QuantaKinome™

A unique, novel mass spectrometry-based multiplexed endogenous kinase activity profiling technology.

  • Robust & established targeted MS

  • Endogenous kinase activities

  • Multiplexed, sensitive and quantitative

  • Covers over 150 human kinases

  • Cells, tissues, (liquid) biopsies

  • Patented activation loop-based assay

  • Developed by world-leading scientists

  • Under development

Phosphoproteomics

Advanced LC-MS Solutions

Our phosphoproteomics services comprise MS-based proteomics solutions for analyses of cells and tissues. This service allows for the identification and quantification of proteins, phosphopeptides, and kinases in a single experiment

 

Protein phosphorylation on serine, threonine and tyrosine residues is a common post-translational modification and occurs on over one-third of all cellular proteins. In humans, 518 protein kinases have been identified that regulate phosphorylation networks and control biological processes such as proliferation, differentiation, and apoptosis. Phosphorylation takes place mainly on serine residues (86.4%), followed by threonine residues (11.8%) and tyrosine residues (1.8%).

 

Workflows

PEPSCOPE’s phosphoproteomics workflows generally require around 1 mg of sample lysate, use urea-based protein digestion, followed by peptide desalting and lyophilization, peptide fractionation using high-pH reversed-phase chromatography. Phosphopeptides are enriched, sometimes multiple times, resulting in numerous LC-MS/MS measurements per biological sample to be analyzed (PEPSCOPE can do this up to 10 different samples).

 

At PEPSCOPE, we multiplex samples to study proteome-wide phosphorylation events through different quantitative mass spectrometry approaches, such as Tandem-Mass-Targets (TMT) labeling. TMT is a chemical derivatization technique used to identify, compare and quantify proteins from multiple samples in one single experiment by mass spectrometry.

Selected publications
  1. PaDuA: a Python library for high-throughput (phospho)proteomic data analysis. Ressa A, Fitzpatrick M, van den Toorn HW, Heck AJR, Altelaar AFM. J Proteome Res. 2019 Feb 1;18(2):576-584. doi: 10.1021/acs.jproteome.8b00576. Epub 2018 Dec 21.

  2. Analysis of NFATc1 amplification in T cells for pharmacodynamic monitoring of tacrolimus in kidney transplant recipients. Kannegieter NM, Hesselink DA, Dieterich M, de Graav GN, Kraaijeveld R, Baan CC. PLoS One. 2018 Jul 23;13(7):e0201113. doi: 10.1371/journal.pone.0201113. eCollection 2018. PubMed PMID: 30036394; PubMed Central PMCID: PMC6056039.

  3. High-Throughput Assessment of Kinome-Wide Activation States (October 30, 2018). Schmidlin T, Rontogianni S, van Gelder CAGH, Stecker KE, van den Eshof BL, Kemper K, Lips EH, van den Biggelaar M, Peeper DS, Heck AJR, Altelaar AFM. Available at SSRN: https://ssrn.com/abstract=3275288 http://dx.doi.org/10.2139/ssrn.3275288

  4. A System-wide Approach to Monitor Responses to Synergistic BRAF and EGFR Inhibition in Colorectal Cancer Cells. Ressa A, Bosdriesz E, de Ligt J, Mainardi S, Maddalo G, Prahallad A, Jager M, de la Fonteijne L, Fitzpatrick M, Groten S, Altelaar AFM, Bernards R, Cuppen E, Wessels L, Heck AJR. Mol Cell Proteomics. 2018 Oct;17(10):1892-1908. doi: 10.1074/mcp.RA117.000486. DOI: 10.1074/mcp.RA117.000486. PMID: 29970458; PubMed Central PMCID: PMC6166676.

  5. Determination of Site-Specific Phosphorylation Ratios in Proteins with Targeted Mass Spectrometry. Dekker LJM, Zeneyedpour L, Snoeijers S, Joore J, Leenstra S, Luider TM. J Proteome Res. 2018 Apr 6;17(4):1654-1663. doi: 10.1021/acs.jproteome.7b00911. Epub 2018 Mar 9. PMID: 29457462

  6. Pharmacodynamic Monitoring of Tacrolimus-Based Immunosuppression in CD14+ Monocytes After Kidney Transplantation. Kannegieter NM, Hesselink DA, Dieterich M, de Graav GN, Kraaijeveld R, Rowshani AT, Leenen PJM, Baan CC. Ther Drug Monit. 2017 Oct;39(5):463-471. doi: 10.1097/FTD.0000000000000426. PubMed PMID: 28640063.

  7. Differential T Cell Signaling Pathway Activation by Tacrolimus and Belatacept after Kidney Transplantation: Post Hoc Analysis of a Randomised-Controlled Trial. Kannegieter NM, Hesselink DA, Dieterich M, de Graav GN, Kraaijeveld R, Baan CC. Sci Rep. 2017 Nov 9;7(1):15135. doi: 10.1038/s41598-017-15542-y. PubMed PMID: 29123208; PubMed Central PMCID: PMC5680251.

  8. Set of Novel Automated Quantitative Microproteomics Protocols for Small Sample Amounts and Its Application to Kidney Tissue Substructures. de Graaf EL, Pellegrini D, McDonnell LA. J Proteome Res. 2016 Dec 2;15(12):4722-4730. Epub 2016 Nov 10

  9. Targeting JAK/STAT Signaling to Prevent Rejection After Kidney Transplantation: A Reappraisal. Baan CC, Kannegieter NM, Felipe CR, Tedesco Silva H Jr. Transplantation. 2016 Sep;100(9):1833-9. doi: 10.1097/TP.0000000000001226. Review. PubMed PMID: 27163538.

