Works (173)

Updated: March 5th, 2024 05:02

2024 journal article

TL;DR: R reverse metabolomics is presented as a discovery strategy, whereby tandem mass spectrometry spectra acquired from newly synthesized compounds are searched for in public metabolomics datasets to uncover phenotypic associations. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: March 4, 2024

2023 article

Aggregated Molecular Phenotype Scores: Enhancing Assessment and Visualization of Mass Spectrometry Imaging Data for Tissue-Based Diagnostics

Chappel, J. R., King, M. E., Fleming, J., Eberlin, L. S., Reif, D. M., & Baker, E. S. (2023, August 14). ANALYTICAL CHEMISTRY, Vol. 8.

By: J. Chappel n, M. King*, J. Fleming n, L. Eberlin*, D. Reif* & E. Baker*

TL;DR: Initial comparisons of cancerous human tissues to their normal or benign counterparts illustrated that AMP scores distinguished phenotypes with high accuracy, sensitivity, and specificity, leading to high diagnostic accuracy and interpretability. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: August 28, 2023

2023 article

Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut

Foley, M. H., Walker, M. E., Stewart, A. K., O'Flaherty, S., Gentry, E. C., Patel, S., … Theriot, C. M. (2023, March 13). NATURE MICROBIOLOGY, Vol. 3.

By: M. Foley n, M. Walker*, A. Stewart n, S. O'Flaherty n, E. Gentry*, S. Patel*, V. Beaty*, G. Allen n ...

MeSH headings : Animals; Mice; Humans; Clostridioides difficile; Clostridioides; Bile Acids and Salts; Amidohydrolases; Clostridium Infections
TL;DR: Insight is provided into the structural basis of BSH mechanisms that shape the BA landscape and promote colonization resistance against C. difficile in vitro and in pre-clinical in vivo models of CDI. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 4, 2023

2023 journal article

Characterizing Adeno-Associated Virus Capsids with Both Denaturing and Intact Analysis Methods

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 34(12), 2811–2821.

By: J. Ryan*, M. Kostelic*, C. Hsieh*, J. Powers n, C. Aspinwall*, J. Dodds*, J. Schiel, M. Marty*, E. Baker*

Source: Web Of Science
Added: December 18, 2023

2023 journal article

Integrative Chemical-Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams

TOXICS, 11(7).

By: A. Cordova*, W. Klaren*, L. Ford*, F. Grimm*, E. Baker*, Y. Zhou n, F. Wright n, I. Rusyn*

author keywords: UVCB; petroleum; regulatory risk assessment; read-across; ion mobility spectrometry
Sources: ORCID, Web Of Science, NC State University Libraries
Added: July 6, 2023

2023 journal article

Using Multidimensional Separations to Distinguish Isomeric Amino Acid-Bile Acid Conjugates and Assess Their Presence and Perturbations in Model Systems

ANALYTICAL CHEMISTRY, 95(41), 15357–15366.

By: A. Stewart n, M. Foley n, M. Dougherty*, S. Mcgill*, A. Gulati*, E. Gentry*, L. Hagey*, P. Dorrestein* ...

TL;DR: This work analyzed 8 core bile acids synthetically conjugated with 22 proteinogenic and nonproteogenic amino acids totaling 176 MCBAs and created an in-house extended bile acid library that was applied to healthy mice dosed with antibiotics and humans having fecal microbiota transplantation (FMT) to assess the MCBA presence and changes in the gut before and after each perturbation. (via Semantic Scholar)
Source: Web Of Science
Added: October 30, 2023

2022 article

A High-Throughput Ion Mobility Spectrometry-Mass Spectrometry Screening Method for Opioid Profiling

Butler, K. E., & Baker, E. S. (2022, September 22). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, Vol. 9.

By: K. Butler n & E. Baker n

MeSH headings : Analgesics, Opioid; High-Throughput Screening Assays; Humans; Ion Mobility Spectrometry / methods; Mass Spectrometry / methods; Solid Phase Extraction
TL;DR: This SPE-IMS-MS approach enabled the rapid screening of urine samples for opioids and presents a major improvement in sample throughput compared to traditional chromatographic analyses coupled with MS, which routinely take several minutes per sample. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: October 3, 2022

2022 journal article

A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows

JOURNAL OF PROTEOME RESEARCH, 21(3), 798–807.

By: A. Bilbao*, B. Gibbons*, S. Stow*, J. Kyle*, K. Bloodsworth*, S. Payne*, R. Smith*, Y. Ibrahim*, E. Baker n, J. Fjeldsted*

author keywords: mass spectrometry; ion mobility spectrometry; preprocessing software; time-of-flight detector saturation; data-independent acquisition; lipid annotation
MeSH headings : Chromatography, Liquid / methods; Humans; Ion Mobility Spectrometry / methods; Ions; Lipids; Mass Spectrometry / methods; Workflow
TL;DR: The PNNL PreProcessor is developed, a standalone and user-friendly software housing various algorithmic implementations to generate new MS-files with enhanced signal quality and in the same instrument format to extend the dynamic range of the detection system, while reducing file sizes for faster and memory-efficient downstream processing. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: May 2, 2022

2022 journal article

Analysis of per- and polyfluoroalkyl substances in Houston Ship Channel and Galveston Bay following a large-scale industrial fire using ion-mobility-spectrometry-mass spectrometry

JOURNAL OF ENVIRONMENTAL SCIENCES, 115, 350–362.

By: A. Valdiviezo*, N. Aly*, Y. Luo*, A. Cordova*, G. Casillas*, M. Foster n, E. Baker n, I. Rusyn*

author keywords: Emergency; Environmental disaster; PFAS
MeSH headings : Animals; Bays; Chromatography, Liquid; Deer; Fluorocarbons / analysis; Ion Mobility Spectrometry; Tandem Mass Spectrometry; Water Pollutants, Chemical / analysis
TL;DR: Untargeted LC-IMS-MS improved the understanding of PFAS presence in complex environmental samples and identified a number of additional PFAS, many known to be components of firefighting foams. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: January 18, 2022

2022 article

Assessing the Fate of Dissolved Organic Compounds in Landfill Leachate and Wastewater Treatment Systems

Doyle, M. G., Odenkirk, M. T., Stewart, A. K., Nelson, J. P., Baker, E. S., & Cruz, F. (2022, November 1). ACS ES&T WATER, Vol. 11.

author keywords: nontargeted analysis; anthropogenic chemicals; wastewater; landfill leachate; reverse osmosis
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: November 2, 2022

2022 article

CCS Predictor 2.0: An Open-Source Jupyter Notebook Tool for Filtering Out False Positives in Metabolomics

Rainey, M. A., Watson, C. A., Asef, C. K., Foster, M. R., Baker, E. S., & Fernandez, F. M. (2022, December 6). ANALYTICAL CHEMISTRY, Vol. 12.

By: M. Rainey*, C. Watson*, C. Asef*, M. Foster n, E. Baker n & F. Fernandez*

MeSH headings : Metabolomics / methods; Mass Spectrometry / methods; Algorithms; Chromatography, High Pressure Liquid; Machine Learning
Sources: Web Of Science, NC State University Libraries
Added: January 3, 2023

2022 journal article

Characterization of compositional variability in petroleum substances

FUEL, 317.

By: A. Roman-Hubers*, A. Cordova*, A. Rohde*, W. Chiu*, T. McDonald*, F. Wright*, J. Dodds n, E. Baker n, I. Rusyn*

author keywords: UVCB; Registration; Variability; IMS-MS
Sources: Web Of Science, NC State University Libraries
Added: May 10, 2022

2022 article

Combining Isotopologue Workflows and Simultaneous Multidimensional Separations to Detect, Identify, and Validate Metabolites in Untargeted Analyses

Dodds, J. N., Wang, L., Patti, G. J., & Baker, E. S. (2022, January 28). ANALYTICAL CHEMISTRY, Vol. 1.

By: J. Dodds n, L. Wang*, G. Patti* & E. Baker n

MeSH headings : Chromatography, Liquid; Ion Mobility Spectrometry; Metabolomics / methods; Tandem Mass Spectrometry; Workflow
TL;DR: The analytical utility of incorporating ion mobility spectrometry (IMS) as an additional separation mechanism into standard LC-MS/MS isotopologue workflows is evaluated to highlight the enhanced separation space and increased annotation confidence afforded by IMS for metabolic characterization and provide a unique perspective for future developments in isotopically labeled MS experiments. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: March 14, 2022

2022 journal article

Cupric Ions Selectively Modulate TRAAK-Phosphatidylserine Interactions

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 144(16), 7048–7053.

By: Y. Zhu*, S. Schrecke*, S. Tang*, M. Odenkirk n, T. Walker*, L. Stover*, J. Lyu*, T. Zhang* ...

MeSH headings : Cations, Divalent / metabolism; Phosphatidylserines; Potassium Channels, Tandem Pore Domain / chemistry; Potassium Channels, Tandem Pore Domain / metabolism
TL;DR: High-resolution native mass spectrometry enables the determination of equilibrium binding constants for distinct Cu2+-bound stoichiometries and uncovered the highest coupling factor corresponds to a 1:1 PS-to-Cu2+ ratio, which brings forth the role of cupric ions as an essential cofactor in selective TRAAK-PS interactions. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: June 6, 2022

2022 article

Empowering women and addressing underrepresentation in the field of mass spectrometry

Rampler, E., Baker, E. S., Kirkwood, K. I., Schwaiger-Haber, M., Tam, M., Jones, M. A., & Sherman, M. (2022, February 16). EXPERT REVIEW OF PROTEOMICS, Vol. 2.

By: E. Rampler*, E. Baker n, K. Kirkwood n, M. Schwaiger-Haber*, M. Tam, M. Jones*, M. Sherman

author keywords: FeMS; ASMS; mass spectrometry; women; diversity
MeSH headings : Female; Humans; Mass Spectrometry; Power, Psychological
UN Sustainable Development Goal Categories
5. Gender Equality (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: March 7, 2022

2022 journal article

Evaluation of Metabolism of a Defined Pesticide Mixture through Multiple In Vitro Liver Models

TOXICS, 10(10).

author keywords: toxicokinetics; chemical mixtures; defined mixtures; human health risk assessment; nontargeted analyses; microphysiological systems
TL;DR: Findings suggest that iHep-based suspension assays maintain higher metabolic activity compared to 2D sandwich and OrganoPlate® 2-lane 96 model, and illustrates that IMS-MS can characterize in vitro metabolite formation following exposure to mixtures of environmental contaminants. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: October 2, 2022

2022 journal article

High-Resolution Demultiplexing (HRdm) Ion Mobility Spectrometry-Mass Spectrometry for Aspartic and Isoaspartic Acid Determination and Screening

ANALYTICAL CHEMISTRY, 94(16), 6191–6199.

