Orbitrap mass spectrometry

Analytical Strategies for Fingerprinting of Antioxidants, Nutritional Substances, and Bioactive Compounds in Foodstuffs Based on High Performance Liquid Chromatography-Mass Spectrometry: An Overview

New technology development and globalisation have led to extreme changes in the agri-food sector in recent years that need an important food supply chain characterisation from plant materials to commercial productions. Many analytical strategies are commonly utilised in the agri-food industry, often using complementary technologies with different purposes. Chromatography on-line coupled to mass spectrometry (MS) is one of the most selective and sensitive analytical methodologies. The purpose of this overview is to present the most recent MS-based techniques applied to food analysis. An entire section is dedicated to the recent applications of high-resolution MS. Covered topics include liquid (LC)– and gas chromatography (GC)–MS analysis of natural bioactive substances, including carbohydrates, flavonoids and related compounds, lipids, phenolic compounds, vitamins, and other different molecules in foodstuffs from the perspectives of food composition, food authenticity and food adulteration. The results represent an important contribution to the utilisation of GC–MS and LC–MS in the field of natural bioactive compound identification and quantification.

Fetal-fluid proteome analyses in late-term healthy pregnant mares and in mares with experimentally induced ascending placentitis

Characterisation of fetal fluids in healthy and disease states of pregnant mares can help to unravel the pathophysiology and to identify putative markers of disease. Thus, this study aimed to compare the protein composition of: (1) amniotic and allantoic fluids of healthy mares obtained immediately after euthanasia and (2) allantoic fluid harvested via centesis before and after experimental induction of placentitis via transcervical inoculation of Streptococcus equi ssp zooepidemicus in healthy mares. Fetal fluids were analysed with a high-throughput proteomic technique after in-gel digestion. Statistical comparisons were performed following normalisation of peptide spectral match. Global normalisation was performed to calculate relative expression. There were 112 unique proteins present in both allantoic and amniotic fluids. There were 13 and 29 proteins defined as amniotic- or allantoic-specific respectively that were present in at least two fluid samples. Another 26 proteins were present in both amniotic and allantoic fluids. Panther DB functional classification grouped fetal-fluid proteins as transfer carriers, signalling molecules, receptors, immunity, hydrolase, enzymes, membrane traffic, cytoskeleton, cell adhesion, calcium binding and extracellular matrix. Experimentally induced placentitis resulted in 10 proteins being upregulated and 10 downregulated in allantoic fluid. Newly identified proteins and changes in the fetal-fluid proteome provide clues about the physiology of pregnancy and pathogenesis of placentitis.

The use of UHPLC, IMS, and HRMS in multiresidue analytical methods: A critical review

Residue chemists who analyse pesticides in vegetables or veterinary drugs in animal-based food are currently facing a situation where there is a requirement to detect more and more compounds at lower and lower concentrations. Conventional tandem quadrupole instruments provide sufficient sensitivity, but speed and selectivity appear as future limitations. This will become an even larger issue when there is a need to not only detect active compounds but also their degradation products and metabolites. This will likely lead to a situation in which the conventional targeted approach must be expanded or augmented by a certain non-targeted strategy. High-resolution mass spectrometry provides such capabilities, but it frequently requires an additional degree of selectivity for the unequivocal confirmation of analytes present at trace levels in highly complex and variable food matrices. The hyphenation of ultrahigh performance liquid chromatography with ion mobility and high-resolution mass spectrometry provides analytical chemists with a new tool for performing such a demanding multiresidue analysis. The objective of this paper is to investigate the benefits of the added ion mobility dimension as well as to critically discuss the current limitations of this commercially available technology.

Increased Single-Spectrum Top-Down Protein Sequence Coverage in Trapping Mass Spectrometers with Chimeric Ion Loading

Fourier transform mass spectrometers routinely provide high mass resolution, mass measurement accuracy, and mass spectral dynamic range. In this work, we utilize 21 T Fourier transform ion cyclotron resonance (FT-ICR) to analyze product ions derived from the application of multiple dissociation techniques and/or multiple precursor ions within a single transient acquisition. This ion loading technique, which we call, "chimeric ion loading", saves valuable acquisition time, decreases sample consumption, and improves top-down protein sequence coverage. In the analysis of MCF7 cell lysate, we show collision-induced dissociation (CID) and electron-transfer dissociation (ETD) on each precursor on a liquid chromatography-mass spectrometry (LC-MS) timescale and improve mean sequence coverage dramatically (CID-only 15% vs chimeric 33%), even during discovery-based acquisition. This approach can also be utilized to multiplex the acquisition of product ion spectra of multiple charge states from a single protein precursor or multiple ETD/proton-transfer reactions (PTR) reaction periods. The analytical utility of chimeric ion loading is demonstrated for top-down proteomics, but it is also likely to be impactful for tandem mass spectrometry applications in other areas.

