Educators:
Dominik Kopczynski, Markus Stepath, Michael Turewicz and Julian Uszkoreit (BioInfra.Prot)

Date:
Monday, 2020-11-23

Location:
online

Contents:
In this one day course we will show some of BioInfra.Prot's tools provided by de.NBI, namely “PIA - Protein Inference Algorithms”, “BIONDA – A Free Biomarker Database” and “CalibraCurve”. Besides the tool based sessions we offer a "Proteomics in the Cloud" session where we show advantages of cloud based bioinformatics and give a tutorial how to access the de.NBI cloud. PIA allows to inspect and combine the results of proteomics search engines. The main focus lays on the integrated inference algorithms for identification and quantification purposes. BIONDA is a free, up-to-date and user-friendly biomarker and biomarker candidate database that facilitates any kind of research on protein biomarkers and the corresponding diseases. CalibraCurve is a tool intended for the generation of calibration curves in the context of MRM (targeted proteomics) experiments. Such calibration curves are necessary for the selection of suitable transitions. In addition the web service STAMPS will be part of this course. It is a pathway-centric service for the development of targeted proteomics assays. In combination with Skyline, it offers a streamlined pipeline for identification and quantification in targeted proteomics analyses and development of targeted proteomics assays.

Learning goals:
Attendees of the course will learn how to use the tools PIA, BIONDA, CalibraCurve and STAMPS effectively for their daily proteomics tasks. Additionally they will learn how to use the de.NBI cloud.

Prerequisites:
This course is for all researches in the field of proteomics. The attendees should have basic knowledge of LC-MS proteomics, but no prior bioinformatics skills are required. Basic knowledge of how to analyse LC-MS data are sufficient. Attendees are required to bring their own laptops. If this is not possible or laptops have very low computing capacities, please contact the organizers.

Keywords:
Proteomics; Data Analysis; Assay Development; Biomarkers; de.NBI Cloud