By: K. Butler n, J. Dodds n, T. Flick*, I. Campuzano* & E. Baker n

MeSH headings : Chromatography, Liquid; Ion Mobility Spectrometry / methods; Isoaspartic Acid / analysis; Mass Spectrometry / methods; Peptides
TL;DR: The rapid high-throughput HRdm DTIMS-MS method was presented to present the first application of HRdm for isoAsp and Asp assessment and demonstrate screening capabilities for isomeric peptides in complex samples, resulting in a workflow highly suitable for biopharmaceutical research needs. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: May 23, 2022

2022 article

Impacts of Gestational FireMaster 550 (FM 550) Exposure on the Neonatal Cortex are Sex Specific and Largely Attributable to the Organophosphate Esters

Witchey, S. K., Doyle, M. G., Fredenburg, J. D., St Armour, G., Horman, B., Odenkirk, M. T., … Patisaul, H. B. (2022, September 8). NEUROENDOCRINOLOGY, Vol. 9.

By: S. Witchey n, M. Doyle n, J. Fredenburg n, G. St Armour n, B. Horman n, M. Odenkirk n, D. Aylor n, E. Baker n, H. Patisaul n

TL;DR: This study reveals multiple mechanisms by which the components of a common FR mixture are developmentally neurotoxic and that the OPFRs may be the compounds of greatest concern. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: September 26, 2022

2022 article

Introducing the Lipidomics Minimal Reporting Checklist

McDonald, J. G., Ejsing, C. S., Kopczynski, D., Holcapek, M., Aoki, J., Arita, M., … Ekroos, K. (2022, August 8). NATURE METABOLISM, Vol. 8.

MeSH headings : Checklist; Lipid Metabolism; Lipidomics; Mass Spectrometry
TL;DR: The creation of a dynamic checklist summarizing key details of lipidomic analyses using a common language has the potential to harmonize the field by improving both traceability and reproducibility. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 22, 2022

2022 article

Stability and Dissociation of Adeno-Associated Viral Capsids by Variable Temperature-Charge Detection-Mass Spectrometry

Kostelic, M. M., Ryan, J. P., Brown, L. S., Jackson, T. W., Hsieh, C.-C., Zak, C. K., … Marty, M. T. (2022, August 18). ANALYTICAL CHEMISTRY, Vol. 8.

By: M. Kostelic*, J. Ryan n, L. Brown*, T. Jackson*, C. Hsieh*, C. Zak*, H. Sanders*, Y. Liu* ...

MeSH headings : Capsid / chemistry; Capsid Proteins / chemistry; Dependovirus / chemistry; Mass Spectrometry; Temperature
TL;DR: This new approach better characterizes the thermal dissociation of AAVs, providing the simultaneous measurement of the stabilities and dissociation pathways of different subpopulations, and observed that pH stress caused a major decrease in thermal stability. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: September 12, 2022

2022 journal article

Surface Modified Nano-Electrospray Needles Improve Sensitivity for Native Mass Spectrometry

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 33(6), 1031–1037.

By: M. Kostelic*, C. Hsieh*, H. Sanders*, C. Zak*, J. Ryan n, E. Baker n, C. Aspinwall*, M. Marty*

author keywords: native mass spectrometry; charge detection mass spectrometry; electrospray ionization; silane chemistry
MeSH headings : Needles; Proteins / analysis; Spectrometry, Mass, Electrospray Ionization / methods
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: June 20, 2022

2022 journal article

Temporal chemical composition changes in water below a crude oil slick irradiated with natural sunlight

MARINE POLLUTION BULLETIN, 185.

By: A. Roman-Hubers*, C. Aeppli*, J. Dodds n, E. Baker n, K. McFarlin*, D. Letinski*, L. Zhao*, D. Mitchell* ...

author keywords: Oil; Photodegradation; Photooxidation; Petroleomics; Toxicity; Spill
MeSH headings : Petroleum; Sunlight; Water; Petroleum Pollution; Seawater
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: February 20, 2023

2022 journal article

Uncovering PFAS and Other Xenobiotics in the Dark Metabolome Using Ion Mobility Spectrometry, Mass Defect Analysis, and Machine Learning

ENVIRONMENTAL SCIENCE & TECHNOLOGY, 56(12), 9133–9143.

By: M. Foster n, M. Rainey*, C. Watson*, J. Dodds n, K. Kirkwood n, F. Fernandez*, E. Baker n

author keywords: xenobiotics; per- and polyfluoroalkyl substances; ion mobility spectrometry; mass spectrometry; mass defect; machine learning; PFAS
MeSH headings : Fluorocarbons; Humans; Ion Mobility Spectrometry / methods; Machine Learning; Metabolome; Xenobiotics
TL;DR: A xenobiotic structural annotation workflow using ion mobility spectrometry coupled with MS (IMS-MS), mass defect filtering, and machine learning to uncover potential xenobiotics classes and species in large metabolomic feature lists is evaluated. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: July 5, 2022

2022 journal article

Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (PFAS)

ENVIRONMENTAL SCIENCE & TECHNOLOGY, 56(6), 3441–3451.

By: K. Kirkwood n, J. Fleming n, H. Nguyen n, D. Reif n, E. Baker n & S. Belcher n

author keywords: Biomonitoring; contamination; per- and polyfluoroalkyl substances; fluoroethers; ion mobility; mass spectrometry; PFAS
MeSH headings : Alkanesulfonic Acids / analysis; Chromatography, Liquid; Fluorocarbons / analysis; United States; United States Environmental Protection Agency
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: February 18, 2022

2022 article

Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions

Kirkwood, K. I., Pratt, B. S., Shulman, N., Tamura, K., MacCoss, M. J., MacLean, B. X., & Baker, E. S. (2022, July 13). NATURE PROTOCOLS, Vol. 7.

By: K. Kirkwood n, B. Pratt*, N. Shulman*, K. Tamura*, M. MacCoss*, B. MacLean*, E. Baker n

MeSH headings : Ion Mobility Spectrometry; Lipidomics; Chromatography, Liquid / methods; Mass Spectrometry / methods; Lipids
TL;DR: This protocol describes how to use the free, vendor-neutral software Skyline to process and annotate multidimensional lipidomic data by using expanded features such as predicted retention times, spectral libraries and ion mobility filtering. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: July 26, 2022

2021 journal article

A Comparative Analysis of Analytical Techniques for Rapid Oil Spill Identification

ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, 40(4), 1034–1049.

By: A. Roman-Hubers*, T. McDonald*, E. Baker n, W. Chiu* & I. Rusyn*

author keywords: Ion mobility spectrometry– mass spectrometry; Fingerprinting; Petroleum
MeSH headings : Gas Chromatography-Mass Spectrometry; Gasoline; Hydrocarbons; Petroleum / analysis; Petroleum Pollution / analysis
TL;DR: The utility of IMS‐MS as a technique for rapid fingerprinting of complex samples and its advantages over traditional GC‐MS‐based analyses when used for decision‐making in emergency situations are demonstrated. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: April 5, 2021

2021 journal article

Data Processing Workflow to Identify Structurally Related Compounds in Petroleum Substances Using Ion Mobility Spectrometry-Mass Spectrometry

ENERGY & FUELS, 35(13), 10529–10539.

By: A. Roman-Hubers*, A. Cordova*, N. Aly*, T. McDonald*, D. Lloyd n, F. Wright n, E. Baker n, W. Chiu*, I. Rusyn*

TL;DR: This work demonstrates how rapid untargeted IMS-MS analysis and the proposed data processing workflow can be used to provide confident compositional characterization of hydrocarbon-containing substances. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: July 26, 2021

2021 article

Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity

Kirkwood, K. I., Christopher, M. W., Burgess, J. L., Littau, S. R., Foster, K., Richey, K., … Baker, E. S. (2021, December 7). JOURNAL OF PROTEOME RESEARCH, Vol. 12.

By: K. Kirkwood n, M. Christopher n, J. Burgess*, S. Littau*, K. Foster*, K. Richey*, B. Pratt*, N. Shulman* ...

author keywords: lipidomics; ion mobility spectrometry; spectral libraries; data annotation; smoke inhalation
MeSH headings : Chromatography, Liquid; Humans; Ion Mobility Spectrometry; Lipidomics; Lipids; Smoke Inhalation Injury
Sources: Web Of Science, NC State University Libraries
Added: December 20, 2021

2021 review

From Pesticides to Per- and Polyfluoroalkyl Substances: An Evaluation of Recent Targeted and Untargeted Mass Spectrometry Methods for Xenobiotics

[Review of ]. ANALYTICAL CHEMISTRY, 93(1), 641–656.

By: J. Dodds n, N. Alexander n, K. Kirkwood n, M. Foster n, Z. Hopkins n, D. Knappe n, E. Baker n

MeSH headings : Fluorocarbons / analysis; Mass Spectrometry; Xenobiotics / analysis
Sources: Web Of Science, NC State University Libraries, ORCID
Added: February 4, 2021

2021 journal article

From Plants to Ants: Fungal Modification of Leaf Lipids for Nutrition and Communication in the Leaf-Cutter Ant Fungal Garden Ecosystem

MSYSTEMS, 6(2).

author keywords: 18:2; 18:3; alpha-linolenic acid; fungal garden ecosystem; interkingdom communication; leaf-cutter ants; lignocellulose degradation; linoleic acid; lipidomics; mass spectrometry
TL;DR: This work demonstrates the role of lipids in both the transfer of energy and as an interkingdom communication tool in leaf-cutter ant fungal gardens and provides insights as to how the fungus modifies plant lipids into a usable source for the ants. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: April 28, 2021

2021 journal article

From Prevention to Disease Perturbations: A Multi-Omic Assessment of Exercise and Myocardial Infarctions

BIOMOLECULES, 11(1).

author keywords: lipidomics; metabolomics; multi-omics; planned myocardial infarction (PMI); myocardial infarction (MI); exercise; heart; cheminformatics
MeSH headings : Exercise; Exercise Test; Female; Humans; Lipidomics; Lipids / blood; Lipids / genetics; Male; Metabolomics; Middle Aged; Myocardial Infarction / blood; Myocardial Infarction / genetics; Myocardial Infarction / physiopathology; Myocardial Infarction / prevention & control; Risk Factors
TL;DR: Different lipidomic perturbations were observed for these events, as could be expected from their vastly different stresses on the body, and these results were combined with previously published metabolomic characterizations of the same patients to give a more holistic understanding of the molecular changes associated with each. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: January 4, 2021

2021 journal article

Improving the Speed and Selectivity of Newborn Screening Using Ion Mobility Spectrometry-Mass Spectrometry

ANALYTICAL CHEMISTRY, 93(51), 17094–17102.

