Educators:
Robert Heyer, Dirk Benndorf, Patrick Hellwig, Kay Schallert, Daniel Kautzner, Claudia Best (BiGi/MetaProtServ)

Date:
09.12.2024 – 13.12.2024

Location:
Magdeburg, Germany (Universitätsplatz 2, Building 28.217)

Contents:
The field of microbiome research is experiencing significant growth, with Meta-Omics data offering valuable insights into microbial communities that impact human health and biochemical cycles. Metaproteomics, a branch of Meta-Omics, focuses on analyzing proteins to identify expressed genes and their corresponding functions. Unlike metagenomics or metatranscriptomics, metaproteomics requires the extraction and analysis of proteins from human or environmental samples, a complex and challenging process.

The de.NBI course on Applied Metaproteomics is designed to train participants in the complete metaproteomics workflow, from experimental design and sample preparation to measurement and bioinformatics analysis of high-resolution mass spectrometry (MS) data. The course accommodates a maximum of 10 participants, who are encouraged to bring their own samples to begin their metaproteomics projects.

The workshop will be held at the Otto-von-Guericke University Magdeburg by Prof. Dirk Benndorf and Prof. Robert Heyer. Participants will have the opportunity to work with leading experts in the field, gaining practical experience and expert guidance throughout the course.

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
13:00-13:30 Safety instructions (Claudia Best)
13:30-18:00 Sample preparation I (protein extraction, protein quantification: Claudia Best, Backup-Max)

Tuesday
08:00-11:00 Sample preparation II (FASP digest, SDS-PAGE: Claudia Best)
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: Claudia Best)
14:00-16:00 Introduction to the MPA 2.0 (lecture: Kay Schallert)
18:00-20.00 Sightseeing in Magdeburg
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 Training at MS (calibration, setup of LC-MS methods, solvent exchange, trouble shooting, Jan)

Thursday
09:00-13:00 MPA 2.0 exercise III (analyzing own data: Kay Schallert)
13:00-14:00 Lunch
14:00-15:00 TBA (lecture and training: NN)
15:00-17:00 Metaproteomics Initiative and NFDI Standardization I (Kay Schallert)
18:30-20:00 Dinner (Restaurant “Lago di Garda”)

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 Metaproteomics Initiative and NFDI Standardization II (Kay Schallert)
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: 100 €
- Οwn Laptop
- Own samples could be analyzed while workshop (but we could also provide samples)

Keywords:
Microbiome, MPA, Metaproteomics, MetaProteomeAnalyzer,

Tools:
MetaproteomeAnalyzer