bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2021–10–17
twenty-one papers selected by
Giovanny Rodríguez Blanco, University of Edinburgh
  1. A DMS Shotgun Lipidomics Workflow Application to Facilitate High-Throughput, Comprehensive Lipidomics.
  2. The Role of Non-essential Amino Acids in T Cell Function and Anti-tumour Immunity.
  3. Capillary Electrophoresis-Mass Spectrometry for Metabolomics: Possibilities and Perspectives.
  4. Yeast-based reference materials for quantitative metabolomics.
  5. Alternating in-source fragmentation with single-stage high-resolution mass spectrometry with high annotation confidence in non-targeted metabolomics.
  6. Liquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-based Cell-free Systems.
  7. A Method to Monitor the NAD+ Metabolome-From Mechanistic to Clinical Applications.
  8. Plasma lipidomic profiles of kidney, breast and prostate cancer patients differ from healthy controls.
  9. mTOR-dependent immunometabolism as Achilles' heel of anticancer therapy.
  10. Liquid Chromatography-Mass Spectrometry for Clinical Metabolomics: An Overview.
  11. Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling.
  12. Proteomics with Enhanced In-Source Fragmentation/Annotation: Applying XCMS-EISA Informatics and Q-MRM High-Sensitivity Quantification.
  13. Simultaneous quantification of 26 NAD-related metabolites in plasma, blood, and liver tissue using UHPLC-MS/MS.
  14. SLC1A5 provides glutamine and asparagine necessary for bone development in mice.
  15. High-confidence structural annotation of metabolites absent from spectral libraries.
  16. Enriching extracellular vesicles for mass spectrometry.
  17. Practical Considerations in Method Development for Gas Chromatography-Based Metabolomic Profiling.
  18. Biological Applications for LC-MS-Based Proteomics.
  19. Analytical Platforms for Mass Spectrometry-Based Metabolomics of Polar and Ionizable Metabolites.
  20. An Integrated Strategy for Mass Spectrometry-Based Multiomics Analysis of Single Cells.
  21. Metabolomics in Clinical Practice: Improving Diagnosis and Informing Management.
  1. J Am Soc Mass Spectrom. 2021 Oct 12.
    A DMS Shotgun Lipidomics Workflow Application to Facilitate High-Throughput, Comprehensive Lipidomics.
    Baolong Su, Lisa F Bettcher, Wei-Yuan Hsieh, Daniel Hornburg, Mackenzie J Pearson, Niek Blomberg, Martin Giera, Michael P Snyder, Daniel Raftery, Steven J Bensinger, Kevin J Williams.
      Differential mobility spectrometry (DMS) is highly useful for shotgun lipidomic analysis because it overcomes difficulties in measuring isobaric species within a complex lipid sample and allows for acyl tail characterization of phospholipid species. Despite these advantages, the resulting workflow presents technical challenges, including the need to tune the DMS before every batch to update compensative voltages settings within the method. The Sciex Lipidyzer platform uses a Sciex 5500 QTRAP with a DMS (SelexION), an LC system configured for direction infusion experiments, an extensive set of standards designed for quantitative lipidomics, and a software package (Lipidyzer Workflow Manager) that facilitates the workflow and rapidly analyzes the data. Although the Lipidyzer platform remains very useful for DMS-based shotgun lipidomics, the software is no longer updated for current versions of Analyst and Windows. Furthermore, the software is fixed to a single workflow and cannot take advantage of new lipidomics standards or analyze additional lipid species. To address this multitude of issues, we developed Shotgun Lipidomics Assistant (SLA), a Python-based application that facilitates DMS-based lipidomics workflows. SLA provides the user with flexibility in adding and subtracting lipid and standard MRMs. It can report quantitative lipidomics results from raw data in minutes, comparable to the Lipidyzer software. We show that SLA facilitates an expanded lipidomics analysis that measures over 1450 lipid species across 17 (sub)classes. Lastly, we demonstrate that the SLA performs isotope correction, a feature that was absent from the original software.
    Keywords:  DMS; flow injection; lipids; lipidyzer; shotgun lipidomics
    DOI:  https://doi.org/10.1021/jasms.1c00203
  2. Arch Immunol Ther Exp (Warsz). 2021 Oct 12. 69(1): 29
    The Role of Non-essential Amino Acids in T Cell Function and Anti-tumour Immunity.
