Label-free quantification using OpenMS and workflows - GCB 2016

Educators:
Julianus Pfeuffer, Timo Sachsenberg (CIBI)

Date:
12-09-2015, 11:30-14:30

Location:
FU Berlin, Institut für Informatik, Takustraße 9, 14195 Berlin

Contents:
Workflow-based analysis in bioinformatics is quickly gaining popularity in the field through its ease of use for researchers with no or little background in computer science, its flexibility, reusability and the reproducibility of its results. However, the ease of use of bioinformatics software and workflows for the analysis of shotgun proteomics experiments may hide the complexity of this analysis and the interdependence of the consecutive tools that are used. This tutorial aims to shed light on basic parts of a proteomics workflow with focus on the application of relative label-free quantification of peptides. The participants will be given an introduction to the theory behind the tools and will then be able to explore and analyze a real-world dataset on their own in a supervised hands-on session. The hands-on session includes a gentle step-by-step tutorial for the usage of the OpenMS plugin within the workflow platform KNIME. Visual exploration will be performed in the software TOPPView. Topics covered are spectrum identification and its statistical validation (with the target-decoy approach), feature finding, map alignment, relative (label-free) quantification and an introduction to workflow systems for data processing in general.

Learning goals:
The participants learn about the basics of workflow-based data analysis in the proteomics area. They will gain an improved understanding of the underlying algorithms and important parameters for a full-featured label-free quantification pipeline that they create on their own using the OpenMS plugin in KNIME. Participants will also be able to manually inspect the quality of their mass-spectrometry data within the software TOPPView and with the help of some built-in visualization features of KNIME.

Prerequisites:
Users should be acquainted with mass spectrometry terms and data.

Keywords:
Bioinformatics for proteomics, workflow systems for data processing, spectrum identification, target-decoy approach, feature finding, map alignment, relative quantification

Tools:
KNIME, OpenMS (incl. TOPPView)

Contact:
Julianus Pfeuffer
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: +49 30 838 75277
Web: http://www.gcb2016.de/program