Mass spectrometry reviews

Cancer is the leading cause of death worldwide characterized by patient heterogeneity and complex tumor microenvironment. While the genomics-based testing has transformed modern medicine, the challenge of diverse clinical outcomes highlights unmet needs for precision oncology. As functional molecules regulating cellular processes, proteins hold great promise as biomarkers and drug targets. Mass spectrometry (MS)-based clinical proteomics has illuminated the molecular features of cancers and facilitated discovery of biomarkers or therapeutic targets, paving the way for innovative strategies that enhance the precision of personalized treatment. In this article, we introduced the tools and current achievements of MS-based proteomics, choice of discovery and targeted MS from discovery to validation phases, profiling sensitivity from bulk samples to single-cell level and tissue to liquid biopsy specimens, current regulatory landscape of MS-based protein laboratory-developed tests (LDTs). The challenges, success and future perspectives in translating research MS assay into clinical applications are also discussed. With well-designed validation studies to demonstrate clinical benefits and meet the regulatory requirements for both analytical and clinical performance, the future of MS-based assays is promising with numerous opportunities to improve cancer diagnosis, treatment, and monitoring.

Mass spectrometry-based proteomics is essential for advancing preventive and personalised medicine. Technological advancements have greatly increased both the number and sensitivity of spectra generated in a single experiment. Traditionally, spectra are identified using database search engines that depend on large and continuously expanding databases. This expansion enlarges the search space, posing challenges for controlling the false discovery rate in peptide identification. While many bioinformatic workflows employ rescoring algorithms as a post-processing step to manage false discoveries, preprocessing spectra offers a promising alternative. One such method, spectral quality assessment, classifies spectra as “high” quality (likely containing a peptide) or “low” quality (predominantly consisting of noise). This review provides a comprehensive perspective on spectral quality assessment, examining existing tools and their underlying principles. We discuss key considerations such as the definition of spectral quality, normalisation, the use of experimental training data, and future research in the field. By highlighting the potential of spectral quality assessment to improve peptide identification and reduce false discoveries, we aim to elaborate on its potential for the proteomics community.

Secondary electrospray ionization (SESI) and extractive electrospray ionization (EESI), as derivative technologies of electrospray ionization (ESI), have empowered the real-time analysis of trace compounds residing in gases and aerosols. Over the past three decades, SESI and EESI have demonstrated remarkable potential in a wide spectrum of applications, spanning disease diagnosis, drug detection, food safety, and environmental surveillance. Concurrently, the strides made in deciphering the ionization mechanisms of SESI and EESI have spurred the creation of diverse ion source configurations that are characterized by enhanced sensitivity and diminished background noise. This comprehensive review encapsulates the ionization mechanisms inherent in SESI and EESI processes, with particular emphasis on the impact of analyte characteristics (such as proton affinity, dipole moment, polarizability, and solubility) and ion source operational parameters (encompassing temperature, humidity, voltage, flow rate and electrospray composition) on ionization efficiency. Additionally, it delves into the progression of SESI and EESI sources, highlights recent breakthroughs, and probes into future trajectories, furnishing novel perspectives for the development of both technologies and the associated instruments.

The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.

Dental caries, a prevalent global infectious condition affecting over 95% of adults, remains elusive in its precise etiology. Addressing the complex dynamics of caries demands a thorough exploration of taxonomic, potential, active, and encoded functions within the oral ecosystem. Metabolomic profiling emerges as a crucial tool, offering immediate insights into microecosystem physiology and linking directly to the phenotype. Identified metabolites, indicative of caries status, play a pivotal role in unraveling the metabolic processes underlying the disease. Despite challenges in metabolite variability, the use of metabolomics, particularly via mass spectrometry and nuclear magnetic resonance spectroscopy, holds promise in caries research. This review comprehensively examines metabolomics in caries prevention, diagnosis, and treatment, highlighting distinct metabolite expression patterns and their associations with disease-related bacterial communities. Pioneering in approach, it integrates singular and combinatory metabolomics methodologies, diverse biofluids, and study designs, critically evaluating prior limitations while offering expert insights for future investigations. By synthesizing existing knowledge, this review significantly advances our comprehension of caries, providing a foundation for improved prevention and treatment strategies.