    Helen Carrasco Hope, Robert J Salmond.
      T cell activation, differentiation and proliferation is dependent upon and intrinsically linked to a capacity to modulate and adapt cellular metabolism. Antigen-induced activation stimulates a transcriptional programme that results in metabolic reprogramming, enabling T cells to fuel anabolic metabolic pathways and provide the nutrients to sustain proliferation and effector responses. Amino acids are key nutrients for T cells and have essential roles as building blocks for protein synthesis as well as in numerous metabolic pathways. In this review, we discuss the roles for uptake and biosynthesis of non-essential amino acids in T cell metabolism, activation and effector function. Furthermore, we highlight the effects of amino acid metabolism and depletion by cancer cells on T cell anti-tumour function and discuss approaches to modulate and improve T cell metabolism for improved anti-tumour function in these nutrient-depleted microenvironments.
    Keywords:  Immunotherapy; Metabolism; Non-essential amino acid; T cell; Tumour microenvironment
    DOI:  https://doi.org/10.1007/s00005-021-00633-6
  3. Adv Exp Med Biol. 2021 ;1336 159-178
    Capillary Electrophoresis-Mass Spectrometry for Metabolomics: Possibilities and Perspectives.
    Nicolas Drouin, Rawi Ramautar.
      Capillary electrophoresis-mass spectrometry (CE-MS) is a very useful analytical technique for the selective and highly efficient profiling of polar and charged metabolites in a wide range of biological samples. Compared to other analytical techniques, the use of CE-MS in metabolomics is relatively low as the approach is still regarded as technically challenging and not reproducible. In this chapter, the possibilities of CE-MS for metabolomics are highlighted with special emphasis on the use of recently developed interfacing designs. The utility of CE-MS for targeted and untargeted metabolomics studies is demonstrated by discussing representative and recent examples in the biomedical and clinical fields. The potential of CE-MS for large-scale and quantitative metabolomics studies is also addressed. Finally, some general conclusions and perspectives are given on this strong analytical separation technique for probing the polar metabolome.
    Keywords:  Applications; Capillary electrophoresis; Interfacing designs; Mass spectrometry; Metabolomics
    DOI:  https://doi.org/10.1007/978-3-030-77252-9_9
  4. Anal Bioanal Chem. 2021 Oct 13.
    Yeast-based reference materials for quantitative metabolomics.
    Hendri Wasito, Gerrit Hermann, Veronika Fitz, Christina Troyer, Stephan Hann, Gunda Koellensperger.
      We introduce a new concept of yeast-derived biological matrix reference material for metabolomics research relying on in vivo synthesis of a defined biomass, standardized extraction followed by absolute quantification with isotope dilution. The yeast Pichia pastoris was grown using full control- and online monitoring fed-batch fermentations followed by fast cold methanol quenching and boiling ethanol extraction. Dried extracts served for the quantification campaign. A metabolite panel of the evolutionarily conserved primary metabolome (amino acids, nucleotides, organic acids, and metabolites of the central carbon metabolism) was absolutely quantified by isotope dilution utilizing uniformly labeled 13C-yeast-based internal standards. The study involved two independent laboratories employing complementary mass spectrometry platforms, namely hydrophilic interaction liquid chromatography-high resolution mass spectrometry (HILIC-HRMS) and gas chromatography-tandem mass spectrometry (GC-MS/MS). Homogeneity, stability tests (on a panel of >70 metabolites over a period of 6 months), and excellent biological repeatability of independent fermentations over a period of 2 years showed the feasibility of producing biological reference materials on demand. The obtained control ranges proved to be fit for purpose as they were either superior or comparable to the established reference materials in the field.
    Keywords:  Absolute quantification; Harmonization; Metabolomics; Pichia pastoris; Reference material; Targeted analysis
    DOI:  https://doi.org/10.1007/s00216-021-03694-w
  5. Talanta. 2022 Jan 01. pii: S0039-9140(21)00749-9. [Epub ahead of print]236 122828
    Alternating in-source fragmentation with single-stage high-resolution mass spectrometry with high annotation confidence in non-targeted metabolomics.
    Hendri Wasito, Tim Causon, Stephan Hann.
