Educators:
Dirk Benndorf, Robert Heyer, Kay Schallert, Roman Zoun (MetaProtServ / BiGi)
Date:
07.03.2018 – 13.03.2018
Location:
Magdeburg, Germany (Universitätsplatz 2, Building 28.205)
Contents:
Microbiome research is rapidly increasing. Meta-Omics data provide insights into microbial community influencing human health and biochemical cycle. Metaproteomics focusses on proteins representing the expressed genes and functions. In contrast to metagenomics or metatranscriptomics, the extraction and the analysis of proteins from human or environmental samples is challenging.
The de.NBI course on Applied Metaproteomics trains the participants to apply a complete workflow starting from design of experiments via sample preparation to measurement and bioinformatics analysis of high-resolution MS data. Maximum 10 participants are strongly encouraged to analyze their own samples to start their own metaproteomics project.
The workshop takes place at chair of bioprocess engineering at Otto-von-Guericke University Magdeburg. The team of microbial communities head by Dr. Dirk Benndorf is well experienced in metaproteomics. The samples will be measured on newly purchased timsTOF Pro MS (Within the German Network for Bioinformatics Infrastructure - de.NBI his group provides the MetaProteomAnalyzer Service facilitating the analysis of of metaproteomic data.)
- Date: 07.-13.03.2018
- Wednesday
-- Arrival
-- Introduction to metaproteomics (lecture)
-- Introduction to the MPA 2.0 (lecture)
-- Design of experiments and sample preparation (including short presentations regarding the participant´s samples)
- Thursday
-- Sample preparation I (protein extraction, protein quantification, FASP digest)
-- Introduction to high resolution mass spectrometry (lecture)
- Friday
-- Sample preparation II (peptide extraction, SDS-PAGE)
-- MPA 2.0 exercise I (working with a small reference dataset, db searching, metaprotein concept)
-- Training at MS I (calibration, setup of LC-MS methods)
-- City Tour ("Nachtwächterführung"", 18:30 at Dom)
-- Dinner (20:00, Wenzel Prager Bierstuben)
- Saturday
-- measurement of participant’s samples I
-- MPA 2.0 exercise II (loading user db, BLAST search of unknown hits, quantitative comparison of datasets, visualization and data export)
- Sunday
-- measurement of participant’s samples II
-- depending on weather optional trip to Berlin or Wernigerode (Harz mountains)
- Monday
-- MPA 2.0 exercise III (analyzing own data)
-- training at MS II (solvent exchange, trouble shooting)
-- presentation of external speakers (Nico Jehmlich, ThiloMuth, …)
- Tuesday
-- MPA IV (exporting data and preparing a presentation)
-- short presentations of participant‘s results
-- departure
Learning goals:
To apply a complete workflow starting from design of experiments via sample preparation to measurement and bioinformatics analysis of high-resolution MS data.
Prerequisites:
Registration via register form at http://www.mpa.ovgu.de/index.php/event/workshop-applied-metaproteomics-workshop-magdeburg-2018/
(Fee: 70 €)
Keywords:
Microbiome, MPA, Metaproteomics, MetaProteomeAnalyzer,
Tools:
MetaproteomeAnalyzer
Contact:
Dirk Benndorf, Robert Heyer, Kay Schallert, Roman Zoun (