Pubmed]
    Vos et al., analyzed the functions of retriever subunits VPS35L and VPS26C in endosomal transport of lipoprotein receptors in hepatocytes. They used targeted proteomics and QconCATs to determine the protein levels of key proteins in COMMD1 or VPS35L-deficient mice and VPS26C-deficient (KO) Hepa1-6 cells and also to determine the protein levels of CCC and retriever subunits in COMMD1-immunoprecipitations.
  • Cov2MS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid Protein.
    Van Puyvelde B, Van Uytfanghe K, Van Oudenhove L, Gabriels R, Van Royen T, Matthys A, Razavi M, Yip R, Pearson T, Drouin N, Claereboudt J, Foley D, Wardle R, Wyndham K, Hankemeier T, Jones D, Saelens X, Martens G, Stove CP, Deforce D, Martens L, Vissers JPC, Anderson NL, Dhaenens M.
    Anal Chem. 2022 Dec 20;94(50):17379-17387. [Pubmed]
    Van Puyvelde et al improved Cov-MS by adding SISCAPA technology to enrich proteotypic peptides of the SARS-CoV-2 nucleocapsid (N) protein from trypsin-digested patient samples. The Cov2MS assay is compatible with most matrices including nasopharyngeal swabs, saliva, and plasma, has increased sensitivity and a strong positive correlation with qPCR detection beyond a quantification cycle of 30-31.
  • Cargo-Specific Role for Retriever Subunit VPS26C in Hepatocyte Lipoprotein Receptor Recycling to Control Postprandial Triglyceride-Rich Lipoproteins
    Vos DY, Wijers M, Smit M, Huijkman N, Kloosterhuis NJ, Wolters JC, Tissink JJ, Pronk ACM, Kooijman S, Rensen PCN, Kuivenhoven JA, van de Sluis B.
    Arterioscler Thromb Vasc Biol. 2022 Nov 10. [Pubmed]
    Vos et al., analyzed the functions of retriever subunits VPS35L and VPS26C in endosomal transport of lipoprotein receptors in hepatocytes. They used targeted proteomics and QconCATs to determine the protein levels of key proteins in COMMD1 or VPS35L-deficient mice and VPS26C-deficient (KO) Hepa1-6 cells and also to determine the protein levels of CCC and retriever subunits in COMMD1-immunoprecipitations.
  • Loss of hepatic SMLR1 causes hepatosteatosis and protects against atherosclerosis due to decreased hepatic VLDL secretion
    van Zwol W, Rimbert A, Wolters JC, Smit M, Bloks VW, Kloosterhuis NJ, Huijkman N, Koster MH, Tharehalli U, de Neck SM, Bournez C, Fuh MM, Kuipers J, Rajan S, de Bruin A, Ginsberg HN, van Westen GJP, Hussain MM, Scheja L, Heeren J, Zimmerman P, van de Sluis B, Kuivenhoven JA.
    Hepatology. 2022 Sep 2 [Pubmed]
    Van Zwol et al. identified small leucine-rich protein 1 (SLMR1) as a player in the VLDL biogenesis pathway and assessed its role by generating a liver-specific knockout mouse. Due to absence of available antibodies, the downregulation of Smlr1 was determined by targeted proteomics.
  • A fast and sensitive absolute quantification assay for the detection of SARS-CoV-2 peptides using parallel reaction monitoring mass spectrometry
    Gajbhiye A, Nalbanta A, Heunisa T, Sidgwick F, Porter A, Tahab Y, Trost M
    Journal of Proteomics. Vol. 265, 15 August 2022. [Pubmed]
    Gajbhiyea et al. developed a high-throughput PRM-MS assay to directly detect viral peptides in nasopharyngeal swab samples. The assay enables sensitive detection and absolute quantification of SARS-CoV-2 nucleocapsid peptides with short turn-around times by using the Cov-MS isotopically labelled synthetic polypeptide as reference standard.
  • Butyrate oxidation attenuates the butyrate-induced improvement of insulin sensitivity in myotubes
    Rios-Morales M, Vieira-Lara MA, Homan E, Langelaar-Makkinje M, Gerding A, Li Z, Huijkman N, Rensen PCN, Wolters JC, Reijngoud DJ, Bakker BM.
    Journal of Proteomics. Biochim Biophys Acta Mol Basis Dis. 2022 Jul 7:166476. [Pubmed]In their study on the regulation of butyrate-induced skeletal muscle metabolism, Rios-Morales et al. examined the effects of butyrate and palmitate treatment on key proteins by quantitative targeted proteomics using QconCAT reference standards.
  • Full humanization of the glycolytic pathway in Saccharomyces cerevisiae
    Boonekamp FJ, Knibbe E, Vieira-Lara MA, Wijsman M, Luttik MAH, van Eunen K, Ridder MD, Bron R, Almonacid Suarez AM, van Rijn P, Wolters JC, Pabst M, Daran JM, Bakker BM, Daran-Lapujade P.
    Cell Rep. 2022 Jun 28;39(13):111010. [Pubmed]
    Boonekamp et al generated and characterized a yeast strain with a humanized glycolytic pathway, providing a new model to study human glycolysis in a simplified context. In their study they used 6 QconCATs to determine absolute concentrations of glycolytic targets by targeted proteomics.
  • A family of QconCATs (Quantification conCATemers) for the quantification of human pharmacological target proteins