      Non-targeted metabolomics is increasingly applied in various applications for understanding biological processes and finding novel biomarkers in living organisms. However, high-confidence identity confirmation of metabolites in complex biological samples is still a significant bottleneck, especially when using single-stage mass analysers. In the current study, a complete workflow for alternating in-source fragmentation on a time-of-flight mass spectrometry (TOFMS) instrument for non-targeted metabolomics is presented. Hydrophilic interaction liquid chromatography (HILIC) was employed to assess polar metabolites in yeast following ESI parameter optimization using experimental design principles, which revealed the key influence of fragmentor voltage for this application. Datasets from alternating in-source fragmentation high resolution mass spectrometry (HRMS) were evaluated using open-source data processing tools combined with public reference mass spectral databases. The significant influence of the selected fragmentor voltages on the abundance of the primary analyte ion of interest and the extent of in-source fragmentation allowed an optimum selection of qualifier fragments for the different metabolites. The new acquisition and evaluation workflow was implemented for the non-targeted analysis of yeast extract samples whereby more than 130 metabolites were putatively annotated with more than 40% considered to be of high confidence. The presented workflow contains a fully elaborated acquisition and evaluation methodology using alternating in-source fragmentor voltages suitable for peak annotation and metabolite identity confirmation for non-targeted metabolomics applications performed on a single-stage HRMS platform.
    Keywords:  All-ions fragmentation; Deconvolution; Design of experiments; Metabolomics; Yeast
    DOI:  https://doi.org/10.1016/j.talanta.2021.122828
  6. J Vis Exp. 2021 Sep 23.
    Liquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-based Cell-free Systems.
    Jaime Lorenzo N Dinglasan, David T Reeves, Robert L Hettich, Mitchel J Doktycz.
      Engineering cellular metabolism for targeted biosynthesis can require extensive design-build-test-learn (DBTL) cycles as the engineer works around the cell's survival requirements. Alternatively, carrying out DBTL cycles in cell-free environments can accelerate this process and alleviate concerns with host compatibility. A promising approach to cell-free metabolic engineering (CFME) leverages metabolically active crude cell extracts as platforms for biomanufacturing and for rapidly discovering and prototyping modified proteins and pathways. Realizing these capabilities and optimizing CFME performance requires methods to characterize the metabolome of lysate-based cell-free platforms. That is, analytical tools are necessary for monitoring improvements in targeted metabolite conversions and in elucidating alterations to metabolite flux when manipulating lysate metabolism. Here, metabolite analyses using high-performance liquid chromatography (HPLC) coupled with either optical or mass spectrometric detection were applied to characterize metabolite production and flux in E. coli S30 lysates. Specifically, this report describes the preparation of samples from CFME lysates for HPLC analyses using refractive index detection (RID) to quantify the generation of central metabolic intermediates and by-products in the conversion of low-cost substrates (i.e., glucose) to various high-value products. The analysis of metabolite conversion in CFME reactions fed with 13C-labeled glucose through reversed-phase liquid chromatography coupled to tandem mass spectrometry (MS/MS), a powerful tool for characterizing specific metabolite yields and lysate metabolic flux from starting materials, is also presented. Altogether, applying these analytical methods to CFME lysate metabolism enables the advancement of these systems as alternative platforms for executing faster or novel metabolic engineering tasks.
    DOI:  https://doi.org/10.3791/62852
  7. Int J Mol Sci. 2021 Sep 30. pii: 10598. [Epub ahead of print]22(19):
    A Method to Monitor the NAD+ Metabolome-From Mechanistic to Clinical Applications.
    Maria Pilar Giner, Stefan Christen, Simona Bartova, Mikhail V Makarov, Marie E Migaud, Carles Canto, Sofia Moco.
      Nicotinamide adenine dinucleotide (NAD+) and its reduced form (NADH) are coenzymes employed in hundreds of metabolic reactions. NAD+ also serves as a substrate for enzymes such as sirtuins, poly(ADP-ribose) polymerases (PARPs) and ADP-ribosyl cyclases. Given the pivotal role of NAD(H) in health and disease, studying NAD+ metabolism has become essential to monitor genetic- and/or drug-induced perturbations related to metabolic status and diseases (such as ageing, cancer or obesity), and its possible therapies. Here, we present a strategy based on liquid chromatography-tandem mass spectrometry (LC-MS/MS), for the analysis of the NAD+ metabolome in biological samples. In this method, hydrophilic interaction chromatography (HILIC) was used to separate a total of 18 metabolites belonging to pathways leading to NAD+ biosynthesis, including precursors, intermediates and catabolites. As redox cofactors are known for their instability, a sample preparation procedure was developed to handle a variety of biological matrices: cell models, rodent tissues and biofluids, as well as human biofluids (urine, plasma, serum, whole blood). For clinical applications, quantitative LC-MS/MS for a subset of metabolites was demonstrated for the analysis of the human whole blood of nine volunteers. Using this developed workflow, our methodology allows studying NAD+ biology from mechanistic to clinical applications.
