Research Groups

Andrej Shevchenko

Mass spectrometry in functional characterization of biological molecules

Previous and Current Research

Advances in mass spectrometric technology together with progress in genomic sequencing and bioinformatics have increased the value of mass spectrometric methods for molecular and cell biology research. Expanding from its previous role as a peptide sequencing tool mass spectrometry is now becoming deeply integrated into the functional characterization of biologically important genes.

However it has also become clear that the identification of important proteins alone does not elucidate the molecular mechanism of complex biological phenomena. The research also has to focus on “small” molecules (such as, lipids), which create the environment enabling the proteins to function. This ultimately requires the development of novel technologies for qualitative and quantitative analysis of biological molecules.

We are now witnessing a “prime time” for the Time – Of – Flight (TOF) mass spectrometry. Hybrid Quadrupole TOF instruments equipped with electrospray (1996) and MALDI (2000) ion sources allowed to combine high throughput identification of proteins in sequence databases with the detailed characterization of individual peptide ions observed in the spectrum of a protein digest in the course of a single experiment.

Future Projects and Goals

In collaboration with various biological research groups we will be characterizing protein complexes – functional units of a molecular machinery of the cell. Our main interest is to develop a generic functional proteomic strategy, which may allow to link protein complexes of different functionality together and thus to decipher protein interaction networks. Currently most of proteomic efforts are focused on organisms whose genome has been fully sequenced. Taking advantage of the unique features of MALDI Quadrupole TOF and electrospray Quadrupole TOF mass spectrometry we will develop analytical approaches for rapid and sensitive characterization of proteins isolated from organisms with yet unknown genomes.

Characterization of lipids will form another pole of our activities. We will apply resent advances of the TOF technology for comprehensive and quantitative profiling of polar lipids in complex mixtures isolated from various cellular compartments.

Methodological and Technical Expertise
  • Mass spectrometry
  • Shotgun lipidomics
  • LC-MS/MS
Selected Publications

Liska, A .J., Shevchenko, A., Pick, U. and Katz, A.
Enhanced photosynthesis and redox energy production contribute to salinity-tolerance in Dunaliella as revealed by homology-based proteomics.
Plant Physiol (2004) (in press)

Liska, A. J., Popov, A., Sunyaev, Sh., Coughlin, P., Habermann, B., Shevchenko, Anna, Bork, P., Karsenti, E. and Shevchenko, A.
Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome.
Proteomics 4 (2004) (in press)

Liska, A. J. and Shevchenko, A.
The expanding organismal scope of proteomics: cross-species protein identification by mass spectrometry and its implications.
Proteomics 3, 19–28 (2003)

Sunyaev, Sh., Liska, A. J., Golod, A., Shevchenko, Anna and Shevchenko, Andrej
MultiTag: Multiple error-tolerant sequence tag search for the sequence similarity identification of proteins by mass spectrometry.
Anal Chem., 75, 1307–1315 (2003)

Liska, A. J. and Shevchenko, A.
Combining mass spectrometry with database interrogation strategies in proteomics.
Trends Anal Chem., 22, 291–298 (2003)


since 2001
Group Leader at the Max Planck Institute of Molecular Cell Biology and Genetics

European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

Institute for Analytical Instrumentation, St. Petersburg


Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstraße 108
01307 Dresden