English

If sufficient demand

Mass spectrometry-based proteomics is showing great potential for giving new biological insight and for discovery of biomarkers. However, the utility of results from proteomics experiments is highly dependent on data analysis and experimental design. The aim of the course is to give the attendants insight into the different steps of data analysis associated with mass spectrometry-based quantitative proteomics experiments, to allow for selection of workflow and to perform basic data analysis.

In this post-graduate course, properties of data from quantitative mass spectrometry-based proteomics will be discussed, based on hands-on examples with practical data analysis. The course attendants will get an overview of existing solutions for analysis of proteomics data. Lectures in the course will cover 1) proteomics experimental planning, encompassing selection of workflow and sample selection, 2) raw data handling and analysis using informatic tools, including validation of peptide and protein identifications, 3) formatting of data for publication and deposition in public repositories, and 4) basic statistical analysis of results, and functional annotation. The exercises will encompass planning of experiments and evaluation of data from two different quantitative proteomics workflows, and discussion of significance and interpretation of the results.

be able to describe basic principles of mass spectrometry-based identification of peptides and proteins.
be able to describe advantages and disadvantages of different quantitative mass spectrometry-based workflows for proteomics.

be able to handle mass spectrometry files in different formats.
be able to perform protein identification from MS/MS data.
be able to generate quantitative peptide reports from LC-MS/MS data.
be able to select mass spectrometry-based workflows for protein measurements in different biological contexts

be able to critically evaluate quantitative proteomics studies.
evaluate consequences of small or large sample groups, as well as of multiple hypothesis testing.

Lectures

Seminars

Exercises

Written assignments

Seminars given by participants

Active participation in lectures, exercises and discussion seminar.

Failed, pass

 

Slides and articles will be distributed

The course is given each autumn through the Postgraduate Courses in the Life Sciences (http://www.cmps.lu.se/life_sciences) if at least 6 students are accepted.

KIM065F

 -11-30

Mats Ohlin