By: J. Dodds n & E. Baker n

MeSH headings : Biomarkers; High-Throughput Screening Assays; Humans; Infant, Newborn; Ion Mobility Spectrometry; Mass Spectrometry; Neonatal Screening
TL;DR: The utility of ion mobility spectrometry (IMS) to enhance the accuracy of MS assays for primary (tier 1) screening is explored and the results suggest that ∼400 IMS resolving power would be required to confidently assess most NBS biomarkers of interest in dried blood spots (DBSs) that currently require follow-up testing. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: February 7, 2022

2021 journal article

In situ imaging reveals disparity between prostaglandin localization and abundance of prostaglandin synthases

COMMUNICATIONS BIOLOGY, 4(1).

MeSH headings : Animals; Cyclooxygenase 1 / genetics; Cyclooxygenase 1 / metabolism; Cyclooxygenase 2 / genetics; Cyclooxygenase 2 / metabolism; Embryo, Mammalian; Mass Spectrometry; Mice; Prostaglandin-Endoperoxide Synthases / metabolism; Prostaglandins / metabolism
TL;DR: A novel mass spectrometry imaging method is applied for direct in situ tissue localization of prostaglandin D2, its precursors, and downstream synthases and reveals that the abundance of COX and prostag landins D2 synthases in cellular regions does not mirror the regional abundance of prostags. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
5. Gender Equality (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 30, 2021

2021 journal article

Ion Mobility Spectrometry Characterization of the Intermediate Hydrogen-Containing Gold Cluster Au-7(PPh3)(7)H-5(2+)

JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 12(10), 2502–2508.

TL;DR: The findings indicate that hydrogen-containing species like Au7(PPh3)7H52+ act as intermediates in the formation of larger phosphine ligated gold clusters, which is necessary for scalable synthesis of clusters with tailored properties. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: April 5, 2021

2021 journal article

Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments

ANALYTICAL CHEMISTRY, 93(22), 7763–7773.

By: M. Odenkirk n, D. Reif n & E. Baker n

MeSH headings : Artificial Intelligence; Big Data; Data Analysis
TL;DR: The present and future capabilities of AI techniques in multiomic studies are discussed while introducing analytical checks and balances to validate the computational conclusions. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: July 19, 2021

2021 article

Per- and polyfluoroalkyl substances (PFAS)-contaminants of emerging concern

Baker, E. S., & Knappe, D. R. U. (2021, December 2). ANALYTICAL AND BIOANALYTICAL CHEMISTRY, Vol. 12.

By: E. Baker n & D. Knappe*

MeSH headings : Anthropogenic Effects; Environmental Pollutants / analysis; Environmental Pollutants / pharmacokinetics; Fluorocarbons / analysis; Fluorocarbons / pharmacokinetics; Humans; Tissue Distribution; United States; United States Environmental Protection Agency
TL;DR: It was imperative to assemble this PFAS topical collection to be a critical resource as Published in the topical collection Perand Polyfluoroalkyl Substances (PFAS) – Contaminants of Emerging Concern with guest editors Erin Baker and Detlef Knappe. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: December 13, 2021

2021 review

Recommendations for good practice in MS-based lipidomics

[Review of ]. JOURNAL OF LIPID RESEARCH, 62.

By: H. Koefeler, R. Ahrends*, E. Baker n, K. Ekroos, X. Han*, N. Hoffmann*, M. Holcapek*, M. Wenk*, G. Liebisch*

author keywords:   lipidomics; metabolomics; MS; chromatography; ion mobility spectrometry; phospholipids; sphingolipids; LC-MS; lipid identification
MeSH headings : Humans; Lipidomics / standards; Lipids / analysis; Mass Spectrometry
TL;DR: It is the intention of this review to highlight the most quality-relevant aspects of the lipidomics workflow, including preanalytics, sample preparation, MS, and lipid species identification and quantitation. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: February 7, 2022

2021 journal article

Relationships between constituents of energy drinks and beating parameters in human induced pluripotent stem cell (iPSC)-Derived cardiomyocytes

FOOD AND CHEMICAL TOXICOLOGY, 149.

By: Y. Luo*, Z. Chen*, A. Blanchette*, Y. Zhou n, F. Wright n, E. Baker n, W. Chiu*, I. Rusyn*

author keywords: Cardiovascular; Heart rate; QT interval; Theophylline; Adenine; Azelate
MeSH headings : Calcium / metabolism; Cell Differentiation; Cell Survival / drug effects; Drug-Related Side Effects and Adverse Reactions; Energy Drinks / analysis; Heart Diseases / chemically induced; Humans; Induced Pluripotent Stem Cells / drug effects; Myocytes, Cardiac / drug effects; Risk Assessment
TL;DR: It was found that some of the energy drinks elicited adverse effects on the cardiomyocytes with the most common being an increase in the beat rate, while QT prolongation was also observed at the lowest concentrations. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 4, 2021

2021 journal article

Spatial Distribution of Polycyclic Aromatic Hydrocarbon Contaminants after Hurricane Harvey in a Houston Neighborhood.

Journal of Health & Pollution.

Erin Baker

TL;DR: Findings from this study highlight the need for fine scale soil testing in residential areas as well as the importance of site-specific risk assessment in response to a major hurricane. (via Semantic Scholar)
Source: ORCID
Added: April 28, 2021

2021 journal article

Utilizing Ion Mobility-Mass Spectrometry to Investigate the Unfolding Pathway of Cu/Zn Superoxide Dismutase

FRONTIERS IN CHEMISTRY, 9.

By: K. Butler n, Y. Takinami, A. Rainczuk, E. Baker n & B. Roberts*

author keywords: ion mobility spectrometry; native mass spectrometry; superoxide dismutase; SOD1; drift tube ion mobility spectrometry; trapped ion mobility spectrometry
TL;DR: The observed CCSvalues were in excellent agreement with computational CCS values predicted from the homo-dimer crystal structure, showcasing the ability to use both IMS-MS platforms to provide valuable structural information for molecular modeling of protein interactions and structural assessments. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: March 15, 2021

2021 article

Utilizing ion mobility spectrometry-mass spectrometry for the characterization and detection of persistent organic pollutants and their metabolites

Aly, N. A., Dodds, J. N., Luo, Y.-S., Grimm, F. A., Foster, M. K., Rusyn, I., & Baker, E. S. (2021, October 20). ANALYTICAL AND BIOANALYTICAL CHEMISTRY, Vol. 10.

By: N. Aly*, J. Dodds n, Y. Luo*, F. Grimm*, M. Foster n, I. Rusyn*, E. Baker n

author keywords: Ion Mobility Spectrometry; Pesticides; Pharmaceuticals; PFAS
MeSH headings : Environmental Monitoring / methods; Humans; Ion Mobility Spectrometry / methods; Mass Spectrometry / methods; Persistent Organic Pollutants / chemistry; Persistent Organic Pollutants / metabolism; Pesticides / analysis; Pesticides / metabolism; Pharmaceutical Preparations / analysis; Pharmaceutical Preparations / metabolism; Polychlorinated Biphenyls / analysis; Polychlorinated Biphenyls / metabolism
TL;DR: This study characterized 64 compounds including parent per- and polyfluoroalkyl substances, pesticides, polychlorinated biphenyls, industrial chemicals, and pharmaceuticals and personal care products, in addition to their metabolites and/or degradants, using ion mobility spectrometry coupled with MS (IMS-MS) as a potential rapid screening technique. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: November 1, 2021

2021 article

Utilizing liquid chromatography, ion mobility spectrometry, and mass spectrometry to assess INLIGHT (TM) derivatized N-linked glycans in biological samples

Butler, K. E., Kalmar, J. G., Muddiman, D. C., & Baker, E. S. (2021, August 4). ANALYTICAL AND BIOANALYTICAL CHEMISTRY, Vol. 8.

By: K. Butler n, J. Kalmar n, D. Muddiman n & E. Baker n

author keywords: Glycomics; Ion mobility spectrometry; INLIGHT (TM); N-Linked glycans; LC-IMS-MS
TL;DR: The combination of IMS and the natural (NAT) and stable-isotope label (SIL) in the INLIGHT™ strategy provided additional confidence for each glycan identification due to the mobility aligned NAT- and SIL-labeled glycans and further capabilities for isomer examinations. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 16, 2021

2020 journal article

Coupling IR-MALDESI with Drift Tube Ion Mobility-Mass Spectrometry for High-Throughput Screening and Imaging Applications

Journal of the American Society for Mass Spectrometry, 31(3), 642–650.

By: M. Ekelof n, J. Dodds n, S. Khodjaniyazova n, K. Garrard n, E. Baker n & D. Muddiman n

author keywords: mass spectrometry imaging; ion mobility spectrometry; IR-MALDESI; high-throughput; isomer resolution
TL;DR: To increase a range of detectable features in IR-MALDESI experiments, the home-built ion source was integrated with a commercially available drift tube ion mobility spec-trometer-mass spectrometer (IMS-MS) and analyzed small polar molecules, lipids, carbohydrates as well as intact proteins. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: ORCID, Web Of Science, NC State University Libraries, Crossref
Added: March 23, 2020

2020 journal article

Enhanced protocol for quantitativeN-linked glycomics analysis using Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT)(TM)

ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 412(27), 7569–7579.

By: J. Kalmar n, K. Butler n, E. Baker n & D. Muddiman n

author keywords: Glycomics; Orbitrap; Sample preparation; INLIGHT (TM); N-linked glycans; HILIC; PGC; Reversed-phase; Chromatography
MeSH headings : Chromatography, Reverse-Phase / methods; Female; Fetuins / chemistry; Glycomics / methods; Glycosylation; Humans; Male; Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase / chemistry; Polysaccharides / analysis; Tandem Mass Spectrometry / methods
TL;DR: To assess the maximum sensitivity and separability of the INLIGHT™ preparation and analysis pipeline, several critical steps were investigated and the identification of low-abundance glycans, such as (Fuc)1(Gal)2(GlcNAc)4(Man)3(NeuAc)3, was possible. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: September 14, 2020

2020 journal article

Metabolite collision cross section prediction without energy-minimized structures

The Analyst, 145(16), 5414–5418.

