Next Article in Journal
Next Article in Special Issue
Previous Article in Journal
Previous Article in Special Issue
Int. J. Mol. Sci. 2014, 15(6), 10169-10184; doi:10.3390/ijms150610169
Article

Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents

,
 and *
Received: 9 April 2014; in revised form: 23 May 2014 / Accepted: 23 May 2014 / Published: 6 June 2014
(This article belongs to the collection Advances in Proteomic Research)
View Full-Text   |   Download PDF [995 KB, uploaded 19 June 2014]
Abstract: Protein recovery is crucial for shotgun metaproteomics to study the in situ functionality of microbial populations from complex biofilms but still poorly addressed by far. To fill this knowledge gap, we systematically evaluated the sample preparation with extraction buffers comprising four detergents for the metaproteomics analysis of a terephthalate-degrading methanogenic biofilm using an on-line two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) system. Totally, 1018 non-repeated proteins were identified with the four treatments. On the whole, each treatment could recover the biofilm proteins with specific distributions of molecular weight, hydrophobicity, and isoelectric point. The extraction buffers containing zwitterionic and anionic detergents were found to harvest the proteins with better efficiency and quality, allowing identification up to 76.2% of total identified proteins with the LC-MS/MS analysis. According to the annotation with a relevant metagenomic database, we further observed different taxonomic profiles of bacterial and archaeal members and discriminable patterns of the functional expression among the extraction buffers used. Overall, the finding of the present study provides first insight to the effect of the detergents on the characteristics of extractable proteins from biofilm and the developed protocol combined with nano 2D-LC/MS/MS analysis can improve the metaproteomics studies on microbial functionality of biofilms in the wastewater treatment systems.
Keywords: metaproteomic; biofilm; protein recovery metaproteomic; biofilm; protein recovery
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Export to BibTeX |
EndNote


MDPI and ACS Style

Huang, H.-J.; Chen, W.-Y.; Wu, J.-H. Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents. Int. J. Mol. Sci. 2014, 15, 10169-10184.

AMA Style

Huang H-J, Chen W-Y, Wu J-H. Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents. International Journal of Molecular Sciences. 2014; 15(6):10169-10184.

Chicago/Turabian Style

Huang, Hung-Jen; Chen, Wei-Yu; Wu, Jer-Horng. 2014. "Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents." Int. J. Mol. Sci. 15, no. 6: 10169-10184.



Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert