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Title: The MPLEx Protocol for Multi-omic Analyses of Soil Samples

Abstract

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required. To address this limitation, a 3-in-1 method for simultaneous metabolite, protein, and lipid extraction (MPLEx) from the exact same soil sample was created by adapting a solvent-based approach. This MPLEx protocol has proven to be simple yet robust for many sample types and even when utilized for limited quantities of complex soil samples. The MPLEx method also greatly enabled the rapid multi-omic measurements needed to gain a better understanding of the members of each microbial community, while evaluating the changes taking place upon biological and environmental perturbations.

Authors:
; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1455290
Report Number(s):
PNNL-SA-129344
Journal ID: ISSN 1940-087X; jove; 48680; 48135; 400412000
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Visualized Experiments; Journal Issue: 135
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

Nicora, Carrie D., Burnum-Johnson, Kristin E., Nakayasu, Ernesto S., Casey, Cameron P., White, Richard A., Roy Chowdhury, Taniya, Kyle, Jennifer E., Kim, Young-Mo, Smith, Richard D., Metz, Thomas O., Jansson, Janet K., and Baker, Erin S.. The MPLEx Protocol for Multi-omic Analyses of Soil Samples. United States: N. p., 2018. Web. doi:10.3791/57343.
Nicora, Carrie D., Burnum-Johnson, Kristin E., Nakayasu, Ernesto S., Casey, Cameron P., White, Richard A., Roy Chowdhury, Taniya, Kyle, Jennifer E., Kim, Young-Mo, Smith, Richard D., Metz, Thomas O., Jansson, Janet K., & Baker, Erin S.. The MPLEx Protocol for Multi-omic Analyses of Soil Samples. United States. doi:10.3791/57343.
Nicora, Carrie D., Burnum-Johnson, Kristin E., Nakayasu, Ernesto S., Casey, Cameron P., White, Richard A., Roy Chowdhury, Taniya, Kyle, Jennifer E., Kim, Young-Mo, Smith, Richard D., Metz, Thomas O., Jansson, Janet K., and Baker, Erin S.. Mon . "The MPLEx Protocol for Multi-omic Analyses of Soil Samples". United States. doi:10.3791/57343.
@article{osti_1455290,
title = {The MPLEx Protocol for Multi-omic Analyses of Soil Samples},
author = {Nicora, Carrie D. and Burnum-Johnson, Kristin E. and Nakayasu, Ernesto S. and Casey, Cameron P. and White, Richard A. and Roy Chowdhury, Taniya and Kyle, Jennifer E. and Kim, Young-Mo and Smith, Richard D. and Metz, Thomas O. and Jansson, Janet K. and Baker, Erin S.},
abstractNote = {Mass spectrometry (MS)-based integrated metaproteomic, metabolomic and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required. To address this limitation, a 3-in-1 method for simultaneous metabolite, protein, and lipid extraction (MPLEx) from the exact same soil sample was created by adapting a solvent-based approach. This MPLEx protocol has proven to be simple yet robust for many sample types and even when utilized for limited quantities of complex soil samples. The MPLEx method also greatly enabled the rapid multi-omic measurements needed to gain a better understanding of the members of each microbial community, while evaluating the changes taking place upon biological and environmental perturbations.},
doi = {10.3791/57343},
journal = {Journal of Visualized Experiments},
number = 135,
volume = ,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2018},
month = {Mon Jan 01 00:00:00 EST 2018}
}