By: M. Soper-Hopper*, J. Vandegrift*, E. Baker n & F. Fernandez*

MeSH headings : Ion Mobility Spectrometry; Mass Spectrometry
TL;DR: It is shown for the first time that accurately predicting CCS values with simple models for the largest library of metabolite cross sections is indeed possible, achieving a root mean square error of 7.0 Å2 (median error of ∼2%) using linear methods accesible to most researchers. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 31, 2020

2020 journal article

Proteomic assessment of serum biomarkers of longevity in older men

AGING CELL, 19(11).

By: E. Orwoll*, J. Wiedrick*, C. Nielson*, J. Jacobs*, E. Baker n, P. Piehowski*, V. Petyuk*, Y. Gao* ...

author keywords: aging; biomarker; inflammation; longevity; men; proteomics
MeSH headings : Aged; Biomarkers / blood; Humans; Longevity; Male; Proteomics / methods
TL;DR: It is suggested that complex pathways, prominently including inflammation, are linked to the likelihood of attaining longevity and may serve to identify novel biomarkers for longevity and to understand the biology underlying lifespan. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: November 2, 2020

2020 journal article

Rapid Characterization of Emerging Per- and Polyfluoroalkyl Substances in Aqueous Film-Forming Foams Using Ion Mobility Spectrometry-Mass Spectrometry

ENVIRONMENTAL SCIENCE & TECHNOLOGY, 54(23), 15024–15034.

MeSH headings : Fluorocarbons / analysis; Ion Mobility Spectrometry; Tandem Mass Spectrometry; Water; Water Pollutants, Chemical / analysis
TL;DR: This work demonstrates that LC-IMS-MS-enabled untargeted analysis of complex formulations, followed by feature identification using data-processing algorithms, can be used for rapid exposure characterization of known and putative PFAS during fire suppression-related contamination events. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: January 19, 2021

2020 journal article

Rapid Characterization of Per- and Polyfluoroalkyl Substances (PFAS) by Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS)

Analytical Chemistry, 92(6), 4427–4435.

MeSH headings : Hydrocarbons, Fluorinated / analysis; Ion Mobility Spectrometry; Mass Spectrometry; Molecular Structure; Polymers / analysis
TL;DR: Results from this study show that the IMS separation provides novel information to support traditional LC-MS PFAS analyses and will greatly benefit the evaluation of unknown pollutants in future environmental studies. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: ORCID, Web Of Science, NC State University Libraries
Added: March 23, 2020

2020 journal article

Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems

ANALYST, 145(22), 7197–7209.

By: M. Odenkirk n, P. Zin n, J. Ash n, D. Reif n, D. Fourches n & E. Baker n

MeSH headings : Cheminformatics; Lipidomics; Lipids; Mass Spectrometry; Phenotype
TL;DR: A Structural-based Connectivity and Omic Phenotype Evaluations (SCOPE) cheminformatics toolbox to aid in these evaluations of lipid species and their respective biological roles is developed. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: November 24, 2020

2020 journal article

Temporal and spatial analysis of per and polyfluoroalkyl substances in surface waters of Houston ship channel following a large-scale industrial fire incident

Environmental Pollution, 265(B), 115009.

By: N. Aly*, Y. Luo*, Y. Liu*, G. Casillas*, T. McDonald*, J. Kaihatu*, M. Jun*, N. Ellis ...

MeSH headings : Drinking Water / analysis; Fires; Fluorocarbons / analysis; Texas; Water Pollutants, Chemical / analysis
TL;DR: A major peak in the level of many PFAS is found in the days and weeks after the ITC incident and a gradual decline over several months with patterns consistent with the tide- and wave-associated water movements. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 31, 2020

2020 journal article

Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools

MOLECULAR OMICS, 16(6).

By: M. Odenkirk n, K. Stratton*, M. Gritsenko*, L. Bramer*, B. Webb-Robertson*, K. Bloodsworth*, K. Weitz*, A. Lipton* ...

MeSH headings : Case-Control Studies; Diabetes, Gestational / genetics; Female; Genomics; Humans; Lipidomics; Metabolic Networks and Pathways; Pre-Eclampsia / genetics; Pregnancy
TL;DR: The multi-omic evaluations performed here provide new insight into the end-stage molecular profiles of each disease, thereby supplying information potentially crucial for earlier diagnosis and treatments. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
5. Gender Equality (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: January 4, 2021

2020 article

Utilizing Drift Tube Ion Mobility Spectrometry for the Evaluation of Metabolites and Xenobiotics

ION MOBILITY-MASS SPECTROMETRY: METHODS AND PROTOCOLS, Vol. 2084, pp. 35–54.

By: M. Odenkirk n & E. Baker n

Contributors: M. Odenkirk n & E. Baker n

author keywords: Ion mobility spectrometry (IMS); Drift tube ion mobility spectrometry (DTIMS); Metabolomics; Exposomics; Collision cross section (CCS)
MeSH headings : Ion Mobility Spectrometry / methods; Metabolome; Metabolomics / methods; Xenobiotics / analysis
TL;DR: A review of relevant parameter considerations for DTIMS application with emphasis on xenobiotics and metabolomics isomer separations is presented. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: December 5, 2019

2019 article

Challenges in Identifying the Dark Molecules of Life

ANNUAL REVIEW OF ANALYTICAL CHEMISTRY, VOL 12, Vol. 12, pp. 177–199.

By: M. Eugenia Monge*, J. Dodds n, E. Baker n, A. Edison* & F. Fernandez*

Contributors: M. Monge*, J. Dodds n, E. Baker n, A. Edison* & F. Fernaacutendez

author keywords: metabolomics; metabolite identification; chromatography; ion mobility; tandem mass spectrometry; nuclear magnetic resonance spectroscopy
MeSH headings : Animals; Chromatography, Liquid / methods; Humans; Ion Mobility Spectrometry / methods; Magnetic Resonance Spectroscopy / methods; Mass Spectrometry / methods; Metabolome; Metabolomics / methods
TL;DR: The state-of-the-art in metabolite identification with specific applications in metabolomics is critically discussed and how technologies such as mass spectrometry, ion mobility, chromatography, and nuclear magnetic resonance currently contribute to this challenging task. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: July 1, 2019

2019 journal article

Evaluating the structural complexity of isomeric bile acids with ion mobility spectrometry

ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 411(19), 4673–4682.

By: X. Zheng*, F. Smith*, N. Aly*, J. Cai*, R. Smith*, A. Patterson*, E. Baker n

Contributors: X. Zheng*, F. Smith*, N. Aly*, J. Cai*, R. Smith*, A. Patterson*, E. Baker n

author keywords: Ion mobility spectrometry; Bile acids; Collisional cross sections
MeSH headings : Bile Acids and Salts / chemistry; Bile Acids and Salts / standards; Copper / chemistry; Humans; Ion Mobility Spectrometry / methods; Isomerism; Molecular Structure; Reference Standards; Zinc / chemistry
TL;DR: In the DTIMS-MS analyses of 12 isomer groups, BAs with smaller m/z values were easily separated in either their deprotonated or sodiated forms (or both). (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: July 29, 2019

2019 journal article

Folding and Assembly of Short α, β, Î-Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures

Journal of the American Chemical Society, 141(36), 14239–14248.

By: Y. Zhang*, Y. Zhong*, A. Connor*, D. Miller*, R. Cao*, J. Shen*, B. Song*, E. Baker* ...

Contributors: Y. Zhang*, Y. Zhong*, A. Connor*, D. Miller*, R. Cao*, J. Shen*, B. Song*, E. Baker* ...

MeSH headings : Crystallography, X-Ray; Hydrogen Bonding; Models, Molecular; Peptides / chemistry; Protein Folding; Protein Structure, Secondary
TL;DR: The folding and assembly of seven short tetrapeptides sharing the same types of α-, β-, and aromatic γ-amino acid residues are reported, demonstrating the unique capability of synthetic foldamers in generating structures with fascinating folding and assembling behavior. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2019 journal article

Ion Mobility Spectrometry: Fundamental Concepts, Instrumentation, Applications, and the Road Ahead

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 30(11), 2185–2195.

By: J. Dodds n & E. Baker n

Contributors: J. Dodds n & E. Baker n

author keywords: Ion mobility spectrometry; IMS; Untargeted metabolomics; Mass spectrometry
TL;DR: This critical insight aims to clarify some common misconceptions for new users in the community pertaining to the fundamental concepts of the various IMS instrumental platforms, while addressing the strengths and shortcomings associated with each. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: November 25, 2019

2019 book

Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses

In Comprehensive Analytical Chemistry (Vol. 83, pp. 123–159).

Contributors: C. Chouinard*, G. Nagy*, R. Smith* & E. Baker*

TL;DR: Ion mobility-mass spectrometry (IMS-MS) has become an advanced proteomics tool not only for bottom-up peptide identification and quantitation but also for the study of native/intact proteins and their role in structural biology and disease progression. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2019 review

Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples

[Review of ]. TRAC-TRENDS IN ANALYTICAL CHEMISTRY, 116, 292–299.

By: K. Burnum-Johnson*, X. Zheng*, J. Dodds n, J. Ash n, D. Fourches n, C. Nicora*, J. Wendler*, T. Metz* ...

Contributors: K. Burnum-Johnson*, X. Zheng*, J. Dodds n, J. Ash n, D. Fourches n, C. Nicora*, J. Wendler*, T. Metz* ...

author keywords: Ion mobility spectrometry; Mass spectrometry; Omics; Proteomics; Lipidomics; Metabolomics; Glycomics; Exposomics
TL;DR: Ion mobility spectrometry has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: July 1, 2019

2019 journal article

Perspectives on Data Analysis in Metabolomics: Points of Agreement and Disagreement from the 2018 ASMS Fall Workshop

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 30(10), 2031–2036.

By: E. Baker n & G. Patti*

Contributors: E. Baker n & G. Patti*

author keywords: Metabolomics; Informatics; ASMS Fall Workshop; Metabolism
MeSH headings : Chromatography, Liquid; Computational Biology / organization & administration; Computational Biology / standards; Humans; Mass Spectrometry; Metabolomics / organization & administration; Metabolomics / standards
TL;DR: Five recurring topics that were covered by multiple presenters are highlighted, including data sharing, artifacts and contaminants, feature degeneracy, database organization, and requirements for metabolite identification, which underscores the diversity of informatic programs currently being used in metabolomics. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: November 11, 2019

2019 journal article

Predicting Ion Mobility Collision Cross-Sections Using a Deep Neural Network: DeepCCS

ANALYTICAL CHEMISTRY, 91(8), 5191–5199.

