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Journal of Proteome Research Jun 2024We introduce single cell Proteoform imaging Mass Spectrometry (), which realizes the benefit of direct solvent extraction and MS detection of intact proteins from single...
We introduce single cell Proteoform imaging Mass Spectrometry (), which realizes the benefit of direct solvent extraction and MS detection of intact proteins from single cells dropcast onto glass slides. Sampling and detection of whole proteoforms by individual ion mass spectrometry enable a scalable approach to single cell proteomics. This new platform addresses the throughput bottleneck in single cell proteomics and boosts the cell processing rate by several fold while accessing protein composition with higher coverage.
Topics: Single-Cell Analysis; Proteomics; Humans; Mass Spectrometry; Proteome
PubMed: 38497708
DOI: 10.1021/acs.jproteome.4c00075 -
Analytical Chemistry Apr 2024PubChem serves as a comprehensive repository, housing over 100 million unique chemical structures representing the breadth of our chemical knowledge across numerous...
PubChem serves as a comprehensive repository, housing over 100 million unique chemical structures representing the breadth of our chemical knowledge across numerous fields including metabolism, pharmaceuticals, toxicology, cosmetics, agriculture, and many more. Rapid identification of these small molecules increasingly relies on electrospray ionization (ESI) paired with tandem mass spectrometry (MS/MS), particularly by comparison to genuine standard MS/MS data sets. Despite its widespread application, achieving consistency in MS/MS data across various analytical platforms remains an unaddressed concern. This study evaluated MS/MS data derived from one hundred molecular standards utilizing instruments from five manufacturers, inclusive of quadrupole time-of-flight (QTOF) and quadrupole orbitrap "exactive" (QE) mass spectrometers by Agilent (QTOF), Bruker (QTOF), SCIEX (QTOF), Waters (QTOF), and Thermo QE. We assessed fragment ion variations at multiple collisional energies (0, 10, 20, and 40 eV) using the cosine scoring algorithm for comparisons and the number of fragments observed. A parallel visual analysis of the MS/MS spectra across instruments was conducted, consistent with a standard procedure that is used to circumvent the still prevalent issue of mischaracterizations as shown for dimethyl sphingosine and C20 sphingosine. Our analysis revealed a notable consistency in MS/MS data and identifications, with fragment ions' / values exhibiting the highest concordance between instrument platforms at 20 eV, the other collisional energies (0, 10, and 40 eV) were significantly lower. While moving toward a standardized ESI MS/MS protocol is required for dependable molecular characterization, our results also underscore the continued importance of corroborating MS/MS data against standards to ensure accurate identifications. Our findings suggest that ESI MS/MS manufacturers, akin to the established norms for gas chromatography mass spectrometry instruments, should standardize the collision energy at 20 eV across different instrument platforms.
Topics: Tandem Mass Spectrometry; Sphingosine; Spectrometry, Mass, Electrospray Ionization; Gas Chromatography-Mass Spectrometry; Ions
PubMed: 38529642
DOI: 10.1021/acs.analchem.3c05576 -
International Journal of Molecular... Mar 2024This Special Issue, "Mass Spectrometric Proteomics 2 [...].
This Special Issue, "Mass Spectrometric Proteomics 2 [...].
Topics: Proteomics; Mass Spectrometry
PubMed: 38474207
DOI: 10.3390/ijms25052960 -
Analytical and Bioanalytical Chemistry Nov 2023Single-cell (SC) analysis offers new insights into the study of fundamental biological phenomena and cellular heterogeneity. The superior sensitivity, high throughput,... (Review)
Review
Single-cell (SC) analysis offers new insights into the study of fundamental biological phenomena and cellular heterogeneity. The superior sensitivity, high throughput, and rich chemical information provided by mass spectrometry (MS) allow MS to emerge as a leading technology for molecular profiling of SC omics, including the SC metabolome, lipidome, and proteome. However, issues such as ionization suppression, low concentration, and huge span of dynamic concentrations of SC components lead to poor MS response for certain types of molecules. It is noted that chemical tagging/derivatization has been adopted in SCMS analysis, and this strategy has been proven an effective solution to circumvent these issues in SCMS analysis. Herein, we review the basic principle and general strategies of chemical tagging/derivatization in SCMS analysis, along with recent applications of chemical derivatization to single-cell metabolomics and multiplexed proteomics, as well as SCMS imaging. Furthermore, the challenges and opportunities for the improvement of chemical derivatization strategies in SCMS analysis are discussed.