    Keywords:  NAD+; mass spectrometry; metabolomics
    DOI:  https://doi.org/10.3390/ijms221910598
  8. Sci Rep. 2021 Oct 13. 11(1): 20322
    Plasma lipidomic profiles of kidney, breast and prostate cancer patients differ from healthy controls.
    Denise Wolrab, Robert Jirásko, Ondřej Peterka, Jakub Idkowiak, Michaela Chocholoušková, Zuzana Vaňková, Karel Hořejší, Ivana Brabcová, David Vrána, Hana Študentová, Bohuslav Melichar, Michal Holčapek.
      Early detection of cancer is one of the unmet needs in clinical medicine. Peripheral blood analysis is a preferred method for efficient population screening, because blood collection is well embedded in clinical practice and minimally invasive for patients. Lipids are important biomolecules, and variations in lipid concentrations can reflect pathological disorders. Lipidomic profiling of human plasma by the coupling of ultrahigh-performance supercritical fluid chromatography and mass spectrometry is investigated with the aim to distinguish patients with breast, kidney, and prostate cancers from healthy controls. The mean sensitivity, specificity, and accuracy of the lipid profiling approach were 85%, 95%, and 92% for kidney cancer; 91%, 97%, and 94% for breast cancer; and 87%, 95%, and 92% for prostate cancer. No association of statistical models with tumor stage is observed. The statistically most significant lipid species for the differentiation of cancer types studied are CE 16:0, Cer 42:1, LPC 18:2, PC 36:2, PC 36:3, SM 32:1, and SM 41:1 These seven lipids represent a potential biomarker panel for kidney, breast, and prostate cancer screening, but a further verification step in a prospective study has to be performed to verify clinical utility.
    DOI:  https://doi.org/10.1038/s41598-021-99586-1
  9. Eur J Immunol. 2021 Oct 14.
    mTOR-dependent immunometabolism as Achilles' heel of anticancer therapy.
    Clarissa Braun, Thomas Weichhart.
      Immune cells are important constituents of the tumor microenvironment and essential in eradicating tumor cells during conventional therapies or novel immunotherapies. The mechanistic target of rapamycin (mTOR) signaling pathway senses the intra- and extracellular nutrient status, growth factor supply and cell stress-related changes to coordinate cellular metabolism and activation dictating effector and memory functions in mainly all hematopoietic immune cells. In addition, the mTOR complex 1 (mTORC1) and mTORC2 are frequently deregulated and become activated in cancer cells to drive cell transformation, survival, neovascularization, and invasion. In this review we provide an overview of the influence of mTOR complexes on immune and cancer cell function and metabolism. We discuss how mTOR inhibitors aiming to target cancer cells will influence immunometabolic cell functions participating either in anti-tumor responses or favoring tumor cell progression in individual immune cells. We suggest immunometabolism as the weak spot of anticancer therapy and propose to evaluate patients according to their predominant immune cell subtype in the cancer tissue. Advances in metabolic drug development that hold promise for more effective treatments in different types of cancer will have to consider their effects on the immune system. This article is protected by copyright. All rights reserved.
    Keywords:  Immunometabolism; cancer treatment; immunotherapy; mTORC1; tumor microenvironment
    DOI:  https://doi.org/10.1002/eji.202149270
  10. Adv Exp Med Biol. 2021 ;1336 179-213
    Liquid Chromatography-Mass Spectrometry for Clinical Metabolomics: An Overview.
    Izadora L Furlani, Estéfane da Cruz Nunes, Gisele A B Canuto, Adriana N Macedo, Regina V Oliveira.
      Metabolomics is a discipline that offers a comprehensive analysis of metabolites in biological samples. In the last decades, the notable evolution in liquid chromatography and mass spectrometry technologies has driven an exponential progress in LC-MS-based metabolomics. Targeted and untargeted metabolomics strategies are important tools in health and medical science, especially in the study of disease-related biomarkers, drug discovery and development, toxicology, diet, physical exercise, and precision medicine. Clinical and biological problems can now be understood in terms of metabolic phenotyping. This overview highlights the current approaches to LC-MS-based metabolomics analysis and its applications in the clinical research.