By: P. Plante*, E. Francovic-Fontaine*, J. May*, J. McLean*, E. Baker n, F. Laviolette*, M. Marchand*, J. Corbeil*

Contributors: P. Plante*, É. Francovic-Fontaine*, J. May*, J. McLean*, E. Baker n, F. Laviolette*, M. Marchand*, J. Corbeil*

MeSH headings : Algorithms; Deep Learning; Ion Mobility Spectrometry; Magnetic Resonance Spectroscopy; Mass Spectrometry; Metabolomics; Neural Networks, Computer
TL;DR: This article successfully developed and trained a prediction model for CCS values requiring only information about a compound's SMILES notation and ion type and was able to outperform all currently available CCS prediction algorithms. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 13, 2019

2018 journal article

A Customizable Flow Injection System for Automated, High Throughput, and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements

Analytical Chemistry, 90(1), 737–744.

By: D. Orton*, M. Tfaily*, R. Moore*, B. Lamarche*, X. Zheng*, T. Fillmore*, R. Chu*, K. Weitz* ...

Contributors: D. Orton*, M. Tfaily*, R. Moore*, B. Lamarche*, X. Zheng*, T. Fillmore*, R. Chu*, K. Weitz* ...

MeSH headings : Escherichia coli / chemistry; Escherichia coli Proteins / chemistry; Flow Injection Analysis / instrumentation; Flow Injection Analysis / methods; Hydrogen-Ion Concentration; Ion Mobility Spectrometry / instrumentation; Ion Mobility Spectrometry / methods; Mass Spectrometry / instrumentation; Mass Spectrometry / methods; Soil / chemistry
TL;DR: An automated, customizable FIA system capable of operating at a range of flow rates to accommodate both low- and high-flow MS ionization sources and showing a highly robust and reproducible platform capable of providing consistent performance over many days without carryover. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2018 journal article

An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies

International Journal of Mass Spectrometry, 427, 91–99.

By: A. Bilbao*, B. Gibbons*, G. Slysz*, K. Crowell*, M. Monroe*, Y. Ibrahim*, R. Smith*, S. Payne*, E. Baker*

Contributors: A. Bilbao*, B. Gibbons*, G. Slysz*, K. Crowell*, M. Monroe*, Y. Ibrahim*, R. Smith*, S. Payne*, E. Baker*

author keywords: Mass spectrometry; Detector saturation; Analog-to-digital converter saturation; Saturation correction; Isotopic envelope; Isotopic ratios; Quantitation
TL;DR: The isotopic envelope for each observed ion above the saturation threshold is compared to its expected theoretical isotopic distribution and the most intense isotopic peak for which saturation does not occur is utilized to re-calculate the precursor m/z and correct the intensity, resulting in both higher mass accuracy and greater dynamic range. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2018 journal article

Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis

Tuberculosis, 112, 52–61.

Contributors: K. Kedia*, J. Wendler*, E. Baker*, K. Burnum-Johnson*, L. Jarsberg*, K. Stratton*, A. Wright*, P. Piehowski* ...

author keywords: Ion mobility spectrometry; Proteomics; Tuberculosis; Antibiotic treatment
MeSH headings : Adolescent; Adult; Antitubercular Agents / therapeutic use; Biomarkers / blood; Blood Proteins / metabolism; Child; Child, Preschool; Chromatography, Liquid; Drug Therapy, Combination; Female; High-Throughput Screening Assays; Host-Pathogen Interactions; Humans; Infant; Infant, Newborn; Ion Mobility Spectrometry; Male; Mass Spectrometry; Middle Aged; North America; Predictive Value of Tests; Prospective Studies; Protein Interaction Maps; Proteomics / methods; South Africa; Spain; Time Factors; Treatment Outcome; Tuberculosis, Pulmonary / blood; Tuberculosis, Pulmonary / diagnosis; Tuberculosis, Pulmonary / drug therapy; Tuberculosis, Pulmonary / microbiology; Uganda; Young Adult
TL;DR: If validated in cohorts with long term follow-up to capture failure and relapse of TB, these protein markers could be developed for monitoring of treatment in clinical trials and in patient care. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: ORCID
Added: December 5, 2019

2018 journal article

Cell type-resolved human lung lipidome reveals cellular cooperation in lung function

Scientific Reports, 8(1).

By: J. Kyle*, G. Clair*, G. Bandyopadhyay*, R. Misra*, E. Zink*, K. Bloodsworth*, A. Shukla*, Y. Du* ...

Contributors: J. Kyle*, G. Clair*, G. Bandyopadhyay*, R. Misra*, E. Zink*, K. Bloodsworth*, A. Shukla*, Y. Du* ...

MeSH headings : Databases, Protein; Female; Humans; Lipid Metabolism / physiology; Lung / cytology; Lung / physiology; Male
TL;DR: Lipidomics analyses showed significant variations in the lipidome across major human lung cell types, with differences most evident at the subclass and intra-subclass level, and lipidomic signatures revealed an overarching posture of high cellular cooperation within the human lung to support critical functions. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2018 journal article

Comparing residential contamination in a Houston environmental justice neighborhood before and after Hurricane Harvey

PLoS ONE, 13(2).

Contributors: J. Horney*, G. Casillas*, E. Baker*, K. Stone*, K. Kirsch*, K. Camargo*, T. Wade*, T. McDonald*

MeSH headings : Cyclonic Storms; Environmental Pollutants / analysis; Gas Chromatography-Mass Spectrometry; Polycyclic Aromatic Hydrocarbons / analysis; Residence Characteristics; Texas
TL;DR: A small longitudinal study to assess domestic exposure to PAHs among residents of Manchester, an environmental justice neighborhood located in the East End of Houston, TX, found evidence of redistribution ofPAHs due to extreme flooding associated with Hurricane Harvey. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2018 journal article

Distinguishing enantiomeric amino acids with chiral cyclodextrin adducts and structures for lossless ion manipulations

Electrophoresis, 39(24), 3148–3155.

author keywords: Chiral separations; Cyclodextrins; Enantiomers; Ion mobility-mass spectrometry; Structures for lossless ion manipulations
MeSH headings : Amino Acids / analysis; Amino Acids / chemistry; Amino Acids / isolation & purification; Cyclodextrins / chemistry; Ions; Mass Spectrometry / methods; Models, Molecular; Stereoisomerism
TL;DR: The SLIM was used to accumulate much larger ion populations than previously feasible for evaluation and therefore allow enantiomeric measurements of higher sensitivity, with gains in resolution from the ultralong path separation capabilities, than previously reported by any other IM–based approach. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2018 journal article

Editorial overview: Omics

Current Opinion in Chemical Biology, 42, A1–A2.

By: P. Barran* & E. Baker*

Contributors: P. Barran* & E. Baker*

MeSH headings : Genomics / methods; Humans; Ion Mobility Spectrometry / methods; Lipid Metabolism; Mass Spectrometry / methods; Metabolomics / methods; Proteomics / methods
Source: ORCID
Added: December 5, 2019

2018 journal article

Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry

Bioanalysis, 10(5), 279–289.

Contributors: J. Kyle*, N. Aly*, X. Zheng*, K. Burnum-Johnson*, R. Smith* & E. Baker*

author keywords: collision cross-section; ion mobility spectrometry; lipid mediators
MeSH headings : Animals; Arachidonic Acid / chemistry; Chromatography, Liquid; Docosahexaenoic Acids / analogs & derivatives; Docosahexaenoic Acids / chemistry; Humans; Influenza A virus / growth & development; Ion Mobility Spectrometry; Isomerism; Linoleic Acid / chemistry; Lung / virology; Mass Spectrometry; Mice; Tissue Extracts / chemistry
TL;DR: Adding IMS separations to conventional LC-MS analyses show great utility for enabling better identification and characterization of LMs in complex biological samples. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2018 journal article

Guest editor's personal foreward

International Journal of Mass Spectrometry, 427, 1–3.

By: E. Baker* & R. Ogorzalek Loo*

Contributors: E. Baker* & R. Ogorzalek Loo*

Source: ORCID
Added: December 5, 2019

2018 journal article

High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men

Aging Cell, 17(2).

By: E. Orwoll*, J. Wiedrick*, J. Jacobs*, E. Baker*, P. Piehowski*, V. Petyuk*, Y. Gao*, T. Shi* ...

Contributors: E. Orwoll*, J. Wiedrick*, J. Jacobs*, E. Baker*, P. Piehowski*, V. Petyuk*, Y. Gao*, T. Shi* ...

author keywords: aging; biomarker; inflammation; men; mortality; proteomics
MeSH headings : Biomarkers / chemistry; Humans; Male; Mortality; Proteomics / methods
TL;DR: The results suggest that complex inflammatory pathways, and proteins in other pathways, are linked to 5‐year mortality risk. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: ORCID
Added: December 5, 2019

2018 journal article

Improved Sensitivity and Separations for Phosphopeptides using Online Liquid Chromotography Coupled with Structures for Lossless Ion Manipulations Ion Mobility-Mass Spectrometry

Analytical Chemistry, 90(18), 10889–10896.

MeSH headings : Amino Acid Sequence; Bacterial Proteins / analysis; Bacterial Proteins / isolation & purification; Chromatography, Reverse-Phase / methods; Humans; Ion Mobility Spectrometry / methods; Isomerism; Mass Spectrometry / methods; Phosphopeptides / analysis; Phosphopeptides / isolation & purification; Shewanella / chemistry
TL;DR: LC-SLIM IM-MS offers great potential for improving the sensitivity, separation, and throughput of phosphoproteomics analyses, with additional gains projected with the future use of longer path SLIM IM separations. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2018 content posted

Lactobacillus acidophilus disrupts collaborative multispecies bile acid metabolism

By: S. Dautel*, N. Khan*, K. Brandvold*, C. Brislawn*, J. Hutchison*, K. Weitz*, H. Heyman*, H. Song* ...

TL;DR: It is discovered that a decrease in ursocholate abundance corresponded with successful weight loss in patients after gastric bypass surgery versus those who did not lose weight after surgery, which highlights a new microbe-to-microbe interaction mediated by bile acids. (via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: December 16, 2019

2018 journal article

Online Ozonolysis Combined with Ion Mobility-Mass Spectrometry Provides a New Platform for Lipid Isomer Analyses

Analytical Chemistry, 90(2), 1292–1300.