Benefits of miniaturized chromatography with various detection modes, such as increased sensitivity, chromatographic efficiency, and speed, were recognized nearly 50 years ago. Over the past two decades, this approach has experienced rapid growth, driven by the emergence of mass spectrometry applications serving -omics sciences and the need for analyzing minute volumes of precious samples with ever higher sensitivity. While nanoscale liquid chromatography (flow rates <1 μL/min) has gained widespread recognition in proteomics, the adoption of microscale setups (flow rates ranging from 1 to 100 μL/min) for low molecular weight compound applications, including metabolomics, has been surprisingly slow, despite the inherent advantages of the approach. Highly heterogeneous matrices and chemical structures accompanied by a relative lack of options for both selective sample preparation and user-friendly equipment are usually reported as major hindrances. To facilitate the wider implementation of microscale analyses, we present here a comprehensive tutorial encompassing important theoretical and practical considerations. We provide fundamental principles in micro-chromatography and guide the reader through the main elements of a microflow workflow, from LC pumps to ionization devices. Finally, based on both our literature overview and experience, illustrated by some in-house data, we highlight the critical importance of the ionization source design and its careful optimization to achieve significant sensitivity improvement.

Liquid chromatography paired with tandem mass spectrometry (LC-MS/MS) is the gold standard in measurement of endocannabinoid concentrations in biomatrices. We conducted a systematic review of literature to identify advances in targeted LC-MS/MS methods in the period 2017–2024. We found that LC-MS/MS methods for endocannabinoid quantification are relatively consistent both across time and across biomatrices. Recent advances have primarily been in three areas: (1) sample preparation techniques, specific to the chosen biomatrix; (2) the range of biomatrices tested, recently favoring blood matrices; and (3) the breadth of endocannabinoid and endocannabinoid-like analytes incorporated into assays. This review provides a summary of the recent literature and a guide for researchers looking to establish the best methods for quantifying endocannabinoids in a range of biomatrices.

Our healthcare system provides reactive sick-care, treating patients after symptoms have appeared by prescription of generic and often suboptimal therapy. This strategy brings along high costs and high pressure which is not sustainable. Alternatively, P5 healthcare is proposed focusing on five key elements: prevention, personalization, prediction, participation, psychocognition, however, changes in current clinical care pathways are required, for which antithrombin deficiency is a prime example. Hereditary antithrombin deficiency (ATD) is a genetic disorder, for which screening is instigated after a thrombotic episode. Current diagnostic tests for ATD lack sensitivity and refinement to correctly classify patients, and generic treatments are prescribed. A molecular understanding of ATD through a molecular diagnostic test that analyzes all clinically relevant features of antithrombin is required. Here, clinically relevant molecular characteristics of antithrombin, the diversity of antithrombin (deficiency) in heath and disease, and the strengths and weaknesses of antithrombin tests are reviewed. A mass spectrometry test that molecularly characterizes a patients antithrombin proteoforms harbors the highest potential to improve the clinical pathway for ATD. Application of this MS-based test in a future enhanced clinical pathway will improve patient management and outcome through molecular characterization of antithrombin and enables the promise of P5 healthcare for ATD.