    Keywords:  Biomarkers; Clinical research; LC-MS; Mass analyzers; Metabolomics; Sample preparation
    DOI:  https://doi.org/10.1007/978-3-030-77252-9_10
  11. J Biol Chem. 2021 Oct 08. pii: S0021-9258(21)01099-1. [Epub ahead of print] 101294
    Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling.
    Paulo A Gameiro, Vesela Encheva, Mariana Silva Dos Santos, James I MacRae, Jernej Ule.
      Tandem mass spectrometry (MS/MS) is an accurate tool to assess modified ribonucleosides and their dynamics in mammalian cells. However, MS/MS quantification of lowly abundant modifications in non-ribosomal RNAs is unreliable, and the dynamic features of various modifications poorly understood. Here, we developed a 13C labeling approach, called 13C-dynamods, to quantify the turnover of base modifications in newly transcribed RNA. This turnover-based approach helped to resolve mRNA from ncRNA modifications in purified RNA or free ribonucleoside samples, and showed the distinct kinetics of the N6-methyladenosine (m6A) versus 7-methylguanosine (m7G) modification in polyA+-purified RNA. We uncovered that N6,N6-dimethyladenosine (m62A) exhibits distinct turnover in small RNAs and free ribonucleosides when compared to known m62A-modified large rRNAs. Finally, combined measurements of turnover and abundance of these modifications informed on the transcriptional versus posttranscriptional sensitivity of modified ncRNAs and mRNAs, respectively, to stress conditions. Thus, 13C-dynamods enables studies of the origin of modified RNAs at steady-state and subsequent dynamics under non-stationary conditions. These results open new directions to probe the presence and biological regulation of modifications in particular RNAs.
    Keywords:  7-methylguanosine; Isotopic labeling; N6,N6-dimethyladenosine; N6-methyladenosine; RNA modifications; RNA turnover; mass spectrometry; metabolic stress; metabolism; methylation dynamics
    DOI:  https://doi.org/10.1016/j.jbc.2021.101294
  12. J Am Soc Mass Spectrom. 2021 Oct 11.
    Proteomics with Enhanced In-Source Fragmentation/Annotation: Applying XCMS-EISA Informatics and Q-MRM High-Sensitivity Quantification.
    Jingchuan Xue, Rico J E Derks, Linh Hoang, Martin Giera, Gary Siuzdak.
      Enhanced in-source fragmentation/annotation (EISA) has recently been shown to produce fragment ions that match tandem mass spectrometry data across a wide range of small molecules. EISA has been developed to facilitate data-dependent acquisition (DDA), data-independent acquisiton (DIA), and multiple-reaction monitoring (MRM), enabling molecular identifications in untargeted metabolomics and targeted quantitative single-quadrupole MRM (Q-MRM) analyses. Here, EISA has been applied to peptide-based proteomic analysis using optimized in-source fragmentation to generate fragmentation patterns for a mixture of 38 peptides, which were comparable to the b- and y-type fragment ions typically observed in tandem MS experiments. The optimal in-source fragmentation conditions at which high-abundance peptide fragments and precursor ions coexist were compared with automated data-dependent acquisition (DDA) in the same quadrupole time-of-flight (QTOF-MS) mass spectrometer, generating a significantly higher fragment percentage of peptides from both singly and doubly charged b- and y-type fragment (b+, y+, b2+, and y2+) ions. Higher fragment percentages were also observed for these fragment ion series over linear ion trap instrumentation. An XCMS-EISA annotation/deconvolution program was developed, making use of the retention time and peak shape continuity between precursor fragment ions, to perform automated proteomic data analysis on the enhanced in-source fragments. Post-translational modification (PTM) characterization on peptides was demonstrated with EISA, producing fragment ions corresponding to a neutral loss of phosphoric acid with greater intensity than observed with DDA on a QTOF-MS. Moreover, Q-MRM demonstrated the ability to use EISA for peptide quantification. The availability of more sophisticated in-source fragmentation informatics, beyond XCMS-EISA, will further enable EISA for sensitive autonomous identification and Q-MRM quantitative analyses in proteomics.
