bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2024‒07‒14
six papers selected by
Giovanny Rodriguez Blanco, University of Edinburgh
  1. Metabolomics 2023 workshop report: moving toward consensus on best QA/QC practices in LC-MS-based untargeted metabolomics.
  2. A Facile LC-MS Method for Profiling Cholesterol and Cholesteryl Esters in Mammalian Cells and Tissues.
  3. Analysis of Sphingosine and Sphinganine from the Aqueous Humor for Signaling Studies Using Ultrahigh-Performance Liquid Chromatography-Mass Spectrometry.
  4. PGFinder, an Open-Source Software for Peptidoglycomics: The Structural Analysis of Bacterial Peptidoglycan by LC-MS.
  5. Detailed Protocol for Solid-Phase Extraction for Lipidomic Analysis.
  6. The Interplay of Lipid Signaling in Musculoskeletal Cross Talk: Implications for Health and Disease.
  1. Metabolomics. 2024 Jul 09. 20(4): 73
    Metabolomics 2023 workshop report: moving toward consensus on best QA/QC practices in LC-MS-based untargeted metabolomics.
    Metabolomics Quality Assurance, Quality Control Consortium (mQACC)
      INTRODUCTION: During the Metabolomics 2023 conference, the Metabolomics Quality Assurance and Quality Control Consortium (mQACC) presented a QA/QC workshop for LC-MS-based untargeted metabolomics.OBJECTIVES: The Best Practices Working Group disseminated recent findings from community forums and discussed aspects to include in a living guidance document.
    METHODS: Presentations focused on reference materials, data quality review, metabolite identification/annotation and quality assurance.
    RESULTS: Live polling results and follow-up discussions offered a broad international perspective on QA/QC practices.
    CONCLUSIONS: Community input gathered from this workshop series is being used to shape the living guidance document, a continually evolving QA/QC best practices resource for metabolomics researchers.
    Keywords:  Data quality; Liquid chromatography–mass spectrometry (LC–MS); Metabolite annotation; Metabolite identification; Metabolomics; Quality assurance; Quality control (QC) samples; Reference materials
    DOI:  https://doi.org/10.1007/s11306-024-02135-w
  2. Biochemistry. 2024 Jul 10.
    A Facile LC-MS Method for Profiling Cholesterol and Cholesteryl Esters in Mammalian Cells and Tissues.
    Aakash Chandramouli, Siddhesh S Kamat.
      Cholesterol is central to mammalian lipid metabolism and serves many critical functions in the regulation of diverse physiological processes. Dysregulation in cholesterol metabolism is causally linked to numerous human diseases, and therefore, in vivo, the concentrations and flux of cholesterol and cholesteryl esters (fatty acid esters of cholesterol) are tightly regulated. While mass spectrometry has been an analytical method of choice for detecting cholesterol and cholesteryl esters in biological samples, the hydrophobicity, chemically inert nature, and poor ionization of these neutral lipids have often proved a challenge in developing lipidomics compatible liquid chromatography-mass spectrometry (LC-MS) methods to study them. To overcome this problem, here, we report a reverse-phase LC-MS method that is compatible with existing high-throughput lipidomics strategies and capable of identifying and quantifying cholesterol and cholesteryl esters from mammalian cells and tissues. Using this sensitive yet robust LC-MS method, we profiled different mammalian cell lines and tissues and provide a comprehensive picture of cholesterol and cholesteryl esters content in them. Specifically, among cholesteryl esters, we find that mammalian cells and tissues largely possess monounsaturated and polyunsaturated variants. Taken together, our lipidomics compatible LC-MS method to study this lipid class opens new avenues in understanding systemic and tissue-level cholesterol metabolism under various physiological conditions.
    DOI:  https://doi.org/10.1021/acs.biochem.4c00160
  3. Methods Mol Biol. 2024 ;2816 35-40
    Analysis of Sphingosine and Sphinganine from the Aqueous Humor for Signaling Studies Using Ultrahigh-Performance Liquid Chromatography-Mass Spectrometry.
    Meher A Saleem, Molly Kennedy, Omar Badla, Emily J Neag, Sanjoy K Bhattacharya.
      Sphingolipids, including sphingosine and sphinganine, are one of the major classes of lipids. They serve as constituents of cell membranes and lipid rafts and aid in the performance of cell-cell communication and adhesion. Abnormal levels of sphingolipids in the aqueous humor can indicate impaired sphingolipid metabolism and associated ocular pathologies. Sphingolipids can be extracted from the aqueous humor by the methyl-tert-butyl ether (MTBE) lipid extraction method and subsequently analyzed by liquid chromatography-mass spectrometry (LC-MS). This chapter describes a modified protocol for an MTBE lipid extraction from the aqueous humor, followed by analysis with ultrahigh-performance liquid chromatography-mass spectrometry (UHPLC-MS).
