Oliver Kohlbacher, Julianus Pfeuffer, Timo Sachsenberg (CIBI)

May 1-3, 2017

Northeastern University
315 and 320 Shillman Hall
115 Forsyth Street, Boston, Massachusetts 02115, USA

Keynote Speakers:
Oliver Kohlbacher (CIBI)

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 ( 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.

Tentative schedule:
Monday, May 1
8:00 a.m. Registration
9:00 a.m. Keynote: Oliver Kohlbacher. Fundamentals of non-targeted proteomics and metabolomics
10:30 a.m. Refreshments
11:00 a.m. Hands-on: Tutorial: Introduction to OpenMS and KNIME
12:30 p.m. Lunch
1:30 p.m. Lecture: Database search, peptide-spectrum matches.
2:00 p.m. Hands-on: Peptide and protein identification by database search.
3:00 p.m. Refreshments
3:30 p.m. Lecture: FDR estimation, protein inference, quality control.
4:00 p.m. Hand-on: Peptide and protein identification by database search.
5:00 p.m. Improvised poster session
6:00 p.m. Adjourn

Tuesday, May 2
8:00 a.m. Bring your own data
9:00 a.m. Lecture: Label-free quantitative proteomics.
10:30 a.m. Refreshments
11:00 a.m. Hands-on: Label-free quantification workflows
12:30 p.m. Lunch
1:30 p.m. Lecture: Introduction to non-targeted metabolomics.
2:30 p.m. Hands-on: Metabolite profiling workflow.
3:00 p.m. Refreshments
3:30 p.m. Hands-on: Differential quantification of metabolites, visualization, report generation
5:00 p.m. Questions and practice with own data
6:00 p.m. Adjourn

Wednesday, May 3
8:00 a.m. Bring your own data
9:00 a.m. Lecture: Metabolite identification
10:30 a.m. Refreshments
11:00 a.m. Hands-on: Metabolite identification through spectral databases and structure databases
12:30 p.m. Wrap-up and jeopardy
1:30 p.m. Adjourn

Software Requirements:
The participants should bring their own laptop computers. Instructions regarding downloading and installing all required software (Windows, OSX, or Linux) will be provided prior to the course. Installer versions of all required software will be available.

LC-MS based proteomics and metabolomics, OpenMS, workflows, KNIME, data analysis


Scientific and program questions:
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