    DOI:  https://doi.org/10.1021/jasms.1c00188
  13. Anal Biochem. 2021 Oct 11. pii: S0003-2697(21)00310-9. [Epub ahead of print] 114409
    Simultaneous quantification of 26 NAD-related metabolites in plasma, blood, and liver tissue using UHPLC-MS/MS.
    Hartmut Cuny, Esther Kristianto, Mark P Hodson, Sally L Dunwoodie.
      Nicotinamide adenine dinucleotide (NAD) is a key metabolic intermediate found in all cells and involved in numerous cellular functions. Perturbances in the NAD metabolome are linked to various diseases such as diabetes and schizophrenia, and to congenital malformations and recurrent miscarriage. Mouse models are central to the investigation of these and other NAD-related conditions because mice can be readily genetically modified and treated with diets with altered concentrations of NAD precursors. Simultaneous quantification of as many metabolites of the NAD metabolome as possible is required to understand which pathways are affected in these disease conditions and what are the functional consequences. Here, we report the development of a fit-for-purpose method to simultaneously quantify 26 NAD-related metabolites and creatinine in mouse plasma, whole blood, and liver tissue using ultra-high performance liquid chromatography - tandem mass spectrometry (UHPLC-MS/MS). The included metabolites represent dietary precursors, intermediates, enzymatic cofactors, and excretion products. Sample preparation was optimized for each matrix and included 21 isotope-labeled internal standards. The method reached adequate precision and accuracy for the intended context of use of exploratory pathway-related biomarker discovery in mouse models. The method was tested by determining metabolite levels in mice fed a special diet with defined precursor content.
    Keywords:  LC-MS/MS; Liver; Method development; NAD metabolism; Plasma; Vitamin B3
    DOI:  https://doi.org/10.1016/j.ab.2021.114409
  14. Elife. 2021 Oct 14. pii: e71595. [Epub ahead of print]10
    SLC1A5 provides glutamine and asparagine necessary for bone development in mice.
    Deepika Sharma, Yilin Yu, Leyao Shen, Guo-Fang Zhang, Courtney M Karner.
      Osteoblast differentiation is sequentially characterized by high rates of proliferation followed by increased protein and matrix synthesis, processes that require substantial amino acid acquisition and production. How osteoblasts obtain or maintain intracellular amino acid production is poorly understood. Here we identify SLC1A5 as a critical amino acid transporter during bone development. Using a genetic and metabolomic approach, we show SLC1A5 acts cell autonomously to regulate protein synthesis and osteoblast differentiation. SLC1A5 provides both glutamine and asparagine which are essential for osteoblast differentiation. Mechanistically, glutamine and to a lesser extent asparagine support amino acid biosynthesis. Thus, osteoblasts depend on Slc1a5 to provide glutamine and asparagine, which are subsequently used to produce non-essential amino acids and support osteoblast differentiation and bone development.
    Keywords:  cell biology; developmental biology; mouse
    DOI:  https://doi.org/10.7554/eLife.71595
  15. Nat Biotechnol. 2021 Oct 14.
    High-confidence structural annotation of metabolites absent from spectral libraries.
    Martin A Hoffmann, Louis-Félix Nothias, Marcus Ludwig, Markus Fleischauer, Emily C Gentry, Michael Witting, Pieter C Dorrestein, Kai Dührkop, Sebastian Böcker.
      Untargeted metabolomics experiments rely on spectral libraries for structure annotation, but, typically, only a small fraction of spectra can be matched. Previous in silico methods search in structure databases but cannot distinguish between correct and incorrect annotations. Here we introduce the COSMIC workflow that combines in silico structure database generation and annotation with a confidence score consisting of kernel density P value estimation and a support vector machine with enforced directionality of features. On diverse datasets, COSMIC annotates a substantial number of hits at low false discovery rates and outperforms spectral library search. To demonstrate that COSMIC can annotate structures never reported before, we annotated 12 natural bile acids. The annotation of nine structures was confirmed by manual evaluation and two structures using synthetic standards. In human samples, we annotated and manually validated 315 molecular structures currently absent from the Human Metabolome Database. Application of COSMIC to data from 17,400 metabolomics experiments led to 1,715 high-confidence structural annotations that were absent from spectral libraries.
    DOI:  https://doi.org/10.1038/s41587-021-01045-9
  16. Mass Spectrom Rev. 2021 Oct 11.
    Enriching extracellular vesicles for mass spectrometry.
