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Clinical Biochemistry Aug 2020
Topics: Humans; Mass Spectrometry
PubMed: 32511963
DOI: 10.1016/j.clinbiochem.2020.06.003 -
Mass Spectrometry Reviews May 2021The boost of research output in lipidomics during the last decade is tightly linked to improved instrumentation in mass spectrometry. Associated with this trend is the... (Review)
Review
The boost of research output in lipidomics during the last decade is tightly linked to improved instrumentation in mass spectrometry. Associated with this trend is the shift from low resolution-toward high-resolution lipidomics platforms. This review article summarizes the state of the art in the lipidomics field with a particular focus on the merits of high mass resolution. Following some theoretical considerations on the benefits of high mass resolution in lipidomics, it starts with a historical perspective on lipid analysis by sector instruments and moves further to today's instrumental approaches, including shotgun lipidomics, liquid chromatography-mass spectrometry, matrix-assisted laser desorption ionization-time-of-flight, and imaging lipidomics. Subsequently, several data processing and data analysis software packages are critically evaluated with all their pros and cons. Finally, this article emphasizes the importance and necessity of quality standards as the field evolves from its pioneering phase into a mature and robust omics technology and lists various initiatives for improving the applicability of lipidomics. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.
Topics: Chromatography, Liquid; Humans; Lipidomics; Lipids; Mass Spectrometry; Software; Spectrometry, Mass, Electrospray Ionization; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 32233039
DOI: 10.1002/mas.21627 -
Analytical Chemistry Jan 2018
Review
Topics: Animals; Clinical Chemistry Tests; Humans; Mass Spectrometry; Single-Cell Analysis
PubMed: 29155564
DOI: 10.1021/acs.analchem.7b04733 -
Essays in Biochemistry Mar 2023Hydrogen deuterium exchange mass spectrometry (HDX-MS) is becoming part of the standard repertoire of techniques used by molecular biologists to investigate protein... (Review)
Review
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is becoming part of the standard repertoire of techniques used by molecular biologists to investigate protein structure and dynamics. This is partly due to the increased use of automation in all stages of the technique and its versatility of application-many proteins that present challenges with techniques such as X-ray crystallography and cryoelectron microscopy are amenable to investigation with HDX-MS. The present review is aimed at scientists who are curious about the technique, and how it may aid their research. It describes the fundamental basis of solvent exchange, the basics of a standard HDX-MS experiment, as well as highlighting emerging novel experimental advances, which point to where the field is heading.
Topics: Hydrogen Deuterium Exchange-Mass Spectrometry; Mass Spectrometry; Cryoelectron Microscopy; Deuterium Exchange Measurement; Proteins
PubMed: 36251047
DOI: 10.1042/EBC20220111 -
Methods in Molecular Biology (Clifton,... 2018Metabolomics based on mass spectrometry can provide quantitative and qualitative information of the pool of metabolites (metabolome) present intracellularly or...
Metabolomics based on mass spectrometry can provide quantitative and qualitative information of the pool of metabolites (metabolome) present intracellularly or extracellularly in a given biological system. A typical metabolomics workflow requires several key steps such as quick and robust sample preparations with quenching of metabolism, chemical derivatization if needed, instrumental measurement, data-processing with/without database information and further statistical analysis and interpretation. Here, we introduce general metabolomics workflows for global and targeted analyses using gas chromatography or liquid chromatography coupled with mass spectrometers.
Topics: Chromatography, Liquid; Gas Chromatography-Mass Spectrometry; Mass Spectrometry; Metabolome; Metabolomics
PubMed: 29876813
DOI: 10.1007/978-1-4939-7804-5_10 -
Current Opinion in Chemical Biology Feb 2021Crosslinking mass spectrometry has become a core technology in structural biology and is expanding its reach towards systems biology. Its appeal lies in a rapid... (Review)
Review
Crosslinking mass spectrometry has become a core technology in structural biology and is expanding its reach towards systems biology. Its appeal lies in a rapid workflow, high sensitivity and the ability to provide data on proteins in complex systems, even in whole cells. The technology depends heavily on crosslinking reagents. The anatomy of crosslinkers can be modular, sometimes comprising combinations of functional groups. These groups are defined by concepts including: reaction selectivity to increase information density, enrichability to improve detection, cleavability to enhance the identification process and isotope-labelling for quantification. Here, we argue that both concepts and functional groups need more thorough experimental evaluation, so that we can show exactly how and where they are useful when applied to crosslinkers. Crosslinker design should be driven by data, not only concepts. We focus on two crosslinker concepts with large consequences for the technology, namely reactive group reaction kinetics and enrichment groups.
