A Fast-Pass, Desorption Electrospray Ionization Mass Spectrometry Strategy for Untargeted Metabolic Phenotyping

Shepard, Hawkins S.; May, Jody C.; Zuniga, Baltazar E.; Abraham, Joshua P.; Pfleger, Brian F.; Young, Jamey D.; McLean, John A.

doi:10.1021/jasms.4c00459

Title: A Fast-Pass, Desorption Electrospray Ionization Mass Spectrometry Strategy for Untargeted Metabolic Phenotyping

Journal Article · 27 January 2025 · Journal of the American Society for Mass Spectrometry

DOI: https://doi.org/10.1021/jasms.4c00459 · OSTI ID:2507134

^[1];

^[1]; Zuniga, Baltazar E. ^[1];

^[2]; Pfleger, Brian F. ^[2];

^[1];

^[1]

Vanderbilt University, Nashville, TN (United States)
University of Wisconsin, Madison, WI (United States)

Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) provides direct analytical readouts of small molecules that can be used to characterize the metabolic phenotypes of genetically engineered bacteria. In an effort to accelerate the time frame associated with the screening of mutant libraries, we have developed a high-throughput DESI-MSI analytical workflow implementing a single raster line-scan strategy that facilitates the collection of location-resolved molecular information from engineered strains on a subminute time scale. Evaluation of this “Fast-Pass” DESI-MSI phenotyping workflow on analytical standards demonstrated the capability of acquiring full metabolic profiling information with a throughput of ~40 s per sample. This Fast-Pass strategy was implemented in the analysis of genetically edited Escherichia coli strains that have been engineered to produce various free-fatty acids (FFAs) for applications relevant to biofuels. Due to the untargeted nature of DESI-MSI, the investigation of these strains yielded molecular information for both global metabolites and targeted detection of accumulated bioproducts, allowing simultaneous readouts of strain-specific chemical profiles and comparative measurements of FFA production levels.

View Journal Article

Cite

Export

Save

Research Organization:: Vanderbilt University, Nashville, TN (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0019404; SC0022207

OSTI ID:: 2507134

Journal Information:: Journal of the American Society for Mass Spectrometry, Journal Name: Journal of the American Society for Mass Spectrometry Journal Issue: 2 Vol. 36; ISSN 1044-0305

Publisher:: American Society for Mass SpectrometryCopyright Statement

Country of Publication:: United States

Language:: English

References (35)