    Jordan B Burton, Nicholas J Carruthers, Paul M Stemmer.
      Extracellular vesicles from plasma, other body fluids and cell culture media hold great promise in the search for biomarkers. Exosomes in particular, the vesicle type that is secreted after being produced in the endocytic pathway and having a diameter of 30-150 nm, are considered to be a conveyance for signaling molecules and, therefore, to hold valuable information regarding the health and activity status of the cells from which they are released. The vesicular nature of exosomes is central to all methods used to separate them from the highly abundant proteins in plasma and other fluids. The enrichment of the vesicles is essential for mass spectrometry-based analysis as they represent only a very small component of all plasma proteins. The progression of isolation techniques for exosomes from ultracentrifugation through chromatographic separation using hydrophobic packing materials shows that effective enrichment is possible and that high throughput approaches to exosome enrichment are achievable.
    Keywords:  biomarker; exosome; liquid biopsy; proteome; vesicle
    DOI:  https://doi.org/10.1002/mas.21738
  17. Adv Exp Med Biol. 2021 ;1336 139-157
    Practical Considerations in Method Development for Gas Chromatography-Based Metabolomic Profiling.
    Andre Cunha Paiva, Amilton Moreira de Oliveira, Juliana Crucello, Roselaine Facanali, Leandro Wang Hantao.
      This chapter discusses the fundamentals of gas chromatography (GC) to improve method development for metabolic profiling of complex biological samples. The selection of column geometry and phase ratio impacts analyte mass transfer, which must be carefully optimized for fast analysis. Stationary phase selection is critical to obtain baseline resolution of critical pairs, but such selection must consider important aspects of metabolomic protocols, such as derivatization and dependence of analyte identification on existing databases. Sample preparation methods are also addressed depending on the sample matrix, including liquid-liquid extraction and solid-phase microextraction.
    Keywords:  Comprehensive two-dimensional gas chromatography; Liquid-liquid extraction; Mass spectrometry; Metabolic profiling; Metabolomics; Sample preparation; Untargeted analysis
    DOI:  https://doi.org/10.1007/978-3-030-77252-9_8
  18. Adv Exp Med Biol. 2021 ;1336 17-29
    Biological Applications for LC-MS-Based Proteomics.
    Bradley J Smith, Daniel Martins-de-Souza.
      Since its inception, liquid chromatography-mass spectrometry (LC-MS) has been continuously improved upon in many aspects, including instrument capabilities, sensitivity, and resolution. Moreover, the costs to purchase and operate mass spectrometers and liquid chromatography systems have decreased, thus increasing affordability and availability in sectors outside of academic and industrial research. Processing power has also grown immensely, cutting the time required to analyze samples, allowing more data to be feasibly processed, and allowing for standardized processing pipelines. As a result, proteomics via LC-MS has become popular in many areas of biological sciences, forging an important seat for itself in targeted and untargeted assays, pure and applied science, the laboratory, and the clinic. In this chapter, many of these applications of LC-MS-based proteomics and an outline of how they can be executed will be covered. Since the field of personalized medicine has matured alongside proteomics, it has also come to rely on various mass spectrometry methods and will be elaborated upon as well. As time goes on and mass spectrometry evolves, there is no doubt that its presence in these areas, and others, will only continue to grow.
    Keywords:  LC-MS-based proteomics; Liquid chromatography-mass spectrometry; Personalized medicine; Proteome; Proteomics
    DOI:  https://doi.org/10.1007/978-3-030-77252-9_2
  19. Adv Exp Med Biol. 2021 ;1336 215-242
    Analytical Platforms for Mass Spectrometry-Based Metabolomics of Polar and Ionizable Metabolites.
    Adriana N Macedo, Andrea T Faccio, Tatiana S Fukuji, Gisele A B Canuto, Marina F M Tavares.
