Premium
Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies
Author(s) -
Nicora Carrie D.,
Anderson Brian J.,
Callister Stephen J.,
Norbeck Angela D.,
Purvine Sam O.,
Jansson Janet K.,
Mason Olivia U.,
David Maude M.,
Jurelevicius Diogo,
Smith Richard D.,
Lipton Mary S.
Publication year - 2013
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201300003
Subject(s) - soil water , chemistry , biology , ecology
Characterization of microbial protein expression provides information necessary to better understand the unique biological pathways that occur within soil microbial communities that contribute to atmospheric CO 2 levels and the earth's changing climate. A significant challenge in studying the soil microbial community proteome is the initial dissociation of bacterial proteins from the complex mixture of particles found in natural soil. The differential extraction of intact bacterial cells limits the characterization of the complete representation of a microbial community. However, in situ lysis of bacterial cells in soil can lead to potentially high levels of protein adsorption to soil particles. Here, we investigated various amino acids for their ability to block soil protein adsorption sites prior to in situ lysis of bacterial cells, as well as their compatibility with both tryptic digestion and mass spectrometric analysis. The treatments were tested by adding proteins from lysed E scherichia coli cells to representative treated and untreated soil samples. The results show that it is possible to significantly increase protein identifications through blockage of binding sites on a variety of soil and sediment textures; use of an optimized desorption buffer further increases the number of identifications.