title: Metaproteomics: Evaluation of protein extraction from activated sludge.
abstract: Metaproteomic studies of full-scale activated sludge systems require reproducible protein extraction methods. A systematic evaluation of three different extractions protocols, each in combination with three different methods of cell lysis, and a commercial kit were evaluated. Criteria used for comparison of each method included the extracted protein concentration and the number of identified proteins and peptides as well as their phylogenetic, cell localization and functional distribution and quantitative reproducibility. Furthermore, the advantage of using specific metagenomes and a 2-step database approach was illustrated. The results recommend a protocol for protein extraction from activated sludge based on the protein extraction reagent B-Per and bead beating. The data have been deposited to the ProteomeXchange with identifier PXD000862 (http://proteomecentral.proteomexchange.org/dataset/PXD000862).
authors.affiliation: Center for Microbial Communities, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark.
authors.forename: Susan Hove
authors.initials: SH
authors.lastname: Hansen
authors.forename: Allan
authors.initials: A
authors.lastname: Stensballe
authors.forename: Per Halkjaer
authors.initials: PH
authors.lastname: Nielsen
authors.forename: Florian-Alexander
authors.initials: FA
authors.lastname: Herbst
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis / Q000302:isolation & purification*; D002853:Chromatography, Liquid; D040901:Proteomics; D012722:Sewage / Q000032:analysis* / Q000382:microbiology*; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins; D012722:Sewage
keywords: Activated sludge; Complex microbial communities; LC-MS/MS; Metaproteomics; Microbiology; Protein extraction