    Vasilogianni AM, El-Khateeb E, Achour B, Alrubia S, Rostami-Hodjegan A, Barber J, Al-Majdoub ZM.
    J Proteomics. 2022 Jun 15;261:104572. [Pubmed]
    In this report, the authors describe the development and characterization of two QconCAT constructs for quantification of 24 enzymes and 21 receptor tyrosine kinases (RTKs), complementing two previously reported QconCATs for the quantification of key enzymes and drug transporters. The QconCATs were successfully applied in quantification of target proteins in human liver.
  • Proteomic quantification of perturbation to pharmacokinetic target proteins in liver disease
    Vasilogianni AM, El-Khateeb E, Al-Majdoub ZM, Alrubia S, Rostami-Hodjegan A, Barber J, Achour B.
    J Proteomics. 2022 May 7:104601. [Pubmed]
    Targeted proteomics is the gold standard for measurement of key pharmacokinetic targets. To determine the suitability of label-free methods for measuring global effects of liver disease on the metabolic capacity of the liver the authors compared targeted measurements using QconCATs to several label-free proteomics methods.
  • Quantitative Proteomics of Hepatic Drug-Metabolizing Enzymes and Transporters in Patients with Colorectal Cancer Metastasis
    Vasilogianni AM, Al-Majdoub ZM, Achour B, Peters SA, Barber J, Rostami-Hodjegan A.
    Clin Pharmacol Ther. 2022 May 3. [Pubmed]
    Vasilogianni et al. studied the impact of liver cancer metastasis on protein abundance of 22 drug-metabolizing enzymes (DMEs) and 25 transporters. They used targeted proteomics and QconCATs as reference standards for analysis of microsome preparations from individuals and cancer patients.
  • A novel role for GalNAc-T2 dependent glycosylation in energy homeostasis
    Verzijl CRC, Oldoni F, Loaiza N, Wolters JC, Rimbert A, Tian E, Yang W, Struik D, Smit M, Kloosterhuis NJ, Fernandez AJ, Samara NL, Ten Hagen KG, Dalal K, Chernish A, McCluggage P, Tabak LA, Jonker JW, Kuivenhoven JA.
    Mol Metab. 2022 Mar 15:101472. [Pubmed]
    Verzijl et al. showed an important role for GalNAc-T2 in whole-body energy homeostatis. In their study they used a QconCAT to simultaneously quantify selected substrates of GalNAc-T2 in plasma samples of Galnt2+/+ and Galnt2-/- mice.
  • CRAF dimerization with ARAF regulates KRAS-driven tumor growth.
    Venkatanarayan A, Liang J, Yen I, Shanahan F, Haley B, Phu L, Verschueren E, Hinkle TB, Kan D, Segal E, Long JE, Lima T, Liau NPD, Sudhamsu J, Li J, Klijn C, Piskol R, Junttila MR, Shaw AS, Merchant M, Chang MT, Kirkpatrick DS, Malek S.
    Cell Rep. 2022 Feb 8;38(6):110351. [PubMed]
    Venkatanarayan et al. used quantitative proteomics to demonstrate increased levels of CRAF:ARAF dimers in KRAS mutant cells and PRM analysis to quantify the stoichiometric relationships between wt and mutant MAPK components using a QconCAT incorporating wild type and mutant sequences for detection of disease associated mutations.
  • Mice with a deficiency in Peroxisomal Membrane Protein 4 (PXMP4) display mild changes in hepatic lipid metabolism
    Blankestijn M, Bloks VW, Struik D, Huijkman N, Kloosterhuis N, Wolters JC, Wanders RJA, Vaz FM, Islinger M, Kuipers F, van de Sluis B, Groen AK, Verkade HJ, Jonker JW.
    Sci Rep. 2022 Feb 15;12(1):2512. [PubMed]
    Blankestijn et al. studied the physiolocial function of the peroxisomal PPARα target PXMP4 by generating a Pxmp4 knockout mouse model. To confirm the absence of PXMP4 in livers of Pxmp4 −/− mice, targeted proteomics were performed, using a QconCAT for providing the reference peptides for Pxmp4.
  • Proteomics of colorectal cancer liver metastasis: A quantitative focus on drug elimination and pharmacodynamics effects
    Vasilogianni AM, Al-Majdoub ZM, Achour B, Peters SA, Rostami-Hodjegan A, Barber J.
    Br J Clin Pharmacol. 2022 Feb;88(4):1811-1823. [Pubmed]
    Vasilogianni et al. used QconCATs to quantify drug-metabolising enzymes, transporters, receptor tyrosine kinases (RTK) and protein markers in samples from colorectal cancer liver metastasis (CLRM) patients. The detected alterations in protein abundance may provide valuable information for diagnosis and therapeutic intervention.

 

Original publications introducing the QconCAT method

  • Beynon R. J., Doherty M. K., Pratt J. M., Gaskell S. J. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides.
    Nature Methods Vol. 2 (8), August 2005, 587-589. [download]
  • Pratt J. M., Simpson D. M., Doherty M. K., Rivers J., Gaskell S. J., Beynon R. J. Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes.
    Nature Protocols Vol. 1 (2), 2006, 1029-1043. [download]

 

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