Topics: Isotope Labeling; Mass Spectrometry
PubMed: 32829152
DOI: 10.1016/j.cbpa.2020.07.008 -
Annual Review of Analytical Chemistry... 2015Developments in forensic mass spectrometry tend to follow, rather than lead, the developments in other disciplines. Examples of techniques having forensic potential born... (Review)
Review
Developments in forensic mass spectrometry tend to follow, rather than lead, the developments in other disciplines. Examples of techniques having forensic potential born independently of forensic applications include ambient ionization, imaging mass spectrometry, isotope ratio mass spectrometry, portable mass spectrometers, and hyphenated chromatography-mass spectrometry instruments, to name a few. Forensic science has the potential to benefit enormously from developments that are funded by other means, if only the infrastructure and personnel existed to adopt, validate, and implement the new technologies into casework. Perhaps one unique area in which forensic science is at the cutting edge is in the area of chemometrics and the determination of likelihood ratios for the evaluation of the weight of evidence. Such statistical techniques have been developed most extensively for ignitable-liquid residue analyses and isotope ratio analysis. This review attempts to capture the trends, motivating forces, and likely impact of developing areas of forensic mass spectrometry, with the caveat that none of this research is likely to have any real impact in the forensic community unless: (a) The instruments developed are turned into robust black boxes with red and green lights for positives and negatives, respectively, or (b) there are PhD graduates in the workforce who can help adopt these sophisticated techniques.
Topics: Forensic Medicine; Humans; Mass Spectrometry
PubMed: 26070716
DOI: 10.1146/annurev-anchem-071114-040335 -
The Analyst Aug 2023The cell is the most basic structural unit and plays a vital role in the function of an organism. Studying the heterogeneity of cells, especially the qualitative and... (Review)
Review
The cell is the most basic structural unit and plays a vital role in the function of an organism. Studying the heterogeneity of cells, especially the qualitative and quantitative analyses of proteins and lipids at the cellular level and even at the subcellular level, is of great significance for the study of some important pathological or physiological processes. Due to the small size of a single cell, low content of analytes and large interference from the biological matrix within the single cell, analytical methods at the single cell level must be highly sensitive and selective. Mass spectrometry is a powerful technology for single-cell analysis, because it has high sensitivity, high selectivity and the ability to monitor multiple chemicals at the same time. In this review, four mass spectrometry-based methods applied to single-cell analysis are introduced and discussed in detail; these are electrospray ionization mass spectrometry (ESI-MS), laser desorption ionization mass spectrometry (LDI-MS), secondary ion mass spectrometry (SIMS) and inductively coupled plasma mass spectrometry (ICP-MS). The recent advances in single-cell analysis with these mass spectrometry-based techniques are summarized. We believe that this review can provide some help and reference for single-cell analysis by mass spectrometry.
Topics: Spectrometry, Mass, Electrospray Ionization; Spectrometry, Mass, Secondary Ion; Proteins; Lasers; Single-Cell Analysis; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 37458146
DOI: 10.1039/d3an00370a -
Methods in Molecular Biology (Clifton,... 2019Metabolites and proteins are potential biomarkers. They can be identified with the help of mass spectrometry (MS). However, measurements obtained by using MS are prone... (Review)
Review
Metabolites and proteins are potential biomarkers. They can be identified with the help of mass spectrometry (MS). However, measurements obtained by using MS are prone to various random and systematic errors. The sensitivity of the technology to the errors poses practical challenges, including concerns about reproducibility of the MS-based assays and the possibility of false findings. Given the sensitivity, the proper design of MS-based experiments becomes of utmost importance. In this chapter, we review the basic experimental-design tools that can be used to prevent occurrence of errors that might cause misleading findings in MS-based experiments. We also present results of an experiment aimed at investigating variability of the intensity measurements produced by a MALDI-TOF mass spectrometer. The knowledge about the potential sources of systematic and random errors is fundamental in order to properly design an MS experiment.
Topics: Analysis of Variance; Mass Spectrometry; Models, Statistical; Proteomics; Research Design; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 30980329
DOI: 10.1007/978-1-4939-9232-4_12 -
Annual Review of Biophysics May 2022Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this... (Review)
Review
Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed.
Topics: Macromolecular Substances; Mass Spectrometry; Proteins
PubMed: 34982572
DOI: 10.1146/annurev-biophys-092721-085421