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This seminar will cover central aspects of modern bottom-up proteome analysis by mass spectrometry with a focus on bioinformatic algorithms and data analysis.
No prior knowledge of LC-MS based proteomics is required.

After a brief introduction to the field of mass spectrometry-based proteomics (instrument types, data properties, overview of bioinformatics challenges) we will explore the big cornerstones, including isotope models and averagines, scoring algorithms for the identification of mass spectra, false-discovery-rate estimation using decoy peptides, absolute and relative quantification of proteins and correlation between mRNA and protein expression.

The first two classes will be lectures, introducing mass-spectrometry based-proteomics (instruments, recording modes, properties of data, etc).

Starting in week 3, we will have student talks on dedicated topics and discussions (critically assessing the merits of the paper and its impact on the field).

The final 1-2 sessions will consist of presentations on the results of the research projects (10-15min each).

Students will:

• give at least one presentation on a chosen topic (see Resources for a list of papers/PDFs); additional proposals of topics by students are encouraged
• develop a small research project (usually based on the topic of the presentation) and present the results at the last sessions of the seminar

This seminar will enable to students to:

• present and discuss research concepts and strategies (in a potentially new field of research)
• discuss pro's and con's of existing computational (and experimental) methods
• conduct small original research project of your own (and present/defend it)

Timeline:

Please decide on a paper which you'd like to present by end of week 2 and send me your choice via email (chris.bielow@fu-berlin.de). A selection of papers is avaible for download in the "Resources" site. Feel free to propose another paper, if you think it fits the scope. I will update the list of papers here (so look at the list before you send your choice). If two students select the same paper, the e-mail with the earlier time-stamp wins.

Assigned talks:

Student Name, Topic.