This seminar will cover central aspects of modern bottom-up proteome analysis by mass spectrometry with a focus on bioinformatic algorithms and data analysis.
After a brief introduction into 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.
Students will learn to read and interpret bioinformatics literature, give presentations and provide/receive feedback (using anonymous feedback forms).
Maximum recommended number of Participants: 11
Preliminary schedule:
| Date | Topic | by |
|---|---|---|
| Apr 20 | Introduction to computational Proteomics | Chris Bielow |
| Apr 27 | Introduction to computational Proteomics II | Chris Bielow |
| May 4 | 3 Averagines and Isotope Distribution (Senko 1995) | Stohwasser Anna Lena |
| May 11 | 4 Peptide Mass Fingerprinting: MOWSE (Pappin 1993) | Krüger Sandra |
| May 18 | 5 Searching Mass Spectra: X! Tandem (Fenyo 2003) | Merrill Sabina |
| May 25 | 6 Selecting Correct Peptides: PeptideProphet (Keller 2002) | Georgi Anja |
| June 1 | 7 Selecting Correct Peptides II: Target-Decoy (Käll 2007) | Tang Ming |
| June 8 | 8 What Proteins are present? ProteinProphet (Nesvizhskii 2003) | Gusewski Florian |
| June 15 | 9 Guest Talk: Protein Inference | Pfeuffer Julianus |
| June 22 | 10 DeNovo Peptide Sequencing in MS/MS: PepNovo (Frank 2005) | Hartkopf Felix |
| June 29 | 11 Predicting retention time: RTPredict (Pfeifer 2007) | Sieg Miriam |
| July 6 | 12 Experimental Design: Randomization & Blocking (Oberg 2008) | Sarfert Melanie |
| July 13 | 13 Verify Data Integrity: Quality Control (Bielow 2015) | Fritz Franziska |
| July 20 | 14 Why is Correlation so bad? mRNA vs. Protein (Poverennaya 2017) |
Papers will be assigned at least 2 weeks in advance. Presentations start in 3rd session (May 4th).
Every student selects at least one paper from a pre-selected list (TBD) and introduces the topic. Presentation of 30-45min + discussion. The talk should not exceed 45 minutes to allow for subsequent discussion.
| Course No | Course Type | Hours |
|---|---|---|
| 19404511 | Seminar | 2 |
| Time Span | 20.04.2018 - 20.07.2018 |
|---|---|
| Instructors |
Chris Bielow
|
| 0089c_MA120 | 2014, MSc Informatik (Mono), 120 LPs |
| 0262b_MA120 | 2012, MSc Bioinformatik (Mono), 120 LPs |
| Day | Time | Location | Details |
|---|---|---|---|
| Friday | 12-14 | T9/049 Seminarraum | 2018-04-20 - 2018-07-20 |