Topics: Mass Spectrometry; Metabolomics; Metabolome; Proteomics; Lipidomics
PubMed: 37466681
DOI: 10.1007/s00216-023-04850-0 -
Talanta Dec 2023Although there are new approaches in both cancer treatment and diagnosis, overall mortality is a major concern. New technologies have attempted to look at breath... (Review)
Review
Although there are new approaches in both cancer treatment and diagnosis, overall mortality is a major concern. New technologies have attempted to look at breath volatile organic compounds (VOCs) detection to diagnose cancer. Gas Chromatography and Mass Spectrometry (GC - MS) have remained the gold standard of VOC analysis for decades, but it has limitations in differentiating VOCs between cancer subtypes. To increase efficacy and accuracy, new methods to analyze these breath VOCs have been introduced, such as Solid Phase Microextraction/Gas Chromatography-Mass Spectrometry (SPME/GC-MS), Selected Ion Flow Tube - Mass Spectrometry (SIFT-MS), Proton Transfer Reaction - Mass Spectrometry (PRT-MS), Ion Mobility Spectrometry (IMS), and Colorimetric Sensors. This article highlights new technologies that have been studied and applied in the detection and quantification of breath VOCs for possible cancer diagnoses.
Topics: Volatile Organic Compounds; Gas Chromatography-Mass Spectrometry; Mass Spectrometry; Breath Tests; Solid Phase Microextraction; Neoplasms
PubMed: 37327663
DOI: 10.1016/j.talanta.2023.124767 -
Essays in Biochemistry Apr 2024Metabolomics has emerged as an indispensable tool for exploring complex biological questions, providing the ability to investigate a substantial portion of the... (Review)
Review
Metabolomics has emerged as an indispensable tool for exploring complex biological questions, providing the ability to investigate a substantial portion of the metabolome. However, the vast complexity and structural diversity intrinsic to metabolites imposes a great challenge for data analysis and interpretation. Liquid chromatography mass spectrometry (LC-MS) stands out as a versatile technique offering extensive metabolite coverage. In this mini-review, we address some of the hurdles posed by the complex nature of LC-MS data, providing a brief overview of computational tools designed to help tackling these challenges. Our focus centers on two major steps that are essential to most metabolomics investigations: the translation of raw data into quantifiable features, and the extraction of structural insights from mass spectra to facilitate metabolite identification. By exploring current computational solutions, we aim at providing a critical overview of the capabilities and constraints of mass spectrometry-based metabolomics, while introduce some of the most recent trends in data processing and analysis within the field.
Topics: Metabolomics; Mass Spectrometry; Chromatography, Liquid; Humans; Computational Biology; Metabolome; Animals
PubMed: 37999335
DOI: 10.1042/EBC20230019 -
Journal of the American Society For... Jul 2023Phospholipids are major components of most eukaryotic cell membranes. Changes in metabolic states are often accompanied by phospholipid structure variations. The...
Phospholipids are major components of most eukaryotic cell membranes. Changes in metabolic states are often accompanied by phospholipid structure variations. The structural changes of phospholipids are the hallmark of disease states, or specific lipid structures have been associated with distinct organisms. Prime examples are microorganisms that synthesize phospholipids with, for example, different branched chain fatty acids. Assignment and relative quantitation of structural isomers of phospholipids that arise from attachment of different fatty acids to the glycerophospholipid backbone are difficult with routine tandem mass spectrometry or with liquid chromatography without authentic standards. In this work, we report on the observation that all investigated phospholipid classes form doubly charged lipid-metal ion complexes during electrospray ionization (ESI) and show that these complexes can be used to assign lipid classes and fatty acid moieties, distinguish isomers of branched chain fatty acids, and relatively quantify these isomers in positive-ion mode. Use of water free methanol and addition of divalent metal salts (100 mol %) to ESI spray solutions afford highly abundant doubly charged lipid-metal ion complexes (up to 70 times of protonated compounds). Higher-energy collisional dissociation and collision-induced dissociation of doubly charged complexes yield a diverse set of lipid class-dependent fragment ions. In common for all lipid classes is the liberation of fatty acid-metal adducts that yield fragment ions from the fatty acid hydrocarbon chain upon activation. This ability is used to pinpoint sites of branching in saturated fatty acids and is showcased for free fatty acids as well as glycerophospholipids. The analytical utility of doubly charged phospholipid-metal ion complexes is demonstrated by distinguishing fatty acid branching-site isomers in phospholipid mixtures and relatively quantifying the corresponding isomeric compounds.
Topics: Tandem Mass Spectrometry; Spectrometry, Mass, Electrospray Ionization; Coordination Complexes; Phospholipids; Fatty Acids; Glycerophospholipids; Ions
PubMed: 37315187
DOI: 10.1021/jasms.3c00126 -
Journal of Pharmaceutical and... Sep 2023Gas chromatography-mass spectrometry (GC-MS) is the first choice for law enforcement agencies in various countries to analyze new psychoactive substances (NPS) because...