Liquid chromatography-mass spectrometry (LC-MS) has become an indispensable tool for elucidating molecular structures and quantifying diverse compounds within complex mixtures. Despite its versatility, it faces various challenges such as ion suppression, low sensitivity, analyte instability, and matrix effects, which are being overcome by different kinds of offline and online derivatization techniques to improve specificity and reduce potential interferences. In this context, considerable advancements have been made in reviewing and critically evaluating a wide range of developed methods and techniques; however, little attention has been given to post-column derivatization (PCD) in LC-MS. Therefore, this comprehensive review highlights state-of-the-art advancements in LC-MS with a specific focus on various types of chemical and physical PCD, and in-source derivatization. It also examines the latest instrumentation developments, highlights methods and influencing factors, and explores applications in food, proteomics, biology, pharmaceuticals, and environmental analysis from the past four decades. Besides, this review critically examines the role of PCD in LC-MS along with outlining its advantages and disadvantages. Furthermore, special emphasis is also made on prospects and insights for developing more versatile LC-PCD-MS techniques and in-source methodologies, to address ongoing challenges and aim to open new research avenues for analysts.

Gas chromatography-mass spectrometry (GC-MS) with Cold electron ionization (EI) is based on interfacing the GC and MS with a supersonic molecular beam (SMB) along with electron ionization of vibrationally cold sample compounds in the SMB in a contact-free fly-through ion source (hence the name Cold EI). Cold EI improves all the central performance aspects of GC-MS, including: a significantly extended range of compounds that are amenable for analysis, enhanced molecular ions, highly improved sample identification, faster analysis (much faster), uniform response to all analytes, greater selectivity and higher signal to noise ratios and lower limits of detection, particularly for compounds that are difficult to analyze. GC-MS with Cold EI executes the analysis of the full range of standard EI applications and most with major improvements of various metrics. Furthermore, it significantly extends the range of compounds and applications amenable for GC-MS analysis. Accordingly, it is a highly superior replacement ion source. In this review article, we describe Cold EI and its main features, discuss its benefits, and demonstrate several of its unique applications including cannabinoids analysis, synthetic organic compounds analysis, whole blood analysis for medical diagnostics, isomer distribution analysis for improved fuels and oils, and explosives analysis.

Monosaccharides play a central role in metabolic networks and in the biosynthesis of glycomolecules, which perform essential functions across all domains of life. Thus, identifying and quantifying these building blocks is crucial in both research and industry. Routine methods have been established to facilitate the analysis of common monosaccharides. However, despite the presence of common metabolites, most organisms utilize distinct sets of monosaccharides and derivatives. These molecules therefore display a large diversity, potentially numbering in the hundreds or thousands, with many still unknown. This complexity presents significant challenges in the study of glycomolecules, particularly in microbes, including pathogens and those with the potential to serve as novel model organisms. This review discusses mass spectrometric techniques for the isomer-sensitive analysis of monosaccharides, their derivatives, and activated forms. Although mass spectrometry allows for untargeted analysis and sensitive detection in complex matrices, the presence of stereoisomers and extensive modifications necessitates the integration of advanced chromatographic, electrophoretic, ion mobility, or ion spectroscopic methods. Furthermore, stable-isotope incorporation studies are critical in elucidating biosynthetic routes in novel organisms.

An intricate network of protein assemblies and protein-protein interactions (PPIs) underlies nearly every biological process in living systems. The organization of these cellular networks is highly dynamic and intimately tied to the genomic and proteomic landscapes of a cell. Disruptions in normal PPIs can impair cellular functions and contribute to the development of human diseases. In recent years, targeting PPIs has emerged as an attractive strategy for drug discovery. Consequently, the identification and characterization of endogenous PPIs—those occurring naturally under physiological conditions—has become crucial for unraveling the molecular mechanisms driving human pathology and for laying the groundwork for novel diagnostics and therapeutics. Owing to numerous technological advancements, mass spectrometry (MS)-based proteomics has transformed the study of PPIs at the systems-level. This review focuses on proteomics approaches that enable the characterization of physiologically relevant endogenous interactions, spanning complex-centric to structure-centric analyses. Additionally, their applications to define native PPIs in the contexts of cancer and viral infectious diseases is highlighted.

