Current Challenges and Recent Developments in Mass Spectrometry–Based Metabolomics

2021 ◽  
Vol 14 (1) ◽  
pp. 467-487
Author(s):  
Stephanie L. Collins ◽  
Imhoi Koo ◽  
Jeffrey M. Peters ◽  
Philip B. Smith ◽  
Andrew D. Patterson
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
High Resolution Mass Spectrometry ◽  
Metabolite Identification ◽  
Feature Reduction ◽  
Compound Identification ◽  
Single Experiment ◽  
Separation Of Isomers ◽  
Mass Detector ◽  
Recent Developments

High-resolution mass spectrometry (MS) has advanced the study of metabolism in living systems by allowing many metabolites to be measured in a single experiment. Although improvements in mass detector sensitivity have facilitated the detection of greater numbers of analytes, compound identification strategies, feature reduction software, and data sharing have not kept up with the influx of MS data. Here, we discuss the ongoing challenges with MS-based metabolomics, including de novo metabolite identification from mass spectra, differentiation of metabolites from environmental contamination, chromatographic separation of isomers, and incomplete MS databases. Because of their popularity and sensitive detection of small molecules, this review focuses on the challenges of liquid chromatography-mass spectrometry–based methods. We then highlight important instrumentational, experimental, and computational tools that have been created to address these challenges and how they have enabled the advancement of metabolomics research.

scholarly journals A Simple and Direct Assay for Monitoring Fatty Acid Synthase Activity and Product-Specificity by High-Resolution Mass Spectrometry

Biomolecules ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 118 ◽  
Author(s):  
Magdalena Topolska ◽  
Fernando Martínez-Montañés ◽  
Christer S. Ejsing
Keyword(s):  
Mass Spectrometry ◽  
Fatty Acid ◽  
High Resolution ◽  
Fatty Acid Synthase ◽  
De Novo ◽  
High Resolution Mass Spectrometry ◽  
Enzymatic Process ◽  
Product Specificity ◽  
High Resolution Mass ◽  
Resolution Mass

De novo fatty acid synthesis is a pivotal enzymatic process in all eukaryotic organisms. It is involved in the conversion of glucose and other nutrients to fatty acyl (FA) chains, that cells use as building blocks for membranes, energy storage, and signaling molecules. Central to this multistep enzymatic process is the cytosolic type I fatty acid synthase complex (FASN) which in mammals produces, according to biochemical textbooks, primarily non-esterified palmitic acid (NEFA 16:0). The activity of FASN is commonly measured using a spectrophotometry-based assay that monitors the consumption of the reactant NADPH. This assay is indirect, can be biased by interfering processes that use NADPH, and cannot report the NEFA chain-length produced by FASN. To circumvent these analytical caveats, we developed a simple mass spectrometry-based assay that affords monitoring of FASN activity and its product-specificity. In this assay (i) purified FASN is incubated with 13C-labeled malonyl-CoA, acetyl-CoA, and NADPH, (ii) at defined time points the reaction mixture is spiked with an internal NEFA standard and extracted, and (iii) the extract is analyzed directly, without vacuum evaporation and chemical derivatization, by direct-infusion high-resolution mass spectrometry in negative ion mode. This assay supports essentially noise-free detection and absolute quantification of de novo synthetized 13C-labled NEFAs. We demonstrate the efficacy of our assay by determining the specific activity of purified cow FASN and show that in addition to the canonical NEFA 16:0 this enzyme also produces NEFA 12:0, 14:0, 18:0, and 20:0. We note that our assay is generic and can be carried out using commonly available high-resolution mass spectrometers with a resolving power as low as 95,000. We deem that our simple assay could be used as high-throughput screening technology for developing potent FASN inhibitors and for enzyme engineering aimed at modulating the activity and the product-landscape of fatty acid synthases.

scholarly journals Automated Pipeline for De Novo Metabolite Identification Using Mass-Spectrometry-Based Metabolomics

2013 ◽  
Vol 85 (7) ◽  
pp. 3576-3583 ◽  
Author(s):  
Julio E. Peironcely ◽  
Miguel Rojas-Chertó ◽  
Albert Tas ◽  
Rob Vreeken ◽  
Theo Reijmers ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
Metabolite Identification ◽  
Automated Pipeline

scholarly journals Lipidomic analysis of bloodstream and procyclic form Trypanosoma brucei