MeSH headings : Chromatography, High Pressure Liquid / instrumentation; Equipment Design; Humans; Ion Mobility Spectrometry / instrumentation; Isomerism; Lipids / analysis; Lipids / blood; Ozone / chemistry; Tandem Mass Spectrometry / instrumentation
TL;DR: The combination of OzID with multidimensional separations shows significant promise for facile profiling of unsaturation patterns within complex lipidomes including human plasma. (via Semantic Scholar)
UN Sustainable Development Goal Categories
16. Peace, Justice and Strong Institutions (OpenAlex)
Source: ORCID
Added: December 5, 2019

2018 journal article

Rapid Ion Mobility Separations of Bile Acid Isomers Using Cyclodextrin Adducts and Structures for Lossless Ion Manipulations

Analytical Chemistry, 90(18), 11086–11091.

MeSH headings : Bile Acids and Salts / chemistry; Bile Acids and Salts / isolation & purification; Cyclodextrins / chemistry; Ions / chemistry; Ions / isolation & purification; Isomerism; Mass Spectrometry / economics; Mass Spectrometry / methods; Models, Molecular; Time Factors
TL;DR: Cyclodextrin adducts were utilized in conjunction with novel ion mobility (IM) separation capabilities provided by structures for lossless ion manipulations (SLIM) that resulted in much higher resolution separations and increased signal intensities for the BA isomers studied. (via Semantic Scholar)
UN Sustainable Development Goal Categories
1. No Poverty (OpenAlex)
Source: ORCID
Added: December 5, 2019

2018 journal article

Recent advances in lipid separations and structural elucidation using mass spectrometry combined with ion mobility spectrometry, ion-molecule reactions and fragmentation approaches

Current Opinion in Chemical Biology, 42, 111–118.

By: X. Zheng*, R. Smith* & E. Baker*

Contributors: X. Zheng*, R. Smith* & E. Baker*

MeSH headings : Ion Mobility Spectrometry / methods; Isomerism; Lipids / chemistry; Lipids / classification; Lipids / isolation & purification; Mass Spectrometry / methods; Molecular Structure
TL;DR: To aid in isomer characterization, ion mobility spectrometry separations, ion-molecule reactions and fragmentation techniques have increasingly been added to lipid analysis workflows and their capabilities for improving the identification of lipid species are reviewed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: ORCID
Added: December 5, 2019

2018 journal article

The MPLEx protocol for multi-omic analyses of soil samples

Journal of Visualized Experiments, 2018(135).

Contributors: C. Nicora*, K. Burnum-Johnson*, E. Nakayasu*, C. Casey*, R. White*, T. Chowdhury*, J. Kyle*, Y. Kim* ...

author keywords: Chemistry; Issue 135; MPLEx; Metaproteomics; Lipidomics; Metabolomics; Multi-omics; Mass Spectrometry
MeSH headings : Mass Spectrometry / methods; Metabolomics / methods; Soil / chemistry
TL;DR: A 3-in-1 method for the simultaneous extraction of metabolites, proteins, and lipids from the same soil sample was created by adapting a solvent-based approach, which has proven to be both simple and robust for many sample types, even when utilized for limited quantities of complex soil samples. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: ORCID
Added: December 5, 2019

2018 journal article

Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS

Journal of the American Society for Mass Spectrometry, 29(5), 817–826.

By: A. Garabedian*, P. Benigni*, C. Ramirez*, E. Baker*, T. Liu*, R. Smith*, F. Fernandez-Lima*

Contributors: A. Garabedian*, P. Benigni*, C. Ramirez*, E. Baker*, T. Liu*, R. Smith*, F. Fernandez-Lima*

author keywords: Discovery and targeted monitoring; Trapped ion mobility spectrometry; Mass; Spectrometry; Biomarker detection; Quantitative proteomics
MeSH headings : Amino Acid Sequence; Biomarkers, Tumor / analysis; Breast Neoplasms / chemistry; Breast Neoplasms / pathology; Female; Humans; Ion Mobility Spectrometry / methods; Peptides / analysis; Proteomics / methods; Spectrometry, Mass, Electrospray Ionization / methods; Tandem Mass Spectrometry / methods; Workflow
TL;DR: The TIMS-TOF MS analysis permitted peptide biomarker detection based on accurate mobility, mass measurements, and high sequence coverage for concentrations in the 10–200 nM range, while simultaneously achieving discovery measurements of not initially targeted peptides as markers from the same proteins and, eventually, other proteins. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2018 journal article

Unraveling the isomeric heterogeneity of glycans: Ion mobility separations in structures for lossless ion manipulations

Chemical Communications, 54(83), 11701–11704.

TL;DR: A structures for lossless ion manipulations (SLIM) serpentine ultra-long path with extended routing (SUPER) ion mobility-mass spectrometry platform to achieve much higher resolution of isomeric glycoforms to address the challenges associated with glycan analyses. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2018 journal article

Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions

Journal of the American Society for Mass Spectrometry, 29(11), 2182–2188.

By: B. MacLean*, B. Pratt*, J. Egertson*, M. MacCoss*, R. Smith* & E. Baker*

Contributors: B. MacLean*, B. Pratt*, J. Egertson*, M. MacCoss*, R. Smith* & E. Baker*

author keywords: Ion mobility spectrometry; Skyline; Data independent acquisition; Proteomics
TL;DR: This study showcases Skyline’s ability to work with the multidimensional LC-IMS-CID-MS data and provide biological and environmental insights rapidly and presents an important informatics development. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2018 journal article

Utilizing Ion Mobility Spectrometry and Mass Spectrometry for the Analysis of Polycyclic Aromatic Hydrocarbons, Polychlorinated Biphenyls, Polybrominated Diphenyl Ethers and Their Metabolites

Analytica Chimica Acta, 1037, 265–273.

By: X. Zheng*, K. Dupuis*, N. Aly*, Y. Zhou*, F. Smith*, K. Tang*, R. Smith*, E. Baker*

Contributors: X. Zheng*, K. Dupuis*, N. Aly*, Y. Zhou*, F. Smith*, K. Tang*, R. Smith*, E. Baker*

author keywords: Ion mobility spectrometry; Collision cross section; Xenobiotics; Polycyclic aromatic hydrocarbons; Polychlorinated biphenyls; Polybrominated diphenyl ethers; Electrospray ionization; Atmospheric pressure chemical ionization; Atmospheric pressure photoionization
MeSH headings : Chromatography, Liquid; Halogenated Diphenyl Ethers / analysis; Halogenated Diphenyl Ethers / metabolism; Ion Mobility Spectrometry; Mass Spectrometry; Molecular Structure; Polybrominated Biphenyls / analysis; Polybrominated Biphenyls / metabolism; Polycyclic Aromatic Hydrocarbons / analysis; Polycyclic Aromatic Hydrocarbons / metabolism
TL;DR: The rapid isomeric and molecular separations possible with IMS-MS showed great promise for quickly distinguishing the parent and metabolized PAH, PCB, and PDBE molecules in complex environmental and biological samples. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: December 5, 2019

2017 journal article

A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry

Chemical Science, 8(11), 7724–7736.

By: X. Zheng*, N. Aly*, Y. Zhou*, K. Dupuis*, A. Bilbao*, V. Paurus*, D. Orton*, R. Wilson* ...

Contributors: X. Zheng*, N. Aly*, Y. Zhou*, K. Dupuis*, A. Bilbao*, V. Paurus*, D. Orton*, R. Wilson* ...

TL;DR: The DTIMS collision cross section database for metabolites and xenobiotics shows clear trends in both the number of xenobiotic molecules and the proportions of these molecules in the blood stream are increasing. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2017 journal article

An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements

Analytical Chemistry, 89(17), 9048–9055.

By: S. Stow*, T. Causon*, X. Zheng*, R. Kurulugama*, T. Mairinger*, J. May*, E. Rennie*, E. Baker* ...

Contributors: S. Stow*, T. Causon*, X. Zheng*, R. Kurulugama*, T. Mairinger*, J. May*, E. Rennie*, E. Baker* ...

MeSH headings : Calibration; Ion Mobility Spectrometry / methods; Laboratories / standards; Lipids / chemistry; Mass Spectrometry / methods; Molecular Structure; Nitrogen / chemistry; Proteins / chemistry; Reproducibility of Results
TL;DR: Improvements on the measurement accuracy of experimental parameters influencing IM separations provide standardized drift tube, nitrogen CCS values (DTCCSN2) for over 120 unique ion species with the lowest measurement uncertainty to date. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Source: ORCID
Added: December 5, 2019

2017 journal article

Characterizing the lipid and metabolite changes associated with placental function and pregnancy complications using ion mobility spectrometry-mass spectrometry and mass spectrometry imaging

Placenta, 60, S67–S72.

By: K. Burnum-Johnson*, E. Baker* & T. Metz*

Contributors: K. Burnum-Johnson*, E. Baker* & T. Metz*

author keywords: Deep placentation; Pregnancy complications; Mass spectrometry imaging; Metabolome; Lipidome; Ion mobility spectrometry-mass spectrometry; Nano-DESI
MeSH headings : Animals; Chromatography, High Pressure Liquid; Embryo Implantation; Female; Humans; Ion Mobility Spectrometry; Lipid Metabolism; Metabolomics / methods; Metabolomics / trends; Models, Biological; Placenta / metabolism; Placenta / physiology; Placenta / physiopathology; Placentation; Pregnancy; Pregnancy Complications / metabolism; Pregnancy Complications / physiopathology; Spectrometry, Mass, Electrospray Ionization; Spectrometry, Mass, Secondary Ion
TL;DR: Current analytical techniques for metabolomic and lipidomic characterization of pregnancy complications are described and the potential for new technologies to contribute to a better understanding of the molecular changes that affect the placenta and pregnancy outcomes is discussed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: ORCID
Added: December 5, 2019

2017 journal article

Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies

Rapid Communications in Mass Spectrometry, 31(5), 447–456.

Contributors: J. Kyle*, C. Casey*, K. Stratton*, E. Zink*, Y. Kim*, X. Zheng*, M. Monroe*, K. Weitz* ...

TL;DR: The difference in the number of statistically significant polar metabolites and lipids indicated that the lipids did not degrade to as great of a degree as the polar metabolites in the DBS samples and lipid quantitation was still possible. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2017 journal article

Compression Ratio Ion Mobility Programming (CRIMP) Accumulation and Compression of Billions of Ions for Ion Mobility-Mass Spectrometry Using Traveling Waves in Structures for Lossless Ion Manipulations (SLIM)

Analytical Chemistry, 89(12), 6432–6439.

By: L. Deng*, S. Garimella*, A. Hamid*, I. Webb*, I. Attah*, R. Norheim*, S. Prost*, X. Zheng* ...

Contributors: L. Deng*, S. Garimella*, A. Hamid*, I. Webb*, I. Attah*, R. Norheim*, S. Prost*, X. Zheng* ...