This review encompasses guided ion beam tandem mass spectrometry studies of hydrated metal dication complexes. Metals include the Group 2 alkaline earths (Mg, Ca, Sr, and Ba), late first-row transition metals (Mn, Fe, Co, Ni, Cu, and Zn), along with Cd. In all cases, threshold collision-induced dissociation experiments are used to quantitatively determine the sequential hydration energies for M2+(H2O) x complexes ranging in size from one to 11 water molecules. Periodic trends in these bond dissociation energies are examined and discussed. Values are compared to other experimental results when available. In addition to dissociation by simple water ligand loss, complexes at a select size (which differs from metal to metal) are also observed to undergo charge separation to yield a hydrated metal hydroxide cation and a hydrated proton. This leads to the concept of a critical size, x crit, and the periodic trends in this value are also discussed.

Starting in the 1960s, flow tube apparatuses have played a central role in the study of ion-molecule kinetics, allowing for immense chemical diversity of cationic, anionic, and neutral reactants. Here, we review studies of oxygen allotropes, excluding ground state O2 ( X 3 ∑ g −), and focusing instead on reactions of cations, anions, and metal chemi-ionization reactions with ground state atomic oxygen (O 3P), vibrationally excited molecular oxygen (O2(v)), electronically excited molecular oxygen (O2 ( a 1 Δ g)), and ozone (O3). Historical outlines of work over several decades are given along with a focus on more recent work by our group at the Air Force Research Laboratory.

The evolution and applications of flow tube mass spectrometry in the study of catalysis promoted by atomic metal ions are tracked from the pioneering days in Boulder, Colorado, to the construction and application of the ICP/SIFT/QqQ and ESI/qQ/SIFT/QqQ instruments at York University and the VISTA-SIFT instrument at the Air Force Research Laboratory. The physical separation of various sources of atomic metal ions from the flow tube in the latter instruments facilitates the spatial resolution of redox reactions and allows the separate measurement of the kinetics of both legs of a two-step catalytic cycle, while also allowing a view of the catalytic cycle in progress downstream in the reaction region of the flow tube. We focus on measurements on O-atom transfer and bond activation catalysis as first identified in Boulder and emphasize fundamental aspects such as the thermodynamic window of opportunity for catalysis, catalytic efficiency, and computed energy landscapes for atomic metal cation catalysis. Gas-phase applications include: the catalytic oxidation of CO to CO2, of H2 to H2O, and of C2H4 to CH3CHO all with N2O as the source of oxygen; the catalytic oxidation of CH4 to CH3OH with O3; the catalytic oxidation of C6H6 with O2. We also address the environmentally important catalytic reduction of NO2 and NO to N2 with CO and H2 by catalytic coupling of two-step catalytic cycles in a multistep cycle. Overall, the power of atomic metal cations in catalysis, and the use of flow tube mass spectrometry in revealing this power, is clearly demonstrated.

Selected ion flow tube mass spectrometry (SIFT-MS) is now recognized as the most versatile analytical technique for the identification and quantification of trace gases down to the parts-per-trillion by volume, pptv, range. This statement is supported by the wide reach of its applications, from real-time analysis, obviating sample collection of very humid exhaled breath, to its adoption in industrial scenarios for air quality monitoring. This review touches on the recent extensions to the underpinning ion chemistry kinetics library and the alternative challenge of using nitrogen carrier gas instead of helium. The addition of reagent anions in the Voice200 series of SIFT-MS instruments has enhanced the analytical capability, thus allowing analyses of volatile trace compounds in humid air that cannot be analyzed using reagent cations alone, as clarified by outlining the anion chemistry involved. Case studies are reviewed of breath analysis and bacterial culture volatile organic compound (VOC), emissions, environmental applications such as air, water, and soil analysis, workplace safety such as transport container fumigants, airborne contamination in semiconductor fabrication, food flavor and spoilage, drugs contamination and VOC emissions from packaging to demonstrate the stated qualities and uniqueness of the new generation SIFT-MS instrumentation. Finally, some advancements that can be made to improve the analytical capability and reach of SIFT-MS are mentioned.