  10. TP53 mutated glioblastoma stem-like cell cultures are sensitive to dual mTORC1/2  inhibition while resistance in TP53 wild type cultures can be overcome by combined inhibition of mTORC1/2 and Bcl-2. Venkatesan S, Hoogstraat M, Caljouw E, Pierson T, Spoor JK, Zeneyedpour L, Dubbink HJ, Dekker LJ, van der Kaaij M, Kloezeman J, Berghauser Pont LM, Besselink NJ, Luider TM, Joore J, Martens JW, Lamfers ML, Sleijfer S, Leenstra S. Oncotarget. 2016 Sep 6;7(36):58435-58444. doi: 10.18632/oncotarget.11205. PubMed PMID: 27533080; PubMed Central PMCID: PMC5295441.

  11. Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots. Scholma J, Fuhler GM, Joore J, Hulsman M, Schivo S, List AF, Reinders MJ, Peppelenbosch MP, Post JNSci Rep. 2016 May 26;6:26695. doi: 10.1038/srep26695. PubMed PMID: 27225531; PubMed Central PMCID: PMC4881024.

  12. Kinome Profiling of Regulatory T Cells: A Closer Look into a Complex Intracellular Network. Tuettenberg A, Hahn SA, Mazur J, Gerhold-Ay A, Scholma J, Marg I, Ulges A, Satoh K, Bopp T, Joore J, Jonuleit H. PLoS One. 2016 Feb 16;11(2):e0149193. doi: 10.1371/journal.pone.0149193. eCollection 2016. PubMed PMID: 26881744; PubMed Central PMCID: PMC4755507.

  13. Signal Transduction Reaction Monitoring Deciphers Site-Specific PI3K-mTOR/MAPK Pathway Dynamics in Oncogene-Induced Senescence. de Graaf EL, Kaplon J, Mohammed S, Vereijken LA, Duarte DP, Redondo Gallego L, Heck AJ, Peeper DS, Altelaar AF. J Proteome Res. 2015 Jul 2;14(7):2906-14. doi: 10.1021/acs.jproteome.5b00236. Epub 2015 Jun 2. PMID: 26011226

  14. Phosphoproteome dynamics in onset and maintenance of oncogene-induced senescence. de Graaf EL, Kaplon J, Zhou H, Heck AJ, Peeper DS, Altelaar AF. Mol Cell Proteomics. 2014 Aug;13(8):2089-100. doi: 10.1074/mcp.M113.035436. Epub 2014 Jun 24. PMID: 24961811

  15. Single-step enrichment by Ti4+-IMAC and label-free quantitation enables in-depth monitoring of phosphorylation dynamics with high reproducibility and temporal resolution. de Graaf EL, Giansanti P, Altelaar AF, Heck AJ. Mol Cell Proteomics. 2014 Sep;13(9):2426-34. doi: 10.1074/mcp.O113.036608. Epub 2014 May 21. PMID: 24850871

  16. Spatio-temporal analysis of molecular determinants of neuronal degeneration in the aging mouse cerebellum. de Graaf EL, Vermeij WP, de Waard MC, Rijksen Y, van der Pluijm I, Hoogenraad CC, Hoeijmakers JH, Altelaar AF, Heck AJ. Mol Cell Proteomics. 2013 May;12(5):1350-62. doi: 10.1074/mcp.M112.024950. Epub 2013 Feb 11. PMID: 23399551

  17. Kinome profiling of non-canonical TRAIL signaling reveals RIP1-Src-STAT3-dependent invasion in resistant non-small cell lung cancer cells. Azijli K, Yuvaraj S, Peppelenbosch MP, Würdinger T, Dekker H, Joore J, van Dijk E, Quax WJ, Peters GJ, de Jong S, Kruyt FA. J Cell Sci. 2012 Oct 1;125(Pt 19):4651-61. doi: 10.1242/jcs.109587. Epub 2012 Jul 13. PubMed PMID: 22797920.

  18. Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra. de Graaf EL, Altelaar AF, van Breukelen B, Mohammed S, Heck AJ. J Proteome Res. 2011 Sep 2;10(9):4334-41. doi: 10.1021/pr200156b. Epub 2011 Jul 21. PMID: 21726076

  19. Monitoring selectivity in kinase-promoted phosphorylation of densely packed peptide monolayers using label-free electrochemical detection. Snir E, Joore J, Timmerman P, Yitzchaik S. Langmuir. 2011 Sep 6;27(17):11212-21. doi:  10.1021/la202247m. Epub 2011 Jul 29. PubMed PMID: 21774536.

  20. Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome. Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, Joore J, Beer MA, Cope L, Pandey A. J Proteomics Bioinform. 2011;4(2):22-35. PubMed PMID: 21720494;  PubMed Central PMCID: PMC3124146.

  21. Multiple reaction monitoring assay for pre-eclampsia related calcyclin peptides in formalin fixed paraffin embedded placenta. Güzel C, Ursem NT, Dekker LJ, Derkx P, Joore J, van Dijk E, Ligtvoet G, Steegers EA, Luider TM. J Proteome Res. 2011 Jul 1;10(7):3274-82. doi: 10.1021/pr1010795. Epub 2011 Mar 24. PubMed PMID: 21329384.