Applied proteomics

Course Coordinator

ECTS points:


Course number:

Course Description


Relation between structure and function of proteins. Proteome as collection of all proteins produced in an organism or cellular system. Proteomics as link of high throughput technologies enabling proteome analysis. Main methods of protein analysis with emphasis on mass spectrometry as qualitative and quantitative standard in proteomics. Reading amino acid sequence from peptide using mass spectra analysis. Application of proteomics in functionality testing of prebiotic strains and virulence of pathogenic strains. Basic concepts of bioinformatics data analysis of data obtained by detection and quantification of proteins with aim of identification of pathogens and probiotic microorganisms on species and strain level and identification of  


  • Name most used algorithms in in silico proteomics.  
  • Debate terms de novo modelling and homology based modelling of proteins.
  • Demonstrate proper usage of HMM and PSI BLAST searches for determining remote homologies between protein families.
  • Discuss difference between PAM and BLOSSUM matrices.
  • Discuss methods of peptide sequencing.
  • Generalize peptide mass fingerprinting method.
  • Analyze MS2 peptide spectra.
  • Locate “b” and “y” series of ions in MS2 peptide spectrum resulting from trypsin digestion and reading out corresponding amino acid sequence.


Lectures: 10 hours

Seminars: 10 hours


  1. Mass Spectrometry-based proteomics. Ruedi Aebersold and Matthias Mann; Nature 422, 198-207 (13 March 2003). DOI:10.1038/nature01511
  2. Proteomics by Mass Spectrometry: Approaches, Advances, and Applications. John R. Yates, Cristian I. Ruse, and Aleksey Nakorchevsky; Annual Review of Biomedical Engineering, Vol. 11: 49-79. DOI: 10.1146/annurev-bioeng-061008-124934
  3. Mass spectrometry in proteomics. Ruedi Aebersold and David R. Goodlett; Chemical reviews 101.2 (2001): 269-296. DOI:10.1021/cr990076h
{* *}