High-resolution mass spectrometry for bioanalytical applications: Is this the new gold standard?

Liquid chromatography coupled to quadrupole-based tandem mass spectrometry (QqQ) is termed the "gold standard" for bioanalytical applications because of its unpreceded selectivity, sensitivity, and the ruggedness of the technology. More recently, however, high-resolution mass spectrometry (HRMS) has become increasingly popular for bioanalytical applications. Nonetheless, this technique is still viewed, either as a screening technology or as a research tool. Although HRMS is actively discussed during scientific conferences, it is yet to be widely utilised in routine laboratory settings and there remains a reluctance to use HRMS for quantitative measurements in regulated environments. This paper does not aim to comprehensively describe the potential of the latest HRMS technology, but rather, it focuses on what results can be obtained and outlines the author's experiences over a period of many years of the routine application of various forms of HRMS instrumentation. Fifteen years ago, some nine different QqQ methods were used in the author's laboratory to analyse a variety of different veterinary drug resides. Today, many more analytes are quantified by seven HRMS methods and just three QqQ methods remain in use for the analysis of a small set of compounds yet to be upgraded to HRMS analysis. This continual upgrading and migration of analytical methods were accompanied by regularly participating in laboratory proficiency tests (PTs). The PT reports (covering a range of analytes and analytical methods) were used to compare the accuracy of HRMS- versus QqQ-based measurements. In the second part of this paper, the particular strengths and limitations of HRMS for both method development and routine measurements are critically discussed. This also includes some anecdotal experiences encountered when replacing QqQ assays with HRMS methods.

MINIATURIZATION IN MASS SPECTROMETRY

Expectations for continuous miniaturization in mass spectrometry are not declining for years. Portable instruments are highly welcome by the industry, science, space agencies, forensic laboratories, and many other units. All are striving for the small, cheap, and as good as possible instruments. This review describes the recent developments of miniature mass spectrometers and also provides selected applications where these devices are used. Upcoming perspectives of further development are also discussed. @ 2019 John Wiley & Sons Ltd. Mass Spec Rev.

Effects of ultrasound on functional properties, structure and glycation properties of proteins: a review

Protein is an indispensable part of life. It provides nutrition for human body and flavor for food. The role of protein depends largely on the functional properties of the protein. Therefore, the elucidation of protein structure and functional properties needs to be further explored. The effects of structural and functional properties of proteins under different ultrasonic treatment conditions were reviewed. The structural changes of protein were studied by hydrogen-deuterium exchange mass spectrometry combined with fluorescence spectrometry and proteomics, and the mechanism of action was determined. The glycation site, the glycation degree, and the glycation characteristics of different sugars were determined. The protein was modified by ultrasound, and the influence of protein structure, physicochemical properties, protein glycation characteristics, and the action mechanism were analyzed by biological mass spectrometry.

Fast and sensitive flow-injection mass spectrometry metabolomics by analyzing sample-specific ion distributions

Mass spectrometry based metabolomics is a widely used approach in biomedical research. However, current methods coupling mass spectrometry with chromatography are time-consuming and not suitable for high-throughput analysis of thousands of samples. An alternative approach is flow-injection mass spectrometry (FI-MS) in which samples are directly injected to the ionization source. Here, we show that the sensitivity of Orbitrap FI-MS metabolomics methods is limited by ion competition effect. We describe an approach for overcoming this effect by analyzing the distribution of ion m/z values and computationally determining a series of optimal scan ranges. This enables reproducible detection of ~9,000 and ~10,000 m/z features in metabolomics and lipidomics analysis of serum samples, respectively, with a sample scan time of ~15 s and duty time of ~30 s; a ~50% increase versus current spectral-stitching FI-MS. This approach facilitates high-throughput metabolomics for a variety of applications, including biomarker discovery and functional genomics screens.

Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications

Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.

An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics

Mass spectrometry (MS)-based proteomics has great potential for overcoming the limitations of antibody-based immunoassays for antibody-independent, comprehensive, and quantitative proteomic analysis of single cells. Indeed, recent advances in nanoscale sample preparation have enabled effective processing of single cells. In particular, the concept of using boosting/carrier channels in isobaric labeling to increase the sensitivity in MS detection has also been increasingly used for quantitative proteomic analysis of small-sized samples including single cells. However, the full potential of such boosting/carrier approaches has not been significantly explored, nor has the resulting quantitation quality been carefully evaluated. Herein, we have further evaluated and optimized our recent boosting to amplify signal with isobaric labeling (BASIL) approach, originally developed for quantifying phosphorylation in small number of cells, for highly effective analysis of proteins in single cells. This improved BASIL (iBASIL) approach enables reliable quantitative single-cell proteomics analysis with greater proteome coverage by carefully controlling the boosting-to-sample ratio (e.g. in general <100×) and optimizing MS automatic gain control (AGC) and ion injection time settings in MS/MS analysis (e.g. 5E5 and 300 ms, respectively, which is significantly higher than that used in typical bulk analysis). By coupling with a nanodroplet-based single cell preparation (nanoPOTS) platform, iBASIL enabled identification of ∼2500 proteins and precise quantification of ∼1500 proteins in the analysis of 104 FACS-isolated single cells, with the resulting protein profiles robustly clustering the cells from three different acute myeloid leukemia cell lines. This study highlights the importance of carefully evaluating and optimizing the boosting ratios and MS data acquisition conditions for achieving robust, comprehensive proteomic analysis of single cells.

Enhancing the selectivity of liquid chromatography-mass spectrometry by using trilinear decomposition on LC-MS data: An application to three-way calibration of coeluting analytes in human plasma

The high selectivities of liquid chromatography and mass spectrometry make liquid chromatography-mass spectrometry one of the most popular tools for quantitative analysis in complex chemical, biological, and environmental systems, while the potential mathematical selectivity of liquid chromatography-mass spectrometry is rarely investigated. This work discussed the mathematical selectivity of liquid chromatography-mass spectrometry by three-way calibration based on the trilinear model, with an application to quantitative analysis of coeluting aromatic amino acids in human plasma. By the trilinear decomposition of the constructed liquid chromatography-mass spectrometry-sample trilinear model and individual regression of the decomposed relative intensity versus concentration, the proposed three-way calibration method successfully achieved quantitative analysis of coeluting aromatic amino acids in human plasma, even in the presence of uncalibrated interferent(s) and a varying background. This analytical method can ease the requirements for sample preparation and complete chromatographic separation of components, reduce the use of organic solvents, decrease the time of chromatographic separation, and increase the peak capacity of liquid chromatography-mass spectrometry. As a "green analytical method", the liquid chromatography-mass spectrometry three-way calibration method can provide a promising tool for direct and fast quantitative analysis in complex systems containing uncalibrated spectral interferents, especially for the situation where the coelution problem is difficult to overcome.

Picoflow Liquid Chromatography-Mass Spectrometry for Ultrasensitive Bottom-Up Proteomics Using 2-μm-i.d. Open Tubular Columns

In many areas of application, key objectives of chemical separation and analysis are to minimize the sample quantity while maximizing the chemical information obtained. Increasing measurement sensitivity is especially critical for proteomics research, especially when processing trace samples and where multiple measurements are desired. A rich collection of technologies has been developed, but the resulting sensitivity remains insufficient for achieving in-depth coverage of proteomic samples as small as single cells. Here, we combine picoliter-scale liquid chromatography (picoLC) with mass spectrometry (MS) to address this issue. The picoLC employs a 2-μm-i.d. open tubular column to reduce the sample input needed to greatly increase the sensitivity achieved using electrospray ionization (ESI) with MS. With this picoLC-MS system, we show that we can identify ∼1000 proteins reliably using only 75 pg of tryptic peptides, representing a 10-100-fold sensitivity improvement compared with the state-of-the-art liquid chromatography (LC) or capillary electrophoresis (CE)-MS methods. PicoLC-MS extends the limit of separation science and is expected to be a powerful tool for single cell proteomics.

