Mass Spectrometry
CS

Proteomics

Routine proteomic analyses

Our group is involved in numerous projects where the MS-based proteomic approaches is required. These projects deal with, for example, the research of Hepatitis B viral infection or analysis of rhomboid dependent proteome changes, etc.


We provide following proteomic analyses:
  • Intact mass analysis

            molecular weight determination of protein or oligonucleotides by MALDI-TOF or ESI-TOF

  • Protein identification

            including protein complexes characterization from gel or solution

  • Characterization of posttranslational modifications

            phosphorylation, acetylation, methylation etc.

  • Protein quantification
            relative quantification (label-free, SILAC labeling)

A) Total ion current chromatogram obtained for the sample of mouse lysate. The MS/MS scan of molecule with retention time of 48.81 min is shown in red rectangle. B) Volcano plots as a result of student's t-test comparison of shotgun LC-MS/MS analysis of proteins co-immunoprecipitated with HBe-HA (left) and HBe3CA-HA (right). Published in Zábranská et al., The FEBS Journal, 2021.

Proteomic research

In our research projects we focus on:

  • analysis of lipoproteins/lipopeptides and membrane proteins

Separation and identification of lipoproteins/lipopeptides is rather challenging due to the limited solubility of lipo-modified segments in water-based solutions, whose are exclusively used within standard proteomic workflows. Therefore, we focus on the implementation of new workflows to the increase the yield of lipo-modified and hydrophobic segments of the proteins.

  •  implementation of novel structural proteomics approaches. In the field of structural proteomics, we implement the following methods:

native MS

protein covalent labelling

protein crosslinking

hydrogen-deuterium exchange MS


These complementary methods allow to study protein structures and characterize not only protein-protein interactions but also interactions of proteins with other biological molecules.

The fragmentation spectrum of the myristoylated peptide GVSGSK obtained by CID and HCD fragmentation technique. In the case of HCD both indicator fragments of myristoylation b0 (m/z 211.205) and b1 (m/z 268.227) were detected.
Ion mobility spectrometry (IMS) of amyloid beta peptide (1-42). Individual chrge states of monomers and oligomers are labeled.
Fosforylasa B značena pomocí D2O ve dvou časových bodech (20 sekund a 2 hodiny). Získaná data byla vynesena do struktury fosforylasy B a stupeň deuterace identifikovaných oblastí byl vyjádřen v barevné škále od modré po červenou. Nepokryté oblasti proteinové sekvence jsou značeny šedě.