Multiplex analysis of sphingolipids using amine-reactive tags (iTRAQ)

Unraveling the complexity of glycosphingolipidome: the key role of mass spectrometry in the structural analysis of glycosphingolipids

Glycosphingolipids (GSL) are a highly heterogeneous class of lipids representing the majority of the sphingolipid category. GSL are fundamental constituents of cellular membranes that have key roles in various biological processes, such as cellular signaling, recognition, and adhesion. Understanding the structural complexity of GSL is pivotal for unraveling their functional significance in a biological context, specifically their crucial role in the pathophysiology of various diseases. Mass spectrometry (MS) has emerged as a versatile and indispensable tool for the structural elucidation of GSL enabling a deeper understanding of their complex molecular structures and their key roles in cellular dynamics and patholophysiology. Here, we provide a thorough overview of MS techniques tailored for the analysis of GSL, emphasizing their utility in probing GSL intricate structures to advance our understanding of the functional relevance of GSL in health and disease. The application of tandem MS using diverse fragmentation techniques, including novel ion activation methodologies, in studying glycan sequences, linkage positions, and fatty acid composition is extensively discussed. Finally, we address current challenges, such as the detection of low-abundance species and the interpretation of complex spectra, and offer insights into potential solutions and future directions by improving MS instrumentation for enhanced sensitivity and resolution, developing novel ionization techniques, or integrating MS with other analytical approaches for comprehensive GSL characterization.

Recent Advances in Understanding of Alzheimer's Disease Progression through Mass Spectrometry-Based Metabolomics

Alzheimer's disease (AD) is the leading cause of dementia in the aging population, but despite extensive research, there is no consensus on the biological cause of AD. While AD research is dominated by protein/peptide-centric research based on the amyloid hypothesis, a theory that designates dysfunction in beta-amyloid production, accumulation, or disposal as the primary cause of AD, many studies focus on metabolomics as a means of understanding the biological processes behind AD progression. In this review, we discuss mass spectrometry (MS)-based AD metabolomics studies, including sample type and preparation, mass spectrometry specifications, and data analysis, as well as biological insights gleaned from these studies, with the hope of informing future AD metabolomic studies.

Perspective on Emerging Mass Spectrometry Technologies for Comprehensive Lipid Structural Elucidation

Lipids and metabolites are of interest in many clinical and research settings because it is the metabolome that is increasingly recognized as a more dynamic and sensitive molecular measure of phenotype. The enormous diversity of lipid structures and the importance of biological structure-function relationships in a wide variety of applications makes accurate identification a challenging yet crucial area of research in the lipid community. Indeed, subtle differences in the chemical structures of lipids can have important implications in cellular metabolism and many disease pathologies. The speed, sensitivity, and molecular specificity afforded by modern mass spectrometry has led to its widespread adoption in the field of lipidomics on many different instrument platforms and experimental workflows. However, unambiguous and complete structural identification of lipids by mass spectrometry remains challenging. Increasingly sophisticated tandem mass spectrometry (MS/MS) approaches are now being developed and seamlessly integrated into lipidomics workflows to meet this challenge. These approaches generally either (i) alter the type of ion that is interrogated or (ii) alter the dissociation method in order to improve the structural information obtained from the MS/MS experiment. In this Perspective, we highlight recent advances in both ion type alteration and ion dissociation methods for lipid identification by mass spectrometry. This discussion is aimed to engage investigators involved in fundamental ion chemistry and technology developments as well as practitioners of lipidomics and its many applications. The rapid rate of technology development in recent years has accelerated and strengthened the ties between these two research communities. We identify the common characteristics and practical figures of merit of these emerging approaches and discuss ways these may catalyze future directions of lipid structural elucidation research.

Recent advances in the mass spectrometric analysis of glycosphingolipidome - A review

Aberrant expression of glycosphingolipids has been implicated in a myriad of diseases, but our understanding of the strucural diversity, spatial distribution, and biological function of this class of biomolecules remains limited. These challenges partly stem from a lack of sensitive tools that can detect, identify, and quantify glycosphingolipids at the molecular level. Mass spectrometry has emerged as a powerful tool poised to address most of these challenges. Here, we review the recent developments in analytical glycosphingolipidomics with an emphasis on sample preparation, mass spectrometry and tandem mass spectrometry-based structural characterization, label-free and labeling-based quantification. We also discuss the nomenclature of glycosphingolipids, and emerging technologies like ion mobility spectrometry in differentiation of glycosphingolipid isomers. The intrinsic advantages and shortcomings of each method are carefully critiqued in line with an individual's research goals. Finally, future perspectives on analytical sphingolipidomics are stated, including a need for novel and more sensive methods in isomer separation, low abundance species detection, and profiling the spatial distribution of glycosphingolipid molecular species in cells and tissues using imaging mass spectrometry.