Gas chromatography-mass spectrometry (GC-MS) is the first choice for law enforcement agencies in various countries to analyze new psychoactive substances (NPS) because of its advantages and complete databases. For synthetic cathinone-type NPS (SCat), alkalization and extraction processes before GC-MS analysis are essential. However, the base form of SCat is unstable, causing it to quickly degrade in solution and cause pyrolysis at the GC-MS injection inlet. In this study, we investigated the degradation of ethyl acetate and pyrolysis at the GC-MS injection inlet of 2-fluoromethcathinone (2-FMC), the most unstable SCat. Using gas chromatography-quadruple/time-of-flight mass spectrometry (GC-Q/TOF-MS) combined with the predicted data from theoretical calculations and the analysis of mass spectrometry (MS) fragmentation, the structures of 15 2-FMC degradation and pyrolysis products were identified. Among them, 11 products were produced during degradation, and six products were obtained from pyrolysis (two of which were the same as the degradation products). At the same time, the degradation and pyrolysis pathways of 2-FMC were provided. The balance between keto-enol and enamine-imine tautomerism triggered the primary degradation pathway of 2-FMC. The subsequent degradation started from the tautomer with a hydroxyimine structure, including imine hydrolysis, oxidation, imine-enamine tautomerism, intramolecular ammonolysis of halobenzene, and hydration to generate a series of degradation products. The secondary degradation reaction was the ammonolysis of ethyl acetate to yield N-[1-(2'-fluorophenyl)-1-oxopropan-2-yl]-N-methylacetamide and the byproduct, N-[1-(2'-fluorophenyl)-1-oxopropan-2-yl]-N-methylformamide. In the pyrolysis of 2-FMC, the major reactions were dehydrogenation, intramolecular ammonolysis of halobenzene, and defluoromethane. The achievements of this manuscript not only study 2-FMC degradation and pyrolysis but also lay the foundation for the study of SCat stability and their accurate analysis by GC-MS.
Topics: Pyrolysis; Gas Chromatography-Mass Spectrometry; Mass Spectrometry; Hydrocarbons, Halogenated; Imines
PubMed: 37320973
DOI: 10.1016/j.jpba.2023.115525 -
Analytical Methods : Advancing Methods... Dec 2023The application of ambient mass spectrometry imaging "MSI" is expanding in the areas of fundamental research on drug delivery and multiple phases of the process of... (Review)
Review
The application of ambient mass spectrometry imaging "MSI" is expanding in the areas of fundamental research on drug delivery and multiple phases of the process of identifying and developing drugs. Precise monitoring of a drug's pharmacological workflows, such as intake, distribution, metabolism, and discharge, is made easier by MSI's ability to determine the concentrations of the initiating drug and its metabolites across dosed samples without losing spatial data. Lipids, glycans, and proteins are just a few of the many phenotypes that MSI may be used to concurrently examine. Each of these substances has a particular distribution pattern and biological function throughout the body. MSI offers the perfect analytical tool for examining a drug's pharmacological features, especially and effectiveness, security, probable toxic effects, and putative molecular pathways, because of its high responsiveness in chemical and physical environments. The utilization of MSI in the field of pharmacy has further extended from the traditional tissue examination to the early stages of drug discovery and development, including examining the structure-function connection, high-throughput capabilities examination, and research on individual cells or tumor spheroids. Additionally, an enormous array of endogenous substances that may function as tissue diagnostics can be scanned simultaneously, giving the specimen a highly thorough characterization. Ambient MSI techniques are soft enough to allow for easy examination of the native sample to gather data on exterior chemical compositions. This paper provides a scientific and methodological overview of ambient MSI utilization in research on pharmaceuticals.
Topics: Pharmaceutical Research; Mass Spectrometry; Diagnostic Imaging; Proteins; Pharmaceutical Preparations
PubMed: 38088775
DOI: 10.1039/d3ay01267k -
Methods in Molecular Biology (Clifton,... 2024Liquid chromatography-mass spectrometry (LC-MS)-based peptidomics methods allow for the detection and identification of many peptides in a complex biological mixture in...
Liquid chromatography-mass spectrometry (LC-MS)-based peptidomics methods allow for the detection and identification of many peptides in a complex biological mixture in an untargeted manner. Quantitative peptidomics approaches allow for comparisons of peptide abundance between different samples, allowing one to draw conclusions about peptide differences as a function of experimental treatment or physiology. While stable isotope labeling is a powerful approach for quantitative proteomics and peptidomics, advances in mass spectrometry instrumentation and analysis tools have allowed label-free methods to gain popularity in recent years. In a general label-free quantitative peptidomics experiment, peak intensity information for each peptide is compared across multiple LC-MS runs. Here, we outline a general approach for label-free quantitative peptidomics experiments, including steps for sample preparation, LC-MS data acquisition, data processing, and statistical analysis. Special attention is paid to address run-to-run variability, which can lead to several major problems in label-free experiments. Overall, our method provides researchers with a framework for the development of their own quantitative peptidomics workflows applicable to quantitation of peptides from a wide variety of different biological sources.
Topics: Peptides; Mass Spectrometry; Liquid Chromatography-Mass Spectrometry
PubMed: 38549012
DOI: 10.1007/978-1-0716-3646-6_7