Faculty of Engineering, LTH

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Proteomics data analysis course

Design and Analysis of Quantitative Proteomics Experiments


Course dates

One week full time. Next course: 7-11 October 2019. The course location is Medicon Village, Building 406, Scheelevägen 2, Lund.

Current course syllabus


Mass spectrometry-based proteomics is showing great potential for giving new biological insight and for discovery of biomarkers. However, the usability of results from proteomics experiments is highly dependent on data analysis and experimental design. In this course, properties of data from quantitative mass spectrometry-based proteomics will be discussed, based on hands-on examples with practical data analysis.


After completion of this course, students are expected to be able to plan quantitative proteomics experiments based on project goals. Factors to consider include possible workflows, time, samples and replicates. An important goal is also to gain insight into how to handle and evaluate data from proteomics experiments. This includes data management, significance evaluation, putting the data into biological context and formatting for publication.


Lectures in the course will cover: Proteomics experimental planning, encompassing selection of workflow and sample selection. Raw data handling and analysis using informatic tools, including validation of peptide and protein identifications. Formatting of data for publication and deposition in public repositories. 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 (isobaric labels and label free), and discussion of significance and interpretation of the results.

Recommended qualifications:

Basic knowledge of mass spectrometry-based proteomics with focus on quantification. For students that are new to proteomics, it is recommended to attend a course covering protein mass spectrometry course first. As an alternative, links to some background reading will be sent out before the course.


Registration through the Postgraduate courses in Life Sciences is now closed. Contact the course leader for possible vacancies.

Contact: Fredrik Levander fredrik.levander (AT)

This course is given in collaboration with:


Postgraduate courses in Life Sciences -

The 2014 version was given in collaboration with EuPA -



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