Hands-on course for sample preparation and data analysis in proteomics

Course overview

The course will give an introduction to the theoretical aspects of the analysis of proteins/peptides by mass spectrometry. Participants will get hands-on experience in sample preparation for a quantitative comparison across samples and perform an in-solution digest using Single-Pot Solid-Phase-enhanced Sample Preparation (SP3) (Hughes et al., Molecular Systems Biology, 2014) and tandem mass tag labelling (TMT). The SP3 technology was developed at EMBL. It enables scientists with a proteomics sample preparation method from nearly any starting buffer conditions (e.g. Laemmli buffer).
Participants will measure their own produced samples using LC-MS/MS and will learn in a session focused on the bioinformatics analysis how the acquired data will be analysed using MSFragger and R. Best practices and Proteomics data management will be a focus of this course.

Audience

All scientists working in the lab from technicians, PhD students to Postdoc’s that use or want to use proteomics for their research. You should have an understanding of protein biology and should know the principle of proteomics. Ideally, you have had experience with proteomics or send samples to a facility or collaboration partner for analysis.

Learning outcomes

Improvement of sample preparation to boost the data quality

Awareness which aspects of sample preparation can influence the outcome of the experiment

Seeing the portfolio of the services of the proteomics core facility

Basic understanding of data analysis

Understanding different visualisations of proteomic data

Warning

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