      Metabolomics studies rely on the availability of suitable analytical platforms to determine a vast collection of chemically diverse metabolites in complex biospecimens. Liquid chromatography-mass spectrometry operated under reversed-phase conditions is the most commonly used platform in metabolomics, which offers extensive coverage for nonpolar and moderately polar compounds. However, complementary techniques are required to obtain adequate separation of polar and ionic metabolites, which are involved in several fundamental metabolic pathways. This chapter focuses on the main mass-spectrometry-based analytical platforms used to determine polar and/or ionizable compounds in metabolomics (GC-MS, HILIC-MS, CE-MS, IPC-MS, and IC-MS). Rather than comprehensively describing recent applications related to GC-MS, HILIC-MS, and CE-MS, which have been covered in a regular basis in the literature, a brief discussion focused on basic principles, main strengths, limitations, as well as future trends is presented in this chapter, and only key applications with the purpose of illustrating important analytical aspects of each platform are highlighted. On the other hand, due to the relative novelty of IPC-MS and IC-MS in the metabolomics field, a thorough compilation of applications for these two techniques is presented here.
    Keywords:  Analytical platforms; CE-MS; GC-MS; HILIC; Ion chromatography; Ion pairing chromatography; Ionic compounds; Ionizable compounds; Metabolomics; Polar compounds
    DOI:  https://doi.org/10.1007/978-3-030-77252-9_11
  20. Anal Chem. 2021 Oct 13.
    An Integrated Strategy for Mass Spectrometry-Based Multiomics Analysis of Single Cells.
    Yuanyuan Li, Hang Li, Yuping Xie, Shuo Chen, Ritian Qin, Hangyan Dong, Yongliang Yu, Jianhua Wang, Xiaohong Qian, Weijie Qin.
      Single-cell-based genomics and transcriptomics analysis have revealed substantial cellular heterogeneity among seemingly identical cells. Knowledge of the cellular heterogeneity at multiomics levels is vital for a better understanding of tumor metastasis and drug resistance, stem cell differentiation, and embryonic development. However, unlike genomics and transcriptomics studies, single-cell characterization of metabolites, proteins, and post-translational modifications at the omics level remains challenging due to the lack of amplification methods and the wide diversity of these biomolecules. Therefore, new tools that are capable of investigating these unamplifiable "omes" from the same single cells are in high demand. In this work, a microwell chip was prepared and the internal surface was modified for hydrophilic interaction liquid chromatography-based tandem extraction of metabolites and proteins and subsequent protein digestion. Next, direct electrospray ionization mass spectrometry was adopted for single-cell metabolome identification, and a data-independent acquisition-mass spectrometry approach was established for simultaneous proteome profiling and phosphoproteome analysis without phosphopeptide enrichment. This integrated strategy resulted in 132 putatively annotated compounds, more than 1200 proteins, and the first large-scale phosphorylation data set from single-cell analysis. Application of this strategy in chemical perturbation studies provides a multiomics view of cellular changes, demonstrating its capability for more comprehensive investigation of cellular heterogeneity.
    DOI:  https://doi.org/10.1021/acs.analchem.0c05209
  21. Clin Chem. 2021 Oct 11. pii: hvab184. [Epub ahead of print]
    Metabolomics in Clinical Practice: Improving Diagnosis and Informing Management.
    John D Odom, V Reid Sutton.
       BACKGROUND: Metabolomics is the study of small molecules to simultaneously identify multiple low molecular weight molecules in a system. Broadly speaking, metabolomics can be subdivided into targeted and untargeted types of analysis, each type having advantages and drawbacks. Targeted metabolomics can quantify analytes but only looks for known or expected analytes related to particular disease(s), whereas untargeted metabolomics is typically nonquantitative but can detect thousands of analytes from an agnostic or nonhypothesis driven perspective, allowing for novel discoveries.
    CONTENT: One application of metabolomics is the study of inborn errors of metabolism (IEM). The biochemical hallmark of IEMs is decreased concentrations of analytes distal to the enzymatic defect and buildup of analytes proximal to the defect. Metabolomics can detect these changes with one test and is effective in screening for and diagnosis of IEMs. Metabolomics has also been used to study many nonmetabolic diseases such as autism spectrum disorder, various cancers, and multiple congenital anomalies syndromes. Metabolomics has led to the discovery of many novel biomarkers of disease. Recent publications demonstrate how metabolomics can be useful clinically in the diagnosis and management of patients, as well as for research and clinical discovery.
    SUMMARY: Metabolomics has proved to be a useful tool clinically for screening and diagnostic purposes and from a research perspective for the detection of novel biomarkers. In the future, metabolomics will likely become a routine part of the evaluation for many diseases as either a supplementary test or it may simply replace historical analyses that require several individual tests and sample types.
    Keywords:  inborn error of metabolism; metabolomics
    DOI:  https://doi.org/10.1093/clinchem/hvab184
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