MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C.; Burnum-Johnson, Kristin E.; Kim, Young-Mo; Kyle, Jennifer E.; Matzke, Melissa M.; Shukla, Anil K.; Chu, Rosalie K.; Schepmoes, Athena A.; Jacobs, Jon M.; Baric, Ralph S.; Webb-Robertson, Bobbie-Jo; Smith, Richard D.; Metz, Thomas O.; Chia, ed., Nicholas

doi:10.1128/mSystems.00043-16

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

Journal Article · Tue Jun 28 00:00:00 EDT 2016 · mSystems

DOI:https://doi.org/10.1128/mSystems.00043-16· OSTI ID:1618370

Nakayasu, Ernesto S. ^[1]; Nicora, Carrie D. ^[1]; Sims, Amy C. ^[2]; Burnum-Johnson, Kristin E. ^[1]; Kim, Young-Mo ^[1]; Kyle, Jennifer E. ^[1]; Matzke, Melissa M. ^[1]; Shukla, Anil K. ^[1]; Chu, Rosalie K. ^[1]; Schepmoes, Athena A. ^[1]; Jacobs, Jon M. ^[1]; Baric, Ralph S. ^[3]; Webb-Robertson, Bobbie-Jo ^[4]; Smith, Richard D. ^[1]; Metz, Thomas O. ^[1]; Chia, ed., Nicholas

Earth &, Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA

In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample.

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Sponsoring Organization:: USDOE

OSTI ID:: 1618370

Alternate ID(s):: OSTI ID: 1327119

Journal Information:: mSystems, Journal Name: mSystems Journal Issue: 3 Vol. 1; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (49)