Validation and Evaluation of High-Resolution Orbitrap Mass Spectrometry on Molecular Characterization of Dissolved Organic Matter

Molecular composition of dissolved organic matter (DOM) is a hot topic in subjects such as environmental science and geochemistry. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has been applied to molecular composition characterization of DOM successfully. However, high instrument and maintenance costs have constrained its wider application. A high-resolution Orbitrap mass spectrometer (Orbitrap MS) can provide approximately 500,000 resolving power (at m/z 200), which is potentially capable of characterizing the molecular composition of DOM. In this paper, the application of high-resolution Orbitrap MS was evaluated by comparing with FT-ICR MS in the aspect of resolution, mass distribution, detection dynamic range, and isotopic peak intensity ratio. The impact of instrument parameters of Orbitrap MS was further investigated, which includes ionization, ion transfer, and mass detection. The result shows that the high-resolution Orbitrap MS is capable or even preferable for molecular characterization of DOM. However, the peak intensity distributions are dependent on the instrument parameters, which could affect the environmental impact assessment caused by the sample itself. The result indicates that development of a universal and comparable method is of great demand.

Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics

The ability to quantitatively probe diverse panels of proteins and their post-translational modifications (PTMs) across multiple samples would aid a broad spectrum of biological, biochemical and pharmacological studies. We report a novel, microarray analytical technology that combines immuno-affinity capture with Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS), which is capable of supporting highly multiplexed, targeted proteomic assays. Termed "Affinity-Bead Assisted Mass Spectrometry" (Affi-BAMS), this LC-free technology enables development of highly specific and customizable assay panels for simultaneous profiling of multiple proteins and PTMs. While affinity beads have been used previously in combination with MS, the Affi-BAMS workflow uses enrichment on a single bead that contains one type of antibody, generally capturing a single analyte (protein or PTM) while having enough binding capacity to enable quantification within approximately 3 orders of magnitude. The multiplexing capability is achieved by combining Affi-BAMS beads with different protein specificities. To enable screening of bead-captured analytes by MS, we further developed a novel method of performing spatially localized elution of targets from individual beads arrayed on a microscope slide. The resulting arrays of micro spots contain highly concentrated analytes localized within 0.5 mm diameter spots that can be directly measured using MALDI MS. While both intact proteins and protein fragments can be monitored by Affi-BAMS, we initially focused on applying this technology for bottom-up proteomics to enable screening of hundreds of samples per day by combining the robust magnetic bead-based workflow with the high throughput nature of MALDI MS acquisition. To demonstrate the variety of applications and robustness of Affi-BAMS, several studies are presented that focus on the response of 4EBP1, RPS6, ERK1/ERK2, mTOR, Histone H3 and C-MET to stimuli including rapamycin, H2O2, EPO, SU11274, Staurosporine and Vorinostat.

Native vs Denatured: An in Depth Investigation of Charge State and Isotope Distributions

New tools and techniques have dramatically accelerated the field of structural biology over the past several decades. One potent and relatively new technique that is now being utilized by an increasing number of laboratories is the combination of so-called "native" electrospray ionization (ESI) with mass spectrometry (MS) for the characterization of proteins and their noncovalent complexes. However, native ESI-MS produces species at increasingly higher m/z with increasing molecular weight, leading to substantial differences when compared to traditional mass spectrometric approaches using denaturing ESI solutions. Herein, these differences are explored both theoretically and experimentally to understand the role that charge state and isotopic distributions have on signal-to-noise (S/N) as a function of complex molecular weight and how the reduced collisional cross sections of proteins electrosprayed under native solution conditions can lead to improved data quality in image current mass analyzers, such as Orbitrap and FT-ICR. Quantifying ion signal differences under native and denatured conditions revealed enhanced S/N and a more gradual decay in S/N with increasing mass under native conditions. Charge state and isotopic S/N models, supported by experimental results, indicate that analysis of proteins under native conditions at 100 kDa will be 17 times more sensitive than analysis under denatured conditions at the same mass. Higher masses produce even larger sensitivity gains. Furthermore, reduced cross sections under native conditions lead to lower levels of ion decay within an Orbitrap scan event over long transient acquisition times, enabling isotopic resolution of species with molecular weights well in excess of those typically resolved under denatured conditions.