Isobaric mass tagging and triple quadrupole mass spectrometry to determine lipid biomarker candidates for Alzheimer's disease

The isobaric tagging method widely used in proteomic and lipidomic fields, with the multiple reaction monitoring (MRM) approach using a triple quadrupole mass spectrometer, was applied to identify biomarker candidates from plasma samples for Alzheimer’s disease (AD). We focused on the following phospholipids that have amino groups as the functional group: phosphatidylethanolamine (PE), Lyso-PE, phosphatidylserine, and Lyso-phosphatidylserine. We also investigated fatty acids that have a carboxy group. A sixplex tandem mass tag (TMT) was used for the isobaric tagging method in this study. The TMT reaction had high reproducibility in human plasma. A total of 196 human plasma samples from three AD cohorts were used for the study, and compared to pooled plasma quality control (QC) samples. The described method required only 40 MRM measurements, including the pooled QC samples, for a full comparison of the data. We found that the content of free fatty acids increased in AD samples in all the three cohorts, alkenyl PEs (ePEs) decreased over a one-year interval in AD patients, and ePEs weakly correlated with amyloid peptide (a-beta) 1–42 in cerebrospinal fluid. In conclusion, total free fatty acids in plasma are a risk factor for AD, and ePEs monitor candidates for AD. Therefore, TMT-lipidomics is a powerful approach for the determination of plasma biomarkers because of the high sample throughput.

Chemical Derivatization and Ultrahigh Resolution and Accurate Mass Spectrometry Strategies for "Shotgun" Lipidome Analysis

Lipids play critical structural and functional roles in the regulation of cellular homeostasis, and it is increasingly recognized that the disruption of lipid metabolism or signaling or both is associated with the onset and progression of certain metabolically linked diseases. As a result, the field of lipidomics has emerged to comprehensively identify and structurally characterize the diverse range of lipid species within a sample of interest and to quantitatively monitor their abundances under different physiological or pathological conditions. Mass spectrometry (MS) has become a critical enabling platform technology for lipidomic researchers. However, the presence of isobaric (i.e., same nominal mass) and isomeric (i.e., same exact mass) lipids within complex lipid extracts means that MS-based identification and quantification of individual lipid species remains a significant analytical challenge. Ultrahigh resolution and accurate mass spectrometry (UHRAMS) offers a convenient solution to the isobaric mass overlap problem, while a range of chromatographic separation, differential extraction, intrasource separation and selective ionization methods, or tandem mass spectrometry (MS/MS) strategies may be used to address some types of isomeric mass lipid overlaps. Alternatively, chemical derivatization strategies represent a more recent approach for the separation of lipids within complex mixtures, including for isomeric lipids. In this Account, we highlight the key components of a lipidomics workflow developed in our laboratory, whereby certain lipid classes or subclasses, namely, aminophospholipids and O-alk-1'-enyl (i.e., plasmalogen) ether-containing lipids, are shifted in mass following sequential functional group selective chemical derivatization reactions prior to "shotgun" nano-ESI-UHRAMS analysis, "targeted" MS/MS, and automated database searching. This combined derivatization and UHRAMS approach resolves both isobaric mass lipids and certain categories of isomeric mass lipids within crude lipid extracts, with no requirement for extensive sample handling prior to analysis, with additional potential for enhanced ionization efficiencies, improved molecular level structural characterization, and multiplexed relative quantification. When integrated with a monophasic method for the simultaneous global extraction of both highly polar and nonpolar lipids, this workflow has been shown to enable the sum composition level identification and relative quantification of 500-600 individual lipid species across four lipid categories and from 36 lipid classes and subclasses, in only 1-2 min data acquisition time and with minimal sample consumption. Thus, while some analytical challenges remain to be addressed, shotgun lipidomics workflows encompassing chemical derivatization strategies have particular promise for the analysis of samples with limited availability that require rapid and unbiased assessment of global lipid metabolism.