Kinetic modeling of free fatty acid production in Escherichia coli based on continuous cultivation of a plasmid free strain Youngquist, J. Tyler; Lennen, Rebecca M.; Ranatunga, Don R. Biotechnology and Bioengineering, Vol. 109, Issue 6, p. 1518-1527 https://doi.org/10.1002/bit.24420	journal	January 2012
A mass spectrometry‐based high‐throughput screening method for engineering fatty acid synthases with improved production of medium‐chain fatty acids Xue, Pu; Si, Tong; Mishra, Shekhar Biotechnology and Bioengineering, Vol. 117, Issue 7 https://doi.org/10.1002/bit.27343	journal	April 2020
Re‐Imagining Drug Discovery using Mass Spectrometry Cooks, R. Graham; Feng, Yunfei; Huang, Kai‐Hung Israel Journal of Chemistry, Vol. 63, Issue 7-8 https://doi.org/10.1002/ijch.202300034	journal	March 2023
Characterization of intact microorganisms by MALDI mass spectrometry Fenselau, Catherine; Demirev, Plamen A. Mass Spectrometry Reviews, Vol. 20, Issue 4 https://doi.org/10.1002/mas.10004	journal	January 2001
Integrating ion mobility into comprehensive multidimensional metabolomics workflows: critical considerations May, Jody C.; McLean, John A. Metabolomics, Vol. 18, Issue 12 https://doi.org/10.1007/s11306-022-01961-0	journal	December 2022
Reducing Spatial Heterogeneity of MALDI Samples with Marangoni Flows During Sample Preparation Lai, Yin-Hung; Cai, Yi-Hong; Lee, Hsun Journal of the American Society for Mass Spectrometry, Vol. 27, Issue 8 https://doi.org/10.1007/s13361-016-1406-0	journal	April 2016
Faster, More Reproducible DESI-MS for Biological Tissue Imaging Tillner, Jocelyn; Wu, Vincen; Jones, Emrys A. Journal of the American Society for Mass Spectrometry, Vol. 28, Issue 10 https://doi.org/10.1007/s13361-017-1714-z	journal	June 2017
MALDI-MS screening of microbial colonies with isomer resolution to select fatty acid desaturase variants Choe, Kisurb; Jindra, Michael A.; Hubbard, Susan C. Analytical Biochemistry, Vol. 672 https://doi.org/10.1016/j.ab.2023.115169	journal	July 2023
Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals Jullesson, David; David, Florian; Pfleger, Brian Biotechnology Advances, Vol. 33, Issue 7 https://doi.org/10.1016/j.biotechadv.2015.02.011	journal	November 2015
Engineering microbial fatty acid metabolism for biofuels and biochemicals Marella, Eko Roy; Holkenbrink, Carina; Siewers, Verena Current Opinion in Biotechnology, Vol. 50 https://doi.org/10.1016/j.copbio.2017.10.002	journal	April 2018
The foundations and development of lipidomics Han, Xianlin; Gross, Richard W. Journal of Lipid Research, Vol. 63, Issue 2 https://doi.org/10.1016/j.jlr.2021.100164	journal	February 2022
Expanding the Biologist’s Toolkit with CRISPR-Cas9 Sternberg, Samuel H.; Doudna, Jennifer A. Molecular Cell, Vol. 58, Issue 4 https://doi.org/10.1016/j.molcel.2015.02.032	journal	May 2015
Engineering Escherichia coli to synthesize free fatty acids Lennen, Rebecca M.; Pfleger, Brian F. Trends in Biotechnology, Vol. 30, Issue 12 https://doi.org/10.1016/j.tibtech.2012.09.006	journal	December 2012
Revisiting metabolic engineering strategies for microbial synthesis of oleochemicals Yan, Qiang; Pfleger, Brian F. Metabolic Engineering, Vol. 58 https://doi.org/10.1016/j.ymben.2019.04.009	journal	March 2020
Evaluation of strategies to narrow the product chain-length distribution of microbially synthesized free fatty acids Jindra, Michael A.; Choe, Kisurb; Chowdhury, Ratul Metabolic Engineering, Vol. 77 https://doi.org/10.1016/j.ymben.2023.02.012	journal	May 2023
Thin-Layer Chromatography and Mass Spectrometry Coupled Using Desorption Electrospray Ionization Van Berkel, Gary J.; Ford, Michael J.; Deibel, Michael A. Analytical Chemistry, Vol. 77, Issue 5 https://doi.org/10.1021/ac048217p	journal	January 2005
Desorption Electrospray Ionization Mass Spectrometry for High-Throughput Analysis of Pharmaceutical Samples in the Ambient Environment Chen, Huanwen; Talaty, Nari N.; Takáts, Zoltán Analytical Chemistry, Vol. 77, Issue 21 https://doi.org/10.1021/ac050989d	journal	November 2005
Imprint Desorption Electrospray Ionization Mass Spectrometry Imaging for Monitoring Secondary Metabolites Production during Antagonistic Interaction of Fungi Tata, Alessandra; Perez, Consuelo; Campos, Michel L. Analytical Chemistry, Vol. 87, Issue 24 https://doi.org/10.1021/acs.analchem.5b03614	journal	November 2015
Spatiochemically Profiling Microbial Interactions with Membrane Scaffolded Desorption Electrospray Ionization-Ion Mobility-Imaging Mass Spectrometry and Unsupervised Segmentation Ellis, Berkley M.; Fischer, Caleb N.; Martin, Leroy B. Analytical Chemistry, Vol. 91, Issue 21 https://doi.org/10.1021/acs.analchem.9b02992	journal	October 2019
