Metaproteomics

• Determine the biodiversity of microbial or viral communities and multi-organism systems
• Large-scale identification and quantification of proteins from microbial communities
• Quantification of per species biomass
• Tracking of substrate metabolisms

Metaproteomics is a rapidly growing research area, addressing the microbial composition of environmental samples (soil, feces, sewage, water etc) [further reading].

We have developed metaproteomics workflows covering protein extraction, peptide separation, LC-MS/MS measurements and data analysis. Our techniques allow us to determine the organisms present in a sample and their proportions as well as comprehensive analysis of the expressed proteins for each organism.

Example:

A protein sample of sewage sludge of unknown composition was solubilized and 30 µg of protein were digested with trypsin. The peptides were then fractionated by binding the peptides to a filter, followed by elution with increasing concentrations of acetonitrile (ACN). The samples were measured on an Orbitrap HF-X mass spectrometer coupled to an AQUITY UPLC system, using a 25 cm M‑Class column. Gradients of 60, 130 or 300 min were used to separate the peptides. Peptides were identified using a de novo peptide sequencing algorithm and by a sectioning database approach, searching against the whole Uniprot bacteria database. The organisms identified in the first round of analysis were used to construct specific databases for more in-depth analysis of the provided sample.