Laboratory of Mass Spectrometry (P. Konik)

Mass Spectrometry is a powerful tool in protein research. The combination of Liquid Chromatography (LC) with a tandem mass spectrometrer (MS/MS) can be used for:

  • Protein identification by database search or De Novo sequencing
  • Quantification of proteins in biological samples (expression levels)
  • Identification of biologically relevant posttranslational modifications (PTM)

The Laboratory of Mass Spectrometry is a service facility of the Department of Molecular Biology.

The most common sample types processed in the laboratory are:

  • protein solutions - isolated proteins, cell lysates, animal/human sera, etc.
  • protein digests - solutions of proteins digested with proteolytic enzymes
  • gel bands - from SDS PAGE, native electrophoresis, 2D gels, etc.

The laboratory uses the following instruments and techniques:

  • Sample digestion with proteolytiv enzymes (Trypsin, S. aureus V8)
  • UPLC (Ultra Performance Liquid Chromatography) separation of peptides on a
    Nano Acquity UPLC (Waters)
  • Peptide Mass Fingerprinting (PMF) and fragment analysis (MS/MS) on a Q-Tof Premier
    Mass Spectrometer (Waters)
  • Data processing and protein identification, quantification and PTM's using
    the PLGS 2.3 software (Waters)
  • For database searching, Uniprot and NCBI public proein databases are used;
    custom databases are also possible

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