Educators:
Dirk Benndorf, Stephan Fuchs, Robert Heyer, Kay Schallert (BiGi/MetaProtServ)

Date:
22.11.2021 – 26.11.2021

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. His group devellopes the MetaProteomAnalyzer service facilitating the analysis of of metaproteomic data. The provision of service is supported by the German Network for Bioinformatics Infrastructure - de.NBI.

Monday
09:00-10:00 Arrival
10:00-11:00 Introduction to metaproteomics (lecture: Dirk Benndorf)
11:00-12:00 Design of experiments and sample preparation (lecture: Robert Heyer)
12:00-13:00 Lunch
13:00-18:00 Sample preparation I (protein extraction, protein quantification: Robert Heyer)
during the afternoon short presentations of participant´s about their samples (each participant max. 10 min)

Tuesday
08:00-11:00 Sample preparation II (FASP digest, SDS-PAGE: Robert Heyer)
11:00-13:00 Introduction to high resolution mass spectrometry (lecture: Dirk Benndorf)
13:00-14:00 Lunch
13:00-14:00 Sample preparation II (peptide extraction: Robert Heyer)
14:00-16:00 Introduction to the MPA 2.0 (lecture: Kay Schallert)
non-stop: measurement of participant’s samples I

Wednesday
non-stop: measurement of participant’s samples I: Dirk Benndorf, Patrick Hellwig
09:00-11:00 MPA 2.0 exercise I (working with a small reference dataset, db searching, metaprotein concept: Kay Schallert, Robert Heyer)
11:00-13:00 MPA 2.0 exercise II (loading user db, BLAST search of unknown hits, quantitative comparison of datasets, visualization and data export: Kay Schallert, Robert Heyer)
13:00-14:00 Lunch
14:00-17:00 Prophane workflow (lecture and training: Stefan Fuchs, external speaker)

Thursday
09:00-13:00 MPA 2.0 exercise III (analyzing own data: Kay Schallert, Robert Heyer)
13:00-14:00 Lunch
14:00-17:00 Training at MS (calibration, setup of LC-MS methods, solvent exchange, trouble shooting, Patrick Hellwig)

Friday
08:00-10:00 MPA 2.0 exercise IV (visualization of data: Robert Heyer)
10:00-12:00 Individual discussion of results and preparation of presentations (Dirk Benndorf, Robert Heyer, Kay Schallert)
12:00-13:00 Short presentations of participant‘s results and conclusion
13:00 Lunch and 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:
Fee: 70 € -> The so-called “3G rule” (the course is only open to those that are vaccinated, recovered, or tested - geimpft, genesen, getestet) will be applied!

Keywords:
Microbiome, MPA, Metaproteomics, MetaProteomeAnalyzer,

Tools:
MetaproteomeAnalyzer