Highly Active C ₈ -Acyl-ACP Thioesterase Variant Isolated by a Synthetic Selection Strategy Hernández Lozada, Néstor J.; Lai, Rung-Yi; Simmons, Trevor R. ACS Synthetic Biology, Vol. 7, Issue 9 https://doi.org/10.1021/acssynbio.8b00215	journal	July 2018
Real-Time Screening of Biocatalysts in Live Bacterial Colonies Yan, Cunyu; Parmeggiani, Fabio; Jones, Emrys A. Journal of the American Chemical Society, Vol. 139, Issue 4 https://doi.org/10.1021/jacs.6b12165	journal	January 2017
Capillary flow as the cause of ring stains from dried liquid drops Deegan, Robert D.; Bakajin, Olgica; Dupont, Todd F. Nature, Vol. 389, Issue 6653, p. 827-829 https://doi.org/10.1038/39827	journal	October 1997
Programming cells by multiplex genome engineering and accelerated evolution Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A. Nature, Vol. 460, Issue 7257, p. 894-898 https://doi.org/10.1038/nature08187	journal	July 2009
Biological synthesis unbounded? Pfleger, Brian F.; Prather, Kristala L. J. Nature Biotechnology, Vol. 33, Issue 11 https://doi.org/10.1038/nbt.3399	journal	November 2015
Engineering fungal de novo fatty acid synthesis for short chain fatty acid production Gajewski, Jan; Pavlovic, Renata; Fischer, Manuel Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms14650	journal	March 2017
Lipid and metabolite profiles of human brain tumors by desorption electrospray ionization-MS Jarmusch, Alan K.; Pirro, Valentina; Baird, Zane Proceedings of the National Academy of Sciences, Vol. 113, Issue 6 https://doi.org/10.1073/pnas.1523306113	journal	January 2016
Accelerating strain phenotyping with desorption electrospray ionization-imaging mass spectrometry and untargeted analysis of intact microbial colonies Ellis, Berkley M.; Babele, Piyoosh K.; May, Jody C. Proceedings of the National Academy of Sciences, Vol. 118, Issue 49 https://doi.org/10.1073/pnas.2109633118	journal	December 2021
Cardinal : an R package for statistical analysis of mass spectrometry-based imaging experiments: Fig. 1. Bemis, Kyle D.; Harry, April; Eberlin, Livia S. Bioinformatics, Vol. 31, Issue 14 https://doi.org/10.1093/bioinformatics/btv146	journal	March 2015
Ambient Mass Spectrometry Cooks, R. G. Science, Vol. 311, Issue 5767 https://doi.org/10.1126/science.1119426	journal	March 2006
Identification of Transport Proteins Involved in Free Fatty Acid Efflux in Escherichia coli Lennen, R. M.; Politz, M. G.; Kruziki, M. A. Journal of Bacteriology, Vol. 195, Issue 1 https://doi.org/10.1128/JB.01477-12	journal	October 2012
Alteration of the specificity and regulation of fatty acid synthesis of Escherichia coli by expression of a plant medium-chain acyl-acyl carrier protein thioesterase. Voelker, T. A.; Davies, H. M. Journal of Bacteriology, Vol. 176, Issue 23, p. 7320-7327 https://doi.org/10.1128/jb.176.23.7320-7327.1994	journal	December 1994
CRISPR–Cas9 Structures and Mechanisms Jiang, Fuguo; Doudna, Jennifer A. Annual Review of Biophysics, Vol. 46, Issue 1 https://doi.org/10.1146/annurev-biophys-062215-010822	journal	May 2017
Increasing medium chain fatty acids production in Yarrowia lipolytica by metabolic engineering Rigouin, Coraline; Croux, Christian; Borsenberger, Vinciane Microbial Cell Factories, Vol. 17, Issue 1 https://doi.org/10.1186/s12934-018-0989-5	journal	September 2018
Lipid extraction by methyl- tert -butyl ether for high-throughput lipidomics Matyash, Vitali; Liebisch, Gerhard; Kurzchalia, Teymuras V. Journal of Lipid Research, Vol. 49, Issue 5 https://doi.org/10.1194/jlr.D700041-JLR200	journal	February 2008
Modulating Membrane Composition Alters Free Fatty Acid Tolerance in Escherichia coli Lennen, Rebecca M.; Pfleger, Brian F. PLoS ONE, Vol. 8, Issue 1 https://doi.org/10.1371/journal.pone.0054031	journal	January 2013

Similar Records

Accelerating strain phenotyping with desorption electrospray ionization-imaging mass spectrometry and untargeted analysis of intact microbial colonies

Journal Article · 2021 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1833748

Ellis, Berkley M.; Babele, Piyoosh K.; May, Jody C.; +4 more

Untargeted Spatial Metabolomics and Spatial Proteomics on the Same Tissue Section

Journal Article · 2024 · Analytical Chemistry · OSTI ID:2544381

Vandergrift, Gregory W.; Veličković, Marija; Day, Le Z.; +4 more

Comprehensive Detection of Genes Causing a Phenotype Using Phenotype Sequencing and Pathway Analysis

Journal Article · 2014 · PLoS ONE · OSTI ID:1904727

Harper, Marc; Gronenberg, Luisa; Liao, James; +1 more

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
DESI-MS
bacteria
genetic engineering
ions
lipidomics
lipids
mass spectrometry imaging
metabolomics
mixtures
molecular engineering
synthetic biology

Title: A Fast-Pass, Desorption Electrospray Ionization Mass Spectrometry Strategy for Untargeted Metabolic Phenotyping

Citation Formats

References (35)

Similar Records

Related Subjects