Metaproteomic Analysis of Extracellular Peptides

For the metaproteomic analyses, filtration is used to separate extracellular peptides from the obtained (poly)peptides. The resulting smaller fractions are then desalted and analysed without proteolytic digestion via liquid chromatography (LC) and mass spectrometry (MS) on an EasyNano-LC coupled online to a QExactive-Plus mass spectrometer (ThermoScientific, Waltham). The identification of ribosomal peptides is done with an integrated catalogue of MG and MT data, while the non-ribosomal peptides are identified using different tools, that is, MyriMatch, DirecTag as well as CycloBranch.45 59 60 (link) The metaproteomic data also allow identification of extracellular (poly)peptides with possible pathogenic functions including protein misfolding and molecular mimicry.61 62 (link)

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Hansen B., Laczny C.C., Aho V.T., Frachet-Bour A., Habier J., Ostaszewski M., Michalsen A., Hanslian E., Koppold D.A., Hartmann A.M., Steckhan N., Mollenhauer B., Schade S., Roomp K., Schneider J.G, & Wilmes P. (2023). Protocol for a multicentre cross-sectional, longitudinal ambulatory clinical trial in rheumatoid arthritis and Parkinson’s disease patients analysing the relation between the gut microbiome, fasting and immune status in Germany (ExpoBiome). BMJ Open, 13(8), e071380.

Publication 2023

EasyNano-LC QExactive-Plus mass spectrometer

Digestion Filtration Liquid chromatography Mass spectrometry Molecular mimicry Pathogenic Peptides Poly Protein Proteolytic Ribosomal

Corresponding Organization : Saarland University

Other organizations : Immanuel Krankenhaus, Charité - Universitätsmedizin Berlin, Hasso Plattner Institute, University of Potsdam, Paracelsus-Kliniken

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Variable analysis

independent variables

Filtration to separate extracellular peptides from (poly)peptides
Desalting of the resulting smaller fractions
Analysis of the fractions without proteolytic digestion via liquid chromatography (LC) and mass spectrometry (MS)

dependent variables

Identification of ribosomal peptides using an integrated catalogue of MG and MT data
Identification of non-ribosomal peptides using tools like MyriMatch, DirecTag, and CycloBranch
Identification of extracellular (poly)peptides with possible pathogenic functions including protein misfolding and molecular mimicry

control variables

EasyNano-LC coupled online to a QExactive-Plus mass spectrometer (ThermoScientific, Waltham) for LC-MS analysis

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