Co-Chair: Tim Van Den Bossche, Ghent University
Co-Chair: Jean Armengaud, University Paris-Saclay

Metaproteomics from Bench to The Clinic, Daniel Figeys, University of Ottawa
Analysis of Functions Expressed by Microbiomes Using Metaproteomics, Pratik Jagtap, University of Minnesota

Metaproteomics is a key methodology for understanding how microbiomes function. The power of metaproteomics comes from efficient connection of genomic and metabolic information. Through the large-scale characterization of the entire protein complement of microbiota and the functional dynamics of the microbiome, metaproteomics has the potential to unravel mechanistic details and identify key regulators of microbial interactions with the host/environment. Functional characterization offers numerous advantages over nucleic acid-based methods that primarily measure taxonomic composition. However, while the techniques in current use for metaproteomics are fundamentally the same as those used for single-organism proteomics, there are a number of key differences in terms of sample preparation, analysis and data processing/interpretation that require specialized expertise and tools for success in metaproteomics experiments.

Metaproteomics from Bench to The Clinic. The first speaker, Dr. Daniel Figeys, will introduce the human gut microbiome and discuss the advantages of using metaproteomics to better understand the biological processes ongoing in this dynamic microbiome environment. He will use a study of pediatric inflammatory bowel disease as an example. 

Analysis of Functions Expressed by Microbiomes Using Metaproteomics. Data analysis of metaproteomics experiments presents unique challenges and requires novel software tools. The second speaker, Dr. Pratik Jagtap, will highlight efforts on the implementation of metaproteomics workflows and their use within the Galaxy bioinformatics platform ( These workflows analyze both the taxonomic and functional state of microbiomes and generate outputs for biological interpretation.

Tim Van Den Bossche
Ghent University, Belgium
Tim Van Den Bossche is working as PhD researcher in the CompOmics lab of prof. Lennart Martens in the field of microbial community proteomics, commonly known as metaproteomics. Here, he led the first-ever, community-driven, multi-site experiment that compared the effects of different state-of-the-art metaproteomics analysis pipelines (wet-lab and computational). Next to this benchmark study, is Tim applying machine learning algorithms on metaproteomics datasets to improve peptide identifications, and downstream taxonomical and functional annotation.
Besides his research, plays he an active role in several scientific communities such as EuBIC-MS and HUPO-PSI, and is moreover a co-founder of the Metaproteomics Initiative.
Jean Armengaud
University Paris-Saclay, France
Jean Armengaud is Chief Deputy of the laboratory of Innovative technologies for Detection and Diagnostics located near Avignon in France. He is also Director of the ProGénoMIX platform, specialized in proteogenomics and metaproteomics. He wishes to contribute to a better understanding of the functioning of complex biological systems and exploit this knowledge for medical and environmental purposes. He received his PhD in Biochemistry in 1994 at the University of Grenoble.
Daniel Figeys
University of Ottawa, Canada
Daniel obtained a B.Sc. and a M.Sc. in chemistry from the Université de Montréal. He obtained a Ph.D. in chemistry from the University of Alberta.  He did his postdoctoral studies at the University of Washington in Molecular Biotechnology. Daniel was previously Senior Vice-President at MDS-Proteomics and more recently co-founder of MedBiome. Daniel is a Professor and a Distinguished Research Chair in the Department of Biochemistry, Microbiology, and Immunology at the University of Ottawa. He is the co-founding director of the Shanghai Institute of Materia Medica-University of Ottawa Joint Center in Systems and Personalized Pharmacology. He was the founding director of the Ottawa Institute of Systems Biology.  His research focuses on the development and applications of technologies and bioinformatic tools to study the human gut microbiome and drug-microbiome interactions. His laboratory has published over 200 papers and has been cited over 17,000 times.
Pratik Jagtap
University of Minnesota, USA
Pratik Jagtap is a Research Assistant Professor at the Department of Biochemistry, Molecular Biology and Biophysics at the University of Minnesota in Minneapolis, Minnesota, He received his Ph.D. degree in 2000 at the Center for Cellular and Molecular Biology, Hyderabad (India). During his post-doctoral research work at the Max-Planck Institute in Tuebingen and later at the University of Michigan in Ann Arbor, he worked on genomic and proteomic analysis of bacteria.
Since 2016 - as a Galaxy-P project co-lead - he has worked with the team to utilize and publish various workflows for multi-omic data analysis. His current research interests include developing workflows for the analysis of complex data, with particular emphasis on MS-based proteomics applications in metaproteomics, proteogenomics, and data-independent acquisition (DIA) data analysis.

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