MeSH headings : Ion Mobility Spectrometry / instrumentation; Ions / chemistry; Mass Spectrometry / instrumentation; Peptides / analysis
TL;DR: It is shown that extended ion accumulation in conjunction with CRIMP compression and multiple passes through the serpentine path provides the basis for a highly desirable combination of ultrahigh sensitivity and SLIM SUPER high-resolution IM separations. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2017 chapter

Conventional and Advanced Separations in Mass Spectrometry-Based Metabolomics: Methodologies and Applications

In Encyclopedia of Spectroscopy and Spectrometry (pp. 376–384).

By: H. Heyman*, X. Zhang*, K. Tang*, E. Baker* & T. Metz*

Contributors: H. Heyman*, X. Zhang*, K. Tang*, E. Baker* & T. Metz*

Sources: ORCID, Crossref, NC State University Libraries
Added: December 5, 2019

2017 book

Coupling front-end separations, ion mobility spectrometry, and mass spectrometry for enhanced multidimensional biological and environmental analyses

In Annual Review of Analytical Chemistry (Vol. 10, pp. 71–92).

author keywords: drift tube IMS; gas chromatography; supercritical fluid chromatography; liquid chromatography; solid-phase extraction; capillary electrophoresis; field asymmetric ion mobility spectrometry; microfluidics; structure for lossless ion manipulations
MeSH headings : Bacterial Toxins / analysis; Chromatography, Liquid; Chromatography, Supercritical Fluid; Environmental Monitoring; Gases / chemistry; Ions / chemistry; Mass Spectrometry / instrumentation; Mass Spectrometry / methods; Microfluidics / methods; Pharmaceutical Preparations / analysis
TL;DR: This review highlights three-dimensional separations using IMS-MS in conjunction with a range of front-end techniques, such as gas chromatography, supercritical fluidchromatography, liquid Chromatography, solid-phase extractions, capillary electrophoresis, field asymmetric ion mobility spectrometry, and microfluidic devices. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2017 journal article

Distinguishing D- and L-aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry

Chemical Communications, 53(56), 7913–7916.

MeSH headings : Amyloid beta-Peptides / chemistry; Aspartic Acid / chemistry; Ion Mobility Spectrometry / methods; Isoaspartic Acid / chemistry; Peptide Fragments / chemistry; Protein Conformation; Stereoisomerism
TL;DR: An ultrahigh resolution ion mobility spectrometry platform coupled with mass Spectrometry (IMS-MS) is utilized to separate amyloid β (Aβ) peptides containing l-aspartic acid, d-as Partic acid; the results illustrate how IMS-MS could be used to better understand age-related diseases or protein folding disorders resulting from amino acid modifications. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: December 5, 2019

2017 journal article

Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses

Analytical and Bioanalytical Chemistry, 409(2), 467–476.

By: X. Zheng*, X. Zhang*, N. Schocker*, R. Renslow*, D. Orton*, J. Khamsi*, R. Ashmus*, I. Almeida* ...

Contributors: X. Zheng*, X. Zhang*, N. Schocker*, R. Renslow*, D. Orton*, J. Khamsi*, R. Ashmus*, I. Almeida* ...

author keywords: Ion mobility spectrometry; Mass spectrometry; Glycans; O-Glycans; Isomers
MeSH headings : Chemistry Techniques, Analytical / methods; Ion Mobility Spectrometry; Ions / chemistry; Isomerism; Mass Spectrometry; Metals / chemistry; Polysaccharides / chemistry; Polysaccharides / isolation & purification
TL;DR: Ims-MS results showed significant differences for the glycan structural isomers when analyzed in positive and negative polarity and complexed with different metal cations, and suggest that specific metal ions or ion polarities could be used to target and baseline separate glycan isomers of interest with IMS-MS. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2017 journal article

Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics

Journal of Bone and Mineral Research, 32(7), 1559–1567.

By: C. Nielson*, J. Wiedrick*, J. Shen*, J. Jacobs*, E. Baker*, A. Baraff*, P. Piehowski*, C. Lee* ...

Contributors: C. Nielson*, J. Wiedrick*, J. Shen*, J. Jacobs*, E. Baker*, A. Baraff*, P. Piehowski*, C. Lee* ...

author keywords: BIOCHEMICAL MARKERS OF BONE TURNOVER; OSTEOPOROSIS; GENERAL POPULATION STUDIES
MeSH headings : Aged; Aged, 80 and over; Biomarkers / blood; Bone Density; Hip; Hip Fractures / blood; Humans; Male; Osteoporosis / blood; Osteoporosis / pathology; Peptides / blood; Proteome / metabolism; Proteomics
TL;DR: Some proteins have been previously associated with fracture risk (eg, CD14 and SHBG), whereas others have roles in cellular senescence and aging and complement activation and innate immunity (CO7, CO9, CFAD). (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2017 journal article

Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go?

Bioanalysis, 9(1), 81–98.

author keywords: collision cross section; exposome; ion mobility spectrometry; mass spectrometry; metabolome
MeSH headings : Animals; Chromatography, Liquid / methods; Computational Biology / methods; High-Throughput Screening Assays / methods; Humans; Mass Spectrometry / methods; Metabolome; Workflow
TL;DR: The state-of-the-art in measuring the exposome is reviewed, the potential use for IMS-MS and the physico-chemical property of collisional cross section in both exposure assessment and molecular identification is discussed. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2017 journal article

Ligand induced structural isomerism in phosphine coordinated gold clusters revealed by ion mobility mass spectrometry

Chemical Communications, 53(53), 7389–7392.

By: M. Ligare*, E. Baker*, J. Laskin* & G. Johnson*

Contributors: M. Ligare*, E. Baker*, J. Laskin* & G. Johnson*

TL;DR: These ligand-dependant structure-property relationships are critical to theoretical modeling of clusters as well as their applications in catalysis and photovoltaics. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2017 journal article

Lipid and Glycolipid Isomer Analyses Using Ultra-High Resolution Ion Mobility Spectrometry Separations

International Journal of Molecular Sciences, 18(1).

author keywords: lipids; glycolipids; isomers; ion mobility spectrometry
MeSH headings : Glycolipids / chemistry; Glycolipids / isolation & purification; Isomerism; Mass Spectrometry / methods
Source: ORCID
Added: December 5, 2019

2017 journal article

New frontiers for mass spectrometry based upon structures for lossless ion manipulations

Analyst, 142(7), 1010–1021.

TL;DR: The evolution of SLIM devices developed over the last three years is reviewed and the basis for previously impractical manipulations, such as very long path length ion mobility separations where ions traverse a serpentine path multiple times are provided. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2017 journal article

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

Bioinformatics (Oxford, England), 33(17), 2715–2722.

By: J. Ma*, C. Casey*, X. Zheng*, Y. Ibrahim*, C. Wilkins*, R. Renslow*, D. Thomas*, S. Payne* ...

Contributors: J. Ma*, C. Casey*, X. Zheng*, Y. Ibrahim*, C. Wilkins*, R. Renslow*, D. Thomas*, S. Payne* ...

MeSH headings : Algorithms; Computational Biology / methods; Mass Spectrometry / methods; Software
TL;DR: To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), the PNNL Ion Mobility Cross Section Extractor (PIXiE) is created. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2017 journal article

Profiling microbial lignocellulose degradation and utilization by emergent omics technologies

Critical Reviews in Biotechnology, 37(5), 626–640.

By: J. Rosnow*, L. Anderson*, R. Nair*, E. Baker* & A. Wright*

Contributors: J. Rosnow*, L. Anderson*, R. Nair*, E. Baker* & A. Wright*

author keywords: Genomics; proteomics; transcriptomics; NMR; fluorescence-activated cell sorting; metabolomics; activity-based probes
MeSH headings : Biofuels; Lignin / metabolism
TL;DR: New technologies are yielding important insights into microbial functions and strategies employed to degrade lignocellulose, providing a mechanistic blueprint in order to advance biofuel production. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: December 5, 2019

2017 journal article

Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations

Analytical Chemistry, 89(8), 4628–4634.

By: L. Deng*, I. Webb*, S. Garimella*, A. Hamid*, X. Zheng*, R. Norheim*, S. Prost*, G. Anderson* ...

Contributors: L. Deng*, I. Webb*, S. Garimella*, A. Hamid*, X. Zheng*, R. Norheim*, S. Prost*, G. Anderson* ...

MeSH headings : Humans; Ion Mobility Spectrometry / methods; Ions / chemistry; Isomerism; Milk, Human / metabolism; Oligosaccharides / chemistry
TL;DR: The new SLIM SUPER high resolution TWIM platform has broad utility in conjunction with MS and is expected to enable a broad range of previously challenging or intractable separations. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2017 journal article

Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry

Journal of Physical Chemistry Letters, 8(7), 1381–1388.

By: X. Zheng*, R. Renslow*, M. Makola*, I. Webb*, L. Deng*, D. Thomas*, N. Govind*, Y. Ibrahim* ...

Contributors: X. Zheng*, R. Renslow*, M. Makola*, I. Webb*, L. Deng*, D. Thomas*, N. Govind*, Y. Ibrahim* ...

TL;DR: This is the first report of successful differentiation of cis/trans diCQA isomers individually, which shows the great promise of IMS coupled with theoretical calculations for determining the structure and activity relationships of different isomers in drug discovery studies. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: ORCID
Added: December 5, 2019

2016 journal article

A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation

Journal of the American Society For Mass Spectrometry, 27(7), 1285–1288.

By: I. Webb*, S. Garimella*, R. Norheim*, E. Baker*, Y. Ibrahim* & R. Smith*

Contributors: I. Webb*, S. Garimella*, R. Norheim*, E. Baker*, Y. Ibrahim* & R. Smith*

author keywords: Collision induced dissociation; Ion mobility spectrometry; rf Confinement; Ion optics; Peptide fragmentation; Manipulation; Conveyor
TL;DR: The SLIM CID module was mounted after an ion mobility (IM) drift tube to enable IM/CID/MS studies, and the efficiency of CID was studied by using the model peptide leucine enkephalin. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2016 journal article

A multi-omic future for microbiome studies

Nature Microbiology, 1(5).

By: J. Jansson* & E. Baker*

Contributors: J. Jansson* & E. Baker*

MeSH headings : Gene Expression Profiling; Humans; Metabolomics; Metagenomics; Microbiota; Proteomics
TL;DR: Integration of multiple ‘omics’ technologies will allow researchers to gain a more complete picture of the constituents and functions of microbial communities and provide far richer information for predictive modelling of community phenotypes. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2016 journal article

Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations

Analytical Chemistry, 88(18), 8949–8956.

