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Karen Jonscher

Proteomics Director


Dr. Karen Jonscher has over 20 years of experience in biological mass spectrometry, including instrument development, method design and data interpretation and validation.  She collaborates with and assists researchers in developing detailed analytical plans and constructing realistic budgets for proteomics-based projects.  She has expertise in a variety of mass spectrometry-based proteomics sample preparation workflows, including protein fractionation, immunoprecipitation, gel electrophoresis, nanscale HPLC and isoelectric separation of peptides.  She has extensive experience in proteomics data interpretation and manual validation that helps ensure the reliability of results obtained from proteomic experiments.  She is affiliated with the Mucosal Inflammation Program and the Center for Hypoxia and Ischemia Research within the Department of Anesthesiology at the University of Colorado Denver.

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Click on this link to view what seems like a typical interaction between a core technician and a researcher: 

  • Quadrupole Ion Trap:  LCQand ITMS, Thermo FIsher; 1100 MSD/SL and Ultra, Agilent
  • Time of Flight:  Voyager DE-RP and STR, Allplied Biosystems; ESI-TOF, Agilent
  • 4000 QTRAP hybrid triple quadrupole/linear ion trap, Applied Biosystems
  • Triple Quadrupole:  TSQ 700, Thermo Fisher; API III, APplied Biosystems
  • Ion Sources:  PicoView, New Objective, Inc.; AP/MALDI, Mass Tech, Inc.; Nanospray, AP-MALDI, HPLC-Chip, Agilent
  • HPLC Pumps:  Eldex, Shimadzu, Michrom BioResources, Agilent, Temo (Applied Biosystems)
  • Ionization techniques:  Microspray, electrospray, MALDI (atmospheric pressure and vaccum), nanospray


  • Chemical derivitization of peptides
  • In gel digestion
  • In solution digestion
  • Immunoprecipitation
  • Reversed Phase HPLC
  • One and two-dimensional gel electrophoresis
  • Western blot analysis
  • Tissue Culture
  • Protein production and purification


  • Manual interpretation of fragmentation spectra
  • Spectral validation

Books and/or chapters


1.             P.R. Griffin, K. Furer-Jonscher, L.E. Hood, J.R. Yates, III, J. Schwartz, and I. Jardine, Analysis of Proteins by Mass Spectrometry, Techniques in Protein Chemistry III, Ed. R.A. Angletti, Academic Press, NY pp. 467-476 (1992).


Papers published or in press


1.         *C.K. Fæste, U. Christians, E. Egaas, and K.R. Jonscher, 2009. Identification and characterization of potential allergens in fenugreek (Trigonella foenum graecum) in foods, J. Proteomics, 73 (7) 1321-33 (2010).

2.             *J. Klawitter, J. Klawitter, E. Kushner, K. Jonscher, J. Bendrick-Peart, D. Leibfritz, U. Christians and V. Schmitz, 2009. Association of Immunosuppressant-induced Protein Changes in the Rat Kidney with Changes in Urine Metabolite Patterns: A Proteo-Metabonomic Study.  J. Proteome Research, 9 (2) 865-875 (2010).

3.             * C.K. Fæste, K.R. Jonscher, L. Sit, J. Klawitter, K.E. Løvberg and L.H. Moen, Differentiating cross-reacting allergens in the immunological analysis of celery (Apium graveolens) by mass spectrometry, J. AOAC Int. 93 (2) 451-461 (2009).

4.             * L. Jin, P.M. Waterman, K.R. Jonscher, C.M. Short, N.A. Reisdorph and J.C. Cambier, MPYS, a novel membrane tetraspanner, is associated with MHC class II and mediates transduction of apoptotic signals, Molecular and Cellular Biology, 28 (16) 5014-5026 (2008).

5.             * L.L. Klein, K.R. Jonscher (joint first authors), R.S. Gibbs, E.J. Kushner, and J.L. McManaman, Proteomic profiling of human vaginal fluid during pregnancy, Reproductive Science, 15 263-273 (2008).

6.             * S. Laudi, W. Steudel, K.R. Jonscher, W. Schoning, B. Schneidewind, U. Kaisers, U. Christians and S. Trump, Comparison of lung proteome profiles in two rodent models of pulmonary arterial hypertension, Proteomics, 7 2469-2478 (2007).

7.             * M. Armstrong, K.R. Jonscher and N. Reisdorph, Analysis of 25 underivatized amino acids in human plasma using ion pairing reversed-phase liquid chromatography/time of flight mass spectrometry, Rapid Communications in Mass Spectrometry, 21 (16) 2717-2726 (2007).

8.             * C. Lambert, J. Li, K.R. Jonscher, M. Quintana and B. Freed, Acrolein, an aldehyde found in cigarette smoke, inhibits NF-kB activity and cytokine production, Journal of Biological Chemistry, 282 (27) 19666-19675 (2007).

9.             * K.A. Resing , K. Meyer-Arendt , A.M. Mendoza, L.D. Aveline-Wolf , K.R. Jonscher, K.G. Pierce , W.M. Old, H.T. Cheung, S. Russell, J.L. Wattawa, G.R. Goehle, R.D. Knight, and N.G. Ahn, Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics, Anal Chem. 76 3556-3568 (2004).

10.          * T.S. Lewis, J. Hunt, L. D. Aveline, K.R. Jonscher, D.F. Louie, J. Yeh, K. A. Resing, and N.G. Ahn, Identification of Novel MAP Kinase Pathway Signaling Targets by Functional Proteomics and Mass Spectrometry, Mol Cell. 6 1343-54 (2000).

11.          * K.R. Jonscher and J.R. Yates, III, Matrix-Assisted Laser Desorption Ionization/Quadrupole Ion Trap Mass Spectrometry of Peptides: Application to the Localization of Phosphorylation Sites on the P Protein from Sendai Virus, J. Biol. Chem. 272 1735-1741 (1997).

12.          * K.R. Jonscher and J.R. Yates, III, Mixture Analysis Using a Hybrid Quadrupole Mass Filter/Quadrupole Ion Trap Mass Spectrometer, Anal. Chem. 68 659-667 (1996).

13.          * K. Jonscher, G. Currie, A.L. McCormack, and J.R. Yates, III, The Analysis of Peptides and Proteins by Matrix-Assisted Laser Desorption Ionization Quadrupole Ion Trap Mass Spectrometry, Rapid Commun. Mass Spectrom. 7 20-26 (1993).

14.          * J.F. Scott, S.J. Shieh, K.R. Furer, N.A. Clark, and W.F. Oliver, Anisotropic Thermal Lens Effect in Ferroelectric Ba2NaNb5O15 at Tc, Phys. Rev. B 41 9330-9335 (1990).

15.          * W. Kutschera, I. Ahmad, P.J. Billquist, B.G. Glagola, K. Furer, R.C. Pardo, M. Paul, K.E. Rehm, P.J. Slota, Jr., R.E. Taylor, and J.L. Yntema, Studies Towards a Method for Radiocalcium Dating of Bones, Radiocarbon 31 311-323 (1989).


                          (* peer reviewed, ** invited paper)

Please check back soon.  Posters and abstracts will be available.