Parasitology ◽  
2010 ◽  
Vol 137 (9) ◽  
pp. 1357-1392 ◽  
Author(s):  
GREGORY S. RICHMOND ◽  
FEDERICA GIBELLINI ◽  
SIMON A. YOUNG ◽  
LOUISE MAJOR ◽  
HELEN DENTON ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Trypanosoma Brucei ◽  
De Novo ◽  
High Resolution Mass Spectrometry ◽  
Negative Ion ◽  
Tandem Mass ◽  
Human Pathogen ◽  
Electrospray Tandem Mass Spectrometry ◽  
Procyclic Form ◽  
Lipidomic Analysis

SUMMARYThe biological membranes of Trypanosoma brucei contain a complex array of phospholipids that are synthesized de novo from precursors obtained either directly from the host, or as catabolised endocytosed lipids. This paper describes the use of nanoflow electrospray tandem mass spectrometry and high resolution mass spectrometry in both positive and negative ion modes, allowing the identification of ~500 individual molecular phospholipids species from total lipid extracts of cultured bloodstream and procyclic form T. brucei. Various molecular species of all of the major subclasses of glycerophospholipids were identified including phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol as well as phosphatidic acid, phosphatidylglycerol and cardolipin, and the sphingolipids sphingomyelin, inositol phosphoceramide and ethanolamine phosphoceramide. The lipidomic data obtained in this study will aid future biochemical phenotyping of either genetically or chemically manipulated commonly used bloodstream and procyclic strains of Trypanosoma brucei. Hopefully this will allow a greater understanding of the bizarre world of lipids in this important human pathogen.

scholarly journals Comparison of a GC-Orbitrap-MS with Parallel GC-FID Capabilities for Metabolomics of Human Serum

2019 ◽  
Author(s):  
Biswapriya B. Misra ◽  
Ekong Bassey ◽  
Michael Olivier
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Human Serum ◽  
Ion Trap ◽  
High Resolution Mass Spectrometry ◽  
Chemical Space ◽  
Metabolite Identification ◽  
Gas Chromatography Mass Spectrometry ◽  
Good Correspondence ◽  
Orbitrap Ms

AbstractGas chromatography mass spectrometry (GC-MS) platforms for use in high throughput and discovery metabolomics have heavily relied on time of flight (ToF), and low resolution quadrupole and ion trap mass spectrometers and are typically run in electron ionization (EI) modes for matching spectral libraries. Traditionally, detectors such as flame ionization detection (FID), have also helped in identification and quantification of compounds in complex samples for diverse clinical applications, i.e., fatty acids. We probed if combination of FID in line with a high-resolution instrument like a GC-Orbitrap-MS may confer advantages over traditional mass spectrometry using EI.We used a commercially available human serum sample to enhance the chemical space of serum using an advanced high resolution mass spectrometry (HR-MS) platform (QExactive Orbitrap-MS) with an FID feature for confident metabolite identification to assess the suitability of the platform for routine clinical metabolomics research. Using the EI mode, we quantified 294 metabolites in human serum using GC-Orbitrap-MS. These metabolites belonged to 89 biological pathways in KEGG. Following a sample split, using an in-line FID analysis, 1117 peaks were quantified. Moreover, representative peaks from FID and their corresponding MS counterparts showed a good correspondence when compared for relative abundance.Our study highlights the benefits of the use of a higher mass accuracy instrument for untargeted GC-MS-based metabolomics not only with EI mode but also orthogonal detection method such as FID, for robust and orthogonal quantification, in future studies addressing complex biological samples in clinical set ups.

scholarly journals Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

2020 ◽  
Author(s):  
Michal Levin ◽  
Marion Scheibe ◽  
Falk Butter
Keyword(s):  
Mass Spectrometry ◽  
Bombyx Mori ◽  
Cell Line ◽  
De Novo ◽  
High Resolution Mass Spectrometry ◽  
Gene Annotation ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
Sequence Information ◽  
A Genome