By: A. Hamid*, S. Garimella*, Y. Ibrahim*, L. Deng*, X. Zheng*, I. Webb*, G. Anderson*, S. Prost* ...

Contributors: A. Hamid*, S. Garimella*, Y. Ibrahim*, L. Deng*, X. Zheng*, I. Webb*, G. Anderson*, S. Prost* ...

MeSH headings : Algorithms; Amino Acid Sequence; Bradykinin / analysis; Equipment Design; Ions / chemistry; Mass Spectrometry / methods; Peptides / analysis
TL;DR: The combined attributes of flexible design, low voltage requirements and lossless ion transmission through multiple turns for the present TW-SLIM module provides a basis for SLIM devices capable of achieving much greater IM resolution via greatly extended ion path lengths and using compact serpentine designs. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: ORCID
Added: December 5, 2019

2016 journal article

Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform

Analytical Chemistry, 88(24), 12152–12160.

By: Y. Ibrahim*, S. Garimella*, S. Prost*, R. Wojcik*, R. Norheim*, E. Baker*, I. Rusyn*, R. Smith*

Contributors: Y. Ibrahim*, S. Garimella*, S. Prost*, R. Wojcik*, R. Norheim*, E. Baker*, I. Rusyn*, R. Smith*

MeSH headings : Algorithms; Animals; Artifacts; Cattle; Equipment Design; Ion Mobility Spectrometry / instrumentation; Ions / analysis; Mass Spectrometry / instrumentation; Petroleum / analysis; Phosphopyruvate Hydratase / chemistry; Proteomics / instrumentation; Serum Albumin, Bovine / chemistry
TL;DR: The new IMS-Orbitrap MS platform was demonstrated by the analysis of proteomic and petroleum samples, where the integration of IMS and high mass resolution proved essential for accurate assignment of molecular formulas. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2016 journal article

Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations

Analytical Chemistry, 88(20), 10143–10150.

By: L. Deng*, Y. Ibrahim*, S. Garimella*, I. Webb*, A. Hamid*, R. Norheim*, S. Prost*, J. Sandoval*, E. Baker*, R. Smith*

Contributors: L. Deng*, Y. Ibrahim*, S. Garimella*, I. Webb*, A. Hamid*, R. Norheim*, S. Prost*, J. Sandoval*, E. Baker*, R. Smith*

TL;DR: Wide m/z range ion transmission is demonstrated, along with significant increases in the signal-to-noise ratios (S/N) due to the larger ion populations injected and a reduction in the chemical background, which was attributed to more efficient desolvation of solvent related clusters over the extended ion accumulation periods. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2016 journal article

Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry

Chemistryselect, 1(10), 2396–2399.

By: L. Deng*, Y. Ibrahim*, E. Baker*, N. Aly*, A. Hamid*, X. Zhang*, X. Zheng*, S. Garimella* ...

Contributors: L. Deng*, Y. Ibrahim*, E. Baker*, N. Aly*, A. Hamid*, X. Zhang*, X. Zheng*, S. Garimella* ...

author keywords: Structures for Lossless Ion Manipulations (SLIM); Ion Mobility Spectrometry; Mass Spectrometry; Isomers
TL;DR: A new approach using Structures for Lossless Ion Manipulations (SLIM) to enable long serpentine path ion mobility spectrometry (IMS) separations followed by MS analyses, which provides previously unachieved resolution for biomolecular species, in conjunction with more effective ion utilization. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: ORCID
Added: December 5, 2019

2016 journal article

Mass spectrometry-based monitoring of millisecond protein-ligand binding dynamics using an automated microfluidic platform

Lab on a Chip, 16(9), 1544–1548.

By: Y. Cong*, S. Katipamula*, C. Trader*, D. Orton*, T. Geng*, E. Baker*, R. Kelly*

Contributors: Y. Cong*, S. Katipamula*, C. Trader*, D. Orton*, T. Geng*, E. Baker*, R. Kelly*

MeSH headings : Algorithms; Automation, Laboratory; Carbonic Anhydrase I / antagonists & inhibitors; Carbonic Anhydrase I / chemistry; Carbonic Anhydrase I / metabolism; Carbonic Anhydrase Inhibitors / chemistry; Carbonic Anhydrase Inhibitors / metabolism; Carbonic Anhydrase Inhibitors / pharmacology; Diffusion; Diuretics / chemistry; Diuretics / metabolism; Diuretics / pharmacology; Equipment Design; Furosemide / chemistry; Furosemide / metabolism; Humans; Kinetics; Lab-On-A-Chip Devices; Ligands; Reproducibility of Results; Spectrometry, Mass, Electrospray Ionization
TL;DR: A novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and an integrated electrospray ionization source for mass spectrometry-based monitoring of protein-ligand binding dynamics is presented. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2016 journal article

Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations

Analytical Chemistry, 88(3), 1728–1733.

By: T. Chen*, Y. Ibrahim*, I. Webb*, S. Garimella*, X. Zhang*, A. Hamid*, L. Deng*, W. Karnesky* ...

Contributors: T. Chen*, Y. Ibrahim*, I. Webb*, S. Garimella*, X. Zhang*, A. Hamid*, L. Deng*, W. Karnesky* ...

MeSH headings : Humans; Ions / chemistry; Mass Spectrometry / methods; Peptides / analysis; Protein Conformation
TL;DR: An ion separation and trapping module and a method based upon SLIM that consists of a linear mobility ion drift region, a switch/tee and a trapping region that allows the isolation and accumulation of mobility-separated species are demonstrated. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2016 journal article

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids

Clinical Mass Spectrometry, 2, 1–10.

By: X. Zhang*, M. Romm*, X. Zheng*, E. Zink*, Y. Kim*, K. Burnum-Johnson*, D. Orton*, A. Apffel* ...

Contributors: X. Zhang*, M. Romm*, X. Zheng*, E. Zink*, Y. Kim*, K. Burnum-Johnson*, D. Orton*, A. Apffel* ...

author keywords: Ion mobility spectrometry; Mass spectrometry; Metabolomics; Exposomics
TL;DR: This SPE-IMS-MS platform overcomes many of the current challenges of large-scale metabolomic and exposomic analyses and offers a viable option for population and patient cohort screening in an effort to gain insights into disease processes and human environmental chemical exposure. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2016 journal article

Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry

Molecular &Amp; Cellular Proteomics, 15(12), 3694–3705.

By: K. Burnum-Johnson*, S. Nie*, C. Casey*, M. Monroe*, D. Orton*, Y. Ibrahim*, M. Gritsenko*, T. Clauss* ...

Contributors: K. Burnum-Johnson*, S. Nie*, C. Casey*, M. Monroe*, D. Orton*, Y. Ibrahim*, M. Gritsenko*, T. Clauss* ...

MeSH headings : Animals; Breast Neoplasms / metabolism; Chromatography, Liquid / methods; Female; Humans; Mass Spectrometry / methods; Mice; Neoplasm Transplantation; Peptides / analysis; Proteome / isolation & purification; Proteomics / methods
TL;DR: A new approach is described that performs both discovery and targeted monitoring (DTM) in a single analysis by combining liquid chromatography, ion mobility spectrometry and mass Spectrometry (LC-IMS-MS). (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2016 journal article

Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry

Journal of the American Society For Mass Spectrometry, 27(6), 1128–1135.

By: S. Garimella*, Y. Ibrahim*, K. Tang*, I. Webb*, E. Baker*, A. Tolmachev*, T. Chen*, G. Anderson*, R. Smith*

Contributors: S. Garimella*, Y. Ibrahim*, K. Tang*, I. Webb*, E. Baker*, A. Tolmachev*, T. Chen*, G. Anderson*, R. Smith*

author keywords: Ion mobility spectrometry; Diffusion; Peak compression; High resolution IMS
MeSH headings : Ion Mobility Spectrometry; Ions; Pressure
TL;DR: A novel concept for ion spatial peak compression is described, and discussed primarily in the context of ion mobility spectrometry (IMS), which can be particularly useful for mitigating diffusion-driven peak broadening over very long path length separations and for achieving higher S/N and IMS resolution over a selected mobility range. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2016 journal article

Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations Using Compression Ratio Ion Mobility Programming

Analytical Chemistry, 88(23), 11877–11885.

By: S. Garimella*, A. Hamid*, L. Deng*, Y. Ibrahim*, I. Webb*, E. Baker*, S. Prost*, R. Norheim*, G. Anderson*, R. Smith*

Contributors: S. Garimella*, A. Hamid*, L. Deng*, Y. Ibrahim*, I. Webb*, E. Baker*, S. Prost*, R. Norheim*, G. Anderson*, R. Smith*

MeSH headings : Electrodes; Ions / chemistry; Ions / isolation & purification; Mass Spectrometry / instrumentation; Mass Spectrometry / methods; Molecular Structure
TL;DR: This work collapses ion distributions in ion mobility (IM) separations into tighter packets providing higher sensitivity measurements in conjunction with mass spectrometry (MS), providing greatly enhanced IM resolution by reducing the detrimental effects of diffusional peak broadening and increasing peak widths. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2016 journal article

Surprising impact of remote groups on the folding-unfolding and dimer-chain equilibria of bifunctional H-bonding unimers

Chemical Communications, 52(19), 3773–3776.

By: R. Liu, S. Cheng*, E. Baker*, R. Smith*, X. Zeng* & B. Gong*

Contributors: R. Liu, S. Cheng*, E. Baker*, R. Smith*, X. Zeng* & B. Gong*

MeSH headings : Amides / chemistry; Dimerization; Hydrogen Bonding; Proton Magnetic Resonance Spectroscopy
TL;DR: Replacing the side chains and end groups ofligoamide 1 with derivatives that show the surprising impact of end groups on the folding and dimer-chain equilibria of the resultant molecules. (via Semantic Scholar)
Source: ORCID
Added: December 5, 2019

2016 journal article

Surprising impact of remote groups on the folding-unfolding and dimer-chain equilibria of bifunctional H-bonding unimers (vol 52, pg 3773, 2016)

Chemical Communications, 52(29), 5205.

By: R. Liu, S. Chen*, E. Baker*, R. Smith*, X. Zeng* & B. Gong*

Contributors: R. Liu, S. Chen*, E. Baker*, R. Smith*, X. Zeng* & B. Gong*

Source: ORCID
Added: December 5, 2019

2016 journal article

The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates

Molecular Ecology, 25(22), 5795–5805.

By: L. Khadempour*, K. Burnum-Johnson*, E. Baker*, C. Nicora*, B. Webb-Robertson*, R. White*,