Advances in proteomics data analysis and display using an accurate mass and time tag approach Zimmer, Jennifer S. D.; Monroe, Matthew E.; Qian, Wei-Jun Mass Spectrometry Reviews, Vol. 25, Issue 3 https://doi.org/10.1002/mas.20071	journal	January 2006
A comparison of cell and tissue extraction techniques using high-resolution1H-NMR spectroscopy Belle, J. E. Le; Harris, N. G.; Williams, S. R. NMR in Biomedicine, Vol. 15, Issue 1 https://doi.org/10.1002/nbm.740	journal	January 2002
Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks Weckwerth, Wolfram; Wenzel, Kathrin; Fiehn, Oliver PROTEOMICS, Vol. 4, Issue 1 https://doi.org/10.1002/pmic.200200500	journal	January 2004
Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry Chertov, Oleg; Biragyn, Arya; Kwak, Larry W. PROTEOMICS, Vol. 4, Issue 4 https://doi.org/10.1002/pmic.200300677	journal	April 2004
A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors Webb-Robertson, Bobbie-Jo M.; Matzke, Melissa M.; Jacobs, Jon M. PROTEOMICS, Vol. 11, Issue 24 https://doi.org/10.1002/pmic.201100078	journal	November 2011
Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics Shi, Tujin; Su, Dian; Liu, Tao PROTEOMICS, Vol. 12, Issue 8 https://doi.org/10.1002/pmic.201100436	journal	April 2012
A reversed-phase capillary ultra-performance liquid chromatography–mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling Gao, Xiaoli; Zhang, Qibin; Meng, Da Analytical and Bioanalytical Chemistry, Vol. 402, Issue 9 https://doi.org/10.1007/s00216-012-5773-5	journal	February 2012
Two strings to the systems biology bow: co-extracting the metabolome and proteome of yeast Schmidt, Simon A.; Jacob, Shana S.; Ahn, Seong Beom Metabolomics, Vol. 9, Issue 1 https://doi.org/10.1007/s11306-012-0437-1	journal	June 2012
Preparation of Lipide Extracts from Brain Tissue Folch, Jordi.; Ascoli, I.; Lees, M. Journal of Biological Chemistry, Vol. 191, Issue 2 https://doi.org/10.1016/S0021-9258(18)55987-1	journal	August 1951
A Simple Method for the Isolation and Purification of Total Lipides from Animal Tissues Folch, Jordi; Lees, M.; Stanley, G. H. Sloane Journal of Biological Chemistry, Vol. 226, Issue 1 https://doi.org/10.1016/S0021-9258(18)64849-5	journal	May 1957
Middle East respiratory syndrome Zumla, Alimuddin; Hui, David S.; Perlman, Stanley The Lancet, Vol. 386, Issue 9997 https://doi.org/10.1016/S0140-6736(15)60454-8	journal	September 2015
Simultaneously extracting DNA, RNA, and protein using kits: Is sample quantity or quality prejudiced? Mathieson, William; Thomas, Gerry A. Analytical Biochemistry, Vol. 433, Issue 1 https://doi.org/10.1016/j.ab.2012.10.006	journal	February 2013
Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes Chen, Rui; Mias, George I.; Li-Pook-Than, Jennifer Cell, Vol. 148, Issue 6 https://doi.org/10.1016/j.cell.2012.02.009	journal	March 2012
Comparison of protein precipitation methods for sample preparation prior to proteomic analysis Jiang, Lei; He, Lin; Fountoulakis, Michael Journal of Chromatography A, Vol. 1023, Issue 2 https://doi.org/10.1016/j.chroma.2003.10.029	journal	January 2004
Simultaneous extraction of proteins and metabolites from cells in culture Sapcariu, Sean C.; Kanashova, Tamara; Weindl, Daniel MethodsX, Vol. 1 https://doi.org/10.1016/j.mex.2014.07.002	journal	January 2014
A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics Stanley, Jeffrey R.; Adkins, Joshua N.; Slysz, Gordon W. Analytical Chemistry, Vol. 83, Issue 16 https://doi.org/10.1021/ac2009806	journal	August 2011
MetaboliteDetector: Comprehensive Analysis Tool for Targeted and Nontargeted GC/MS Based Metabolome Analysis Hiller, Karsten; Hangebrauk, Jasper; Jäger, Christian Analytical Chemistry, Vol. 81, Issue 9 https://doi.org/10.1021/ac802689c	journal	May 2009
Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-Based Proteomics Data Webb-Robertson, Bobbie-Jo M.; McCue, Lee Ann; Waters, Katrina M. Journal of Proteome Research, Vol. 9, Issue 11 https://doi.org/10.1021/pr1005247	journal	November 2010
A Quantitative Study of the Effects of Chaotropic Agents, Surfactants, and Solvents on the Digestion Efficiency of Human Plasma Proteins by Trypsin Proc, Jennifer L.; Kuzyk, Michael A.; Hardie, Darryl B. Journal of Proteome Research, Vol. 9, Issue 10 https://doi.org/10.1021/pr100656u	journal	October 2010
A biomolecular isolation framework for eco-systems biology Roume, Hugo; EL Muller, Emilie; Cordes, Thekla The ISME Journal, Vol. 7, Issue 1 https://doi.org/10.1038/ismej.2012.72	journal	July 2012
Model‐driven multi‐omic data analysis elucidates metabolic immunomodulators of macrophage activation Bordbar, Aarash; Mo, Monica L.; Nakayasu, Ernesto S. Molecular Systems Biology, Vol. 8, Issue 1 https://doi.org/10.1038/msb.2012.21	journal	January 2012
Global quantification of mammalian gene expression control Schwanhäusser, Björn; Busse, Dorothea; Li, Na Nature, Vol. 473, Issue 7347 https://doi.org/10.1038/nature10098	journal	May 2011
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes Hultman, Jenni; Waldrop, Mark P.; Mackelprang, Rachel Nature, Vol. 521, Issue 7551 https://doi.org/10.1038/nature14238	journal	March 2015
Sample extraction techniques for enhanced proteomic analysis of plant tissues Isaacson, Tal; Damasceno, Cynthia M. B.; Saravanan, Ramu S. Nature Protocols, Vol. 1, Issue 2 https://doi.org/10.1038/nprot.2006.102	journal	July 2006
A new method to measure oxygen solubility in organic solvents through optical oxygen sensing Quaranta, Michela; Murkovic, Michael; Klimant, Ingo The Analyst, Vol. 138, Issue 21 https://doi.org/10.1039/c3an36782g	journal	January 2013
Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes Kim, Young-Mo; Schmidt, Brian J.; Kidwai, Afshan S. Molecular BioSystems, Vol. 9, Issue 6 https://doi.org/10.1039/c3mb25598k	journal	January 2013
Decreased abundance of type III secretion system-inducing signals in Arabidopsis mkp1 enhances resistance against Pseudomonas syringae Anderson, J. C.; Wan, Y.; Kim, Y. -M. Proceedings of the National Academy of Sciences, Vol. 111, Issue 18 https://doi.org/10.1073/pnas.1403248111	journal	April 2014
Quantitative Assessment of In-solution Digestion Efficiency Identifies Optimal Protocols for Unbiased Protein Analysis León, Ileana R.; Schwämmle, Veit; Jensen, Ole N. Molecular & Cellular Proteomics, Vol. 12, Issue 10 https://doi.org/10.1074/mcp.M112.025585	journal	June 2013
Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements Webb-Robertson, Bobbie-Jo M.; Matzke, Melissa M.; Datta, Susmita Molecular & Cellular Proteomics, Vol. 13, Issue 12 https://doi.org/10.1074/mcp.M113.030932	journal	November 2014
Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides per Protein Ishihama, Yasushi; Oda, Yoshiya; Tabata, Tsuyoshi Molecular & Cellular Proteomics, Vol. 4, Issue 9 https://doi.org/10.1074/mcp.M500061-MCP200	journal	June 2005
VIPER: an advanced software package to support high-throughput LC-MS peptide identification Monroe, Matthew E.; Tolić, Nikola; Jaitly, Navdeep Bioinformatics, Vol. 23, Issue 15 https://doi.org/10.1093/bioinformatics/btm281	journal	June 2007
DAnTE: a statistical tool for quantitative analysis of -omics data Polpitiya, A. D.; Qian, W. -J.; Jaitly, N. Bioinformatics, Vol. 24, Issue 13 https://doi.org/10.1093/bioinformatics/btn217	journal	May 2008
LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data Sartor, Maureen A.; Leikauf, George D.; Medvedovic, Mario Bioinformatics, Vol. 25, Issue 2 https://doi.org/10.1093/bioinformatics/btn592	journal	November 2008
Improved quality control processing of peptide-centric LC-MS proteomics data Matzke, Melissa M.; Waters, Katrina M.; Metz, Thomas O. Bioinformatics, Vol. 27, Issue 20 https://doi.org/10.1093/bioinformatics/btr479	journal	August 2011
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data Karnovsky, Alla; Weymouth, Terry; Hull, Tim Bioinformatics, Vol. 28, Issue 3 https://doi.org/10.1093/bioinformatics/btr661	journal	November 2011
Assessing the Need for a Standardized Cancer HUman Biobank (caHUB): Findings From a National Survey With Cancer Researchers Massett, H. A.; Atkinson, N. L.; Weber, D. JNCI Monographs, Vol. 2011, Issue 42 https://doi.org/10.1093/jncimonographs/lgr007	journal	June 2011
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Shannon, P. Genome Research, Vol. 13, Issue 11 https://doi.org/10.1101/gr.1239303	journal	November 2003
The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation: Metabolomics of leaf-cutter ant fungus gardens Huang, Eric L.; Aylward, Frank O.; Kim, Young-Mo Environmental Microbiology Reports, Vol. 6, Issue 4 https://doi.org/10.1111/1758-2229.12163	journal	April 2014
A universal protocol for the combined isolation of metabolites, DNA, long RNAs, small RNAs, and proteins from plants and microorganisms Valledor, Luis; Escandón, Mónica; Meijón, Mónica The Plant Journal, Vol. 79, Issue 1 https://doi.org/10.1111/tpj.12546	journal	June 2014
Bilateral Entry and Release of Middle East Respiratory Syndrome Coronavirus Induces Profound Apoptosis of Human Bronchial Epithelial Cells Tao, X.; Hill, T. E.; Morimoto, C. Journal of Virology, Vol. 87, Issue 17 https://doi.org/10.1128/JVI.01562-13	journal	July 2013
Sindbis Virus Entry into Cells Triggers Apoptosis by Activating Sphingomyelinase, Leading to the Release of Ceramide Jan, Jia-Tsrong; Chatterjee, Subroto; Griffin, Diane E. Journal of Virology, Vol. 74, Issue 14 https://doi.org/10.1128/JVI.74.14.6425-6432.2000	journal	July 2000
A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm Aderem, Alan; Adkins, Joshua N.; Ansong, Charles mBio, Vol. 2, Issue 1 https://doi.org/10.1128/mBio.00325-10	journal	February 2011
A Rapid Method of Total Lipid Extraction and Purification Bligh, E. G.; Dyer, W. J. Canadian Journal of Biochemistry and Physiology, Vol. 37, Issue 8 https://doi.org/10.1139/o59-099	journal	August 1959
Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis Pomraning, Kyle R.; Wei, Siwei; Karagiosis, Sue A. PLOS ONE, Vol. 10, Issue 4 https://doi.org/10.1371/journal.pone.0123188	journal	April 2015
Sphingolipids in viral infection Schneider-Schaulies, Jürgen; Schneider-Schaulies, Sibylle Biological Chemistry, Vol. 396, Issue 6-7 https://doi.org/10.1515/hsz-2014-0273	journal	June 2015
Integration of -omics data and networks for biomedical research with VANTED Klukas, Christian; Schreiber, Falk Journal of Integrative Bioinformatics https://doi.org/10.2390/biecoll-jib-2010-112	text	January 2009
Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00109	journal	April 2014
Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms Kim, Young-Mo; Nowack, Shane; Olsen, Millie T. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00209	journal	April 2015
Anti–Dengue Virus Nonstructural Protein 1 Antibodies Cause NO-Mediated Endothelial Cell Apoptosis via Ceramide-Regulated Glycogen Synthase Kinase-3β and NF-κB Activation Chen, Chia-Ling; Lin, Chiou-Feng; Wan, Shu-Wen The Journal of Immunology, Vol. 191, Issue 4 https://doi.org/10.4049/jimmunol.1201976	journal	July 2013

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