Chemical Proteomics


National course. The course is open for current and potential facility users such as PhD students, postdocs, group leaders and core facility staff in need of proteome-wide proteomics skills with aims in drug discovery and proteomics, within all Swedish universities.

This course is supported by SciLifeLab and run by the SciLifeLab Chemical Proteomics & Proteogenomics facility.

Application form

Important dates

Application open

Application deadline: September 23, 2019

Confirmation to accepted participants: September 27, 2019

Responsible teachers: Massimiliano Gaetani, Roman Zubarev

If you have not received any information about your application by October 3, please contact education@scilifelab.uu.se

Course fee

A course fee of 1300 SEK will be invoiced to accepted participants (includes the coffee, lunches and course dinner). NOTE – The university cannot invoice individuals.

Course content

This course will cover most updated Mass Spectrometry (MS)- based quantitative proteomics strategies available for deconvolution of drug / compound target and action mechanism together with other MS-based techniques for drug development.

The course will show the major approaches that our facility uses to provide identification of drug target(s) and mechanism of action and to characterize them. The course will also offer a workshop with research lectures of international level.

Topics:

  • Introduction on MS-based, quantitative proteomics approaches and chemical proteomics
  • Most relevant chemical proteomics approaches, with major focus on unbiased proteome-wide methods using unmodified drug / compound molecules in living cells or cell lysates. In particular, the MS-based quantitative proteomics methods for deconvolution of targets and action mechanism that will be treated are:
    – Functional identification of targets by expression proteomics (FITExP), determining specific regulation of proteome expression / degradation in cells as response to a treatment;
    – Thermal proteome profiling (TPP), based on differential protein melting curves between treated and untreated proteomes (in living cells and cells lysates);
    – ProTargetMiner: proteome signature library of anticancer molecules;
    – Proteome Integral Stability Alteration (PISA) assay: a much higher throughput and lower cost quantitative proteomics assay based on protein stability/solubility (in living cells and lysates).
  • System-wide Identification of Enzyme Substrates by Thermal Analysis (SIESTA), in protein extracts.
  • Elucidation of the interaction interface and mapping of the binding site of a drug with its target protein by Hydrogen/Deuterium (H/D) exchange mass spectrometry (HDX MS).
  • Workshop with research lectures hosting speakers of international level.

Please note that SciLifeLab training courses do not provide any formal university credits.
The course content is estimated to correspond to 
a certain number of credits, however the estimated credits are just guidelines.
If formal credits are crucial, the student needs to confer with the home department before course application, whether the course is valid for formal credits or not.

Entry requirements

  • Knowledge of basic in vitro assays using cells for drug/compound testing
  • Basic knowledge in experimental design and statistical methods
  • Basic knowledge in proteomics analysis
  • Practical interest into unbiased identification and analysis of the interaction between a drug/compound of interest and its protein target(s), and/or into unbiased discovery of the key proteins and their related mechanism of cell responses upon drug/compound treatment.

Due to space constraints, there is a maximum number of allowed participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.