April 30-May 2, 2018: Proteomics and metabolomics with OpenMS
Description
The course introduces key concepts of non-targeted label-free proteomics and metabolomics. Non-targeted methods are ideal for unbiased discovery studies and scale well for large-scale studies (e.g., clinical proteomics/metabolomics). Based on example datasets we will then introduce several open-source software tools for proteomics and metabolomics, primarily focusing on OpenMS (www.OpenMS.org). We will demonstrate how these tools can be combined into complex data analysis workflows including visualization of results. Participants will have the opportunity to bring their own data and design custom analysis workflows together with instructors.
Target audience
- Target audience are experimental scientists with experience in proteomic and/or metabolomic research. We also welcome computational scientists interested in working with raw mass spectrometric data.
Speakers
- Oliver Kohlbacher, Timo Sachsenberg, Julianus Pfeuffer
Tentative schedule
Monday, April 30, 2018
- 8:00 a.m. Registration
- 9:00 a.m. Keynote: Fundamentals of non-targeted proteomics and metabolomics, Oliver Kohlbacher
- 10:30 a.m. Refreshments
- 11:00 a.m. Hands-on: Introduction to OpenMS and KNIME, Timo Sachsenberg, Julianus Pfeuffer
- 12:30 p.m. Lunch
- 1:30 p.m. Lecture: Database search, peptide-spectrum matches , Oliver Kohlbacher
- 2:00 p.m. Hands-on: Peptide and protein identification by database search, Timo Sachsenberg, Julianus Pfeuffer
- 3:00 p.m. Refreshments
- 3:30 p.m. Lecture: FDR estimation, protein inference, quality control, Oliver Kohlbacher
- 4:00 p.m. Hands-on: Peptide and protein identification by database search, Timo Sachsenberg, Julianus Pfeuffer
- 5:00 p.m. Q&A
Tuesday, May 1, 2018
- 8:00 a.m. Q&A
- 9:00 a.m. Lecture: Label-free quantitative proteomics, Oliver Kohlbacher
- 10:30 a.m. Refreshments
- 11:00 a.m. Hands-on: Label-free quantification workflows,Timo Sachsenberg, Julianus Pfeuffer
- 12:30 p.m. Lunch
- 1:30 p.m. Lecture: Introduction to non-targeted metabolomics, Oliver Kohlbacher
- 2:30 p.m. Hands-on: Metabolite profiling workflow, Timo Sachsenberg, Julianus Pfeuffer
- 3:00 p.m. Refreshments
- 3:30 p.m. Hands-on: Differential quantification of metabolites, visualization, report generation, Timo Sachsenberg, Julianus Pfeuffer
- 5:00 p.m. Q&A
Wednesday, May 2, 2018
- 8:00 a.m. Q&A
- 9:00 a.m. Lecture: Metabolite identification, Oliver Kohlbacher
- 10:30 a.m. Refreshments
- 11:00 a.m. Hands-on: Metabolite identification through spectral databases and structure databases, Timo Sachsenberg, Julianus Pfeuffer
- 12:30 p.m. Wrap-up
