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Practical course on proteomics - MB170C112

Title:	Proteomické praktikum
Czech title:	Proteomické praktikum
Form of teaching:	practical classes
Guaranteed by:	Department of Cell Biology (31-151)
Faculty:	Faculty of Science
Actual:	from 2026
Duration in semesters:	1
Semester:	summer
E-Credits:	2
Examination process:	summer s.:
Hours per week, examination:	summer s.:0/1, C [TS]
Capacity:	12
Maximum number of enrolled students:	12
Min. number of students:	unlimited
4EU+:	no
Virtual mobility / capacity:	no
State of the course:	taught
Language:	Czech
Additional information:	http://pavel.talacko@natur.cuni.cz
Note:	enabled for web enrollment

Guarantor:	Mgr. Pavel Talacko

Opinion survey results

Annotation - Czech

Praktikum navazuje na předmět Proteomika - MB170P112 a probíhá turnusově v prostorách Biocev ve Vestci u Prahy. V první části praktika studenti připraví vzorky pro LC/MS experiment (lyze, štěpení trypsinem, odsolení). Následně budou seznámeni s detaily konkrétní metodiky a instrumentace pro LC/MS analýzu. Analýza bude provedena na nejnovějších přístrojích v OMICS servisní laboratoři hmotnostní spektrometrie. Ve druhé části budou studenti vyhodnocovat a interpretovat naměřená data pomoci volně dostupných nástrojů (MaxQuant, Perseus, Skyline).

1. Hughes, C.S., Moggridge, S., Muller, T., Sorensen, P.H., Morin, G.B. and Krijgsveld, J. (2019) Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nat Protoc, 14, 68-85.
2. Cox, J., Hein, M.Y., Luber, C.A., Paron, I., Nagaraj, N. and Mann, M. (2014) Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics, 13, 2513-2526.
3. Tyanova, S., Temu, T., Sinitcyn, P., Carlson, A., Hein, M.Y., Geiger, T., Mann, M. and Cox, J. (2016) The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods, 13, 731-740.
4. Schilling, B., Rardin, M.J., MacLean, B.X., Zawadzka, A.M., Frewen, B.E., Cusack, M.P., Sorensen, D.J., Bereman, M.S., Jing, E., Wu, C.C. et al. (2012) Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Mol Cell Proteomics, 11, 202-214.

Last update: Talacko Pavel, Mgr. (28.08.2026)

Literature -

1. Hughes, C.S., Moggridge, S., Muller, T., Sorensen, P.H., Morin, G.B. and Krijgsveld, J. (2019) Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nat Protoc, 14, 68-85.

2. Cox, J., Hein, M.Y., Luber, C.A., Paron, I., Nagaraj, N. and Mann, M. (2014) Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics, 13, 2513-2526.

3. Tyanova, S., Temu, T., Sinitcyn, P., Carlson, A., Hein, M.Y., Geiger, T., Mann, M. and Cox, J. (2016) The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods, 13, 731-740.

4. Schilling, B., Rardin, M.J., MacLean, B.X., Zawadzka, A.M., Frewen, B.E., Cusack, M.P., Sorensen, D.J., Bereman, M.S., Jing, E., Wu, C.C. et al. (2012) Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Mol Cell Proteomics, 11, 202-214.

Last update: Talacko Pavel, Mgr. (28.08.2026)

Course assessment methods and requirements for successful completion, grading scheme - Czech

Je udělován zápočet po předložení protokolu z praktik.

Last update: Talacko Pavel, Mgr. (28.08.2026)

Syllabus -

- LC/MS sample preparation (lysis, alkylation, reduction, trypsin digestion, desalting)
- Description of used methods and instrumentation (chromatografic gradients, DDA/DIA akvizition, mass spectrometer setup)
- LC/MS analysis of prepared samples
- Data evalutaion and interpretation (MaxQuant, Perseus, Skyline)

Last update: Talacko Pavel, Mgr. (28.08.2026)

The course does not include work placement