    Keywords:  Aqueous humor; LC; LC-MS; Lipid extraction; Lipidomics; Liquid chromatography; MS; MTBE; Mass spectrometry; Sphinganine; Sphingolipidomics; Sphingolipids; Sphingosine; UHPLC; UHPLC-MS; Ultrahigh-performance liquid chromatography
    DOI:  https://doi.org/10.1007/978-1-0716-3902-3_4
  4. Methods Mol Biol. 2024 ;2836 111-132
    PGFinder, an Open-Source Software for Peptidoglycomics: The Structural Analysis of Bacterial Peptidoglycan by LC-MS.
    Brooks J Rady, Stéphane Mesnage.
      Peptidoglycan is a major and essential component of the bacterial cell envelope that confers cell shape and provides protection against internal osmotic pressure. This complex macromolecule is made of glycan strands cross-linked by short peptides, and its structure is continually modified throughout growth via a process referred to as "remodeling." Peptidoglycan remodeling allows cells to grow, adapt to their environment, and release fragments that can act as signaling molecules during host-pathogen interactions. Preparing peptidoglycan samples for structural analysis first requires purification of the peptidoglycan sacculus, followed by its enzymatic digestion into disaccharide peptides (muropeptides). These muropeptides can then be characterized by liquid chromatography coupled mass spectrometry (LC-MS) and used to infer the structure of intact peptidoglycan sacculi. Due to the presence of unusual crosslinks, noncanonical amino acids, and amino sugars, the analysis of peptidoglycan LC-MS datasets cannot be handled by traditional proteomics software. In this chapter, we describe a protocol to perform the analysis of peptidoglycan LC-MS datasets using the open-source software PGFinder. We provide a step-by-step strategy to deconvolute data from various mass spectrometry instruments, generate muropeptide databases, perform a PGFinder search, and process the data output.
    Keywords:   Data deconvolution; LC-MS; Peptidoglycan; Software; Mass spectrometry
    DOI:  https://doi.org/10.1007/978-1-0716-4007-4_8
  5. Methods Mol Biol. 2024 ;2816 151-159
    Detailed Protocol for Solid-Phase Extraction for Lipidomic Analysis.
    Marian N Aziz, Leticia Brotto, Ahmed S Yacoub, Kamal Awad, Marco Brotto.
      Developing robust analytical techniques is a vital phase to facilitate understanding the roles and impacts of various omic profilings in cellular functions. The comprehensive analysis of various biological molecules within a biological system requires a precise sample preparation technique. Solid-Phase Extraction (SPE) has proven to be an indispensable method in lipidomic analysis, providing an uncomplicated and user-friendly technique for extraction and purification of lipid components from complex biological matrices. Of all the factors influencing the reliability and success of SPE, column or adsorbent materials, flow rate, and storage conditions are paramount in terms of their significance. In this chapter, we will discuss in detail the SPE steps for lipidomic analysis in biofluid samples (serum and plasma) and muscle tissues.
    Keywords:  SPE for lipidomic; SPE for muscle; SPE for plasma; SPE for serum; Sample preparation
    DOI:  https://doi.org/10.1007/978-1-0716-3902-3_15
  6. Methods Mol Biol. 2024 ;2816 1-11
    The Interplay of Lipid Signaling in Musculoskeletal Cross Talk: Implications for Health and Disease.
    Ahmed Al Saedi, Ahmed S Yacoub, Kamal Awad, David Karasik, Marco Brotto, Gustavo Duque.
      The intricate interplay between the muscle and bone tissues is a fundamental aspect of musculoskeletal physiology. Over the past decades, emerging research has highlighted the pivotal role of lipid signaling in mediating communication between these tissues. This chapter delves into the multifaceted mechanisms through which lipids, particularly phospholipids, sphingolipids, and eicosanoids, participate in orchestrating cellular responses and metabolic pathways in both muscle and bone. Additionally, we examine the clinical implications of disrupted lipid signaling in musculoskeletal disorders, offering insights into potential therapeutic avenues. This chapter aims to shed light on the complex lipid-driven interactions between the muscle and bone tissues, paving the way for a deeper understanding of musculoskeletal health and disease.
    Keywords:  Cross talk; Fat; Lipid signaling; Lipids; Musculoskeletal cross talk
    DOI:  https://doi.org/10.1007/978-1-0716-3902-3_1
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