Abstract BackgroundThe process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-Seq or mass spectrometry. While satisfactory annotation has been made feasible for well-studied model organisms through great efforts of big consortia, for most systems this kind of data is either absent or not adequately precise. ResultsCombining in-depth transcriptome sequencing and high resolution mass spectrometry, we here use proteotranscriptomics to improve gene annotation of protein-coding genes in the Bombyx mori cell line BmN4 which is an increasingly used tool for the analysis of piRNA biogenesis and function. Using this approach we provide the exact coding sequence and evidence for more than 6,200 genes on the protein level. Furthermore using spatial proteomics, we establish the subcellular localization of thousands of these proteins. We show that our approach outperforms current Bombyx mori annotation attempts in terms of accuracy and coverage. ConclusionsWe show that proteotranscriptomics is an efficient, cost-effective and accurate approach to improve previous annotations or generate new gene models. As this technique is based on de-novo transcriptome assembly, it provides the possibility to study any species also in the absence of genome sequence information for which proteogenomics would be impossible.

scholarly journals Measurement artefacts, ion mobility and other observations in environmental mass spectrometry analyses

2020 ◽  
Author(s):  
◽  
Jeremy R Hart
Keyword(s):  
Mass Spectrometry ◽  
Ion Mobility ◽  
High Resolution Mass Spectrometry ◽  
Structural Information ◽  
Animal Health ◽  
Area Measurement ◽  
Chromatographic Retention ◽  
Compound Identification ◽  
Compliance Requirements ◽  
Pressure Chemical

Many laboratories are engaged in the measurement of persistent organic pollutants, particularly polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzo-furans (PCDFs) and polychlorinated biphenyls (PCBs), to satisfy various investigative needs and compliance requirements worldwide. However, from a mass spectrometry perspective, the current mandated methods have changed little since their origins in the 1980s and 1990s and fail to address certain issues that can lead to the erroneous rejection or filtering of data, and conversely, to the acceptance of data that may be considered questionable. Notwithstanding any legislative requirements, since the goal of these analyses is ultimately related to human or animal health, producing accurate and reliable data is of the utmost importance. This research highlights various areas of concern and aims to improve upon the current peak identification and measurement practices that can lead to such false negatives, false positives and other errors. A key contribution made by this thesis concerns the role of ion statistics in peak area measurement and its subsequent effect on isotope ratio determination – a primary parameter (together with chromatographic retention time) for compound identification in both high-resolution mass spectrometry (HRMS) and tandem mass spectrometry (MS/MS) methods. In an allied area of research, a comprehensive study of all mono- to deca-chlorinated biphenyls using atmospheric pressure chemical ionisation, both for fragmentation analysis and in conjunction with ion mobility spectrometry (IMS), was undertaken. An additional original contribution described in this thesis shows that, in addition to certain structural information – especially in relation to the degree of chlorine ortho substitution – there are some unusual shifts in the measured IMS arrival time distributions of certain PCB isotopologues and isotopomers suggesting the occurrence of isomerisation in the gas phase. Other patterns emerging from these data are indicative of the toxicity of certain PCBs, both correlating with known toxic congeners and others that are currently classified as non-toxic.

Developments in mycotoxin analysis: an update for 2019-2020

2021 ◽  
Vol 14 (1) ◽  
pp. 3-26 ◽  
Author(s):  
S.A. Tittlemier ◽  
J. Brunkhorst ◽  
B. Cramer ◽  
M.C. DeRosa ◽  
V.M.T. Lattanzio ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Quality Control ◽  
Quality Assurance ◽  
High Resolution Mass Spectrometry ◽  
Tandem Mass ◽  
Mass Spectrometry Detection ◽  
Recent Developments ◽  
Mycotoxin Analysis ◽  
Instrumental Methods ◽  
Resolution Mass

This review summarises developments on the analysis of various matrices for mycotoxins published in the period from mid-2019 to mid-2020. Notable developments in all aspects of mycotoxin analysis, from sampling and quality assurance/quality control of analytical results, to the various detection and quantitation technologies ranging from single mycotoxin biosensors to comprehensive instrumental methods are presented and discussed. Aside from sampling and quality control, discussion of this past year’s developments is organised by detection and quantitation technology and covers chromatography with targeted or non-targeted high resolution mass spectrometry, tandem mass spectrometry, detection other than mass spectrometry, biosensors, as well as assays that use alternatives to antibodies. This critical review aims to briefly present the most important recent developments and trends in mycotoxin determination as well as to address limitations of the presented methodologies.

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