Development of two-dimensional gas chromatography (GC×GC) coupled with Orbitrap-technology-based mass spectrometry: Interest in the identification of biofuel composition

Comprehensive gas chromatography (GC) has emerged in recent years as the technique of choice for the analysis of volatile and semivolatile compounds in complex matrices. Coupling it with high-resolution mass spectrometry (MS) makes a powerful tool for identification and quantification of organic compounds. The results obtained in this study showed a significant improvement by using GC×GC-EI-MS in comparison with GC-EI-MS; the separation of chromatogram peaks was highly improved, which facilitated detection and identification. However, the limitation of Orbitrap mass analyzer compared with time-of-flight analyzer is the data acquisition rate; the frequency average was about 25 Hz at a mass resolving power of 15.000, which is barely sufficient for the proper reconstruction of the narrowest chromatographic peaks. On the other hand, the different spectra obtained in this study showed an average mass accuracy of about 1 ppm. Within this average mass accuracy, some reasonable elemental compositions can be proposed and combined with characteristic fragment ions, and the molecules can be identified with precision. At a mass resolving power of 7.500, the scan rate reaches 43 Hz and the GC×GC-MS peaks can be represented by more than 10 data points, which should be sufficient for quantification. The GC×GC-MS was also applied to analyze a cellulose bio-oil sample. Following this, a highly resolved chromatogram was obtained, allowing EI mass spectra containing molecular and fragment ions of many distinct molecules present in the sample to be identified.

Temperature-dependent luminescence spectroscopic and mass spectrometric investigations of U(VI) complexation with aqueous silicates in the acidic pH-range

In this study the complexation of U(VI) with orthosilicic acid (H₄SiO₄) was investigated between pH 3.5 and 5 by combining electrospray ionization mass spectrometry (ESI-MS) and laser-induced luminescence spectroscopy. The ESI-MS experiments performed at a total silicon concentration of 5 · 10^-3M (exceeding the solubility of amorphous silica at both pH-values) revealed the formation of oligomeric sodium-silicates in addition to the UO₂OSi(OH)₃⁺ species. For the luminescence spectroscopic experiments (25 °C), the U(VI) concentration was fixed at 5 · 10^-6M, the silicon concentration was varied between 1.3 · 10^-4-1.3 · 10^-3M (reducing the formation of silicon oligomers) and the ionic strength was kept constant at 0.2 M NaClO₄. The results confirmed the formation of the aqueous UO₂OSi(OH)₃⁺ complex. The conditional complexation constant at 25 °C, log *β = -(0.31 ± 0.24), was extrapolated to infinite dilution using the Davies equation, which led to log *β⁰ = -(0.06 ± 0.24). Further experiments at different temperatures (1-25 °C) allowed the calculation of the molal enthalpy of reaction Δ_rH_m⁰ = 45.8 ± 22.5 kJ·mol^-1 and molal entropy of reaction Δ_rS_m⁰ = 152.5 ± 78.8 J·K^-1·mol^-1 using the integrated van't Hoff equation, corroborating an endothermic and entropy driven complexation process.

The proteome and its dynamics: A missing piece for integrative multi-omics in schizophrenia

The complex and heterogeneous pathophysiology of schizophrenia can be deconstructed by integration of large-scale datasets encompassing genes through behavioral phenotypes. Genome-wide datasets are now available for genetic, epigenetic and transcriptomic variations in schizophrenia, which are then analyzed by newly devised systems biology algorithms. A missing piece, however, is the inclusion of information on the proteome and its dynamics in schizophrenia. Proteomics has lagged behind omics of the genome, transcriptome and epigenome since analytic platforms were relatively less robust for proteins. There has been remarkable progress, however, in the instrumentation of liquid chromatography (LC) and mass spectrometry (MS) (LCMS), experimental paradigms and bioinformatics of the proteome. Here, we present a summary of methodological innovations of recent years in MS based proteomics and the power of new generation proteomics, review proteomics studies that have been conducted in schizophrenia to date, and propose how such data can be analyzed and integrated with other omics results. The function of a protein is determined by multiple molecular properties, i.e., subcellular localization, posttranslational modification (PTMs) and protein-protein interactions (PPIs). Incorporation of these properties poses additional challenges in proteomics and their integration with other omics; yet is a critical next step to close the loop of multi-omics integration. In sum, the recent advent of high-throughput proteome characterization technologies and novel mathematical approaches enable us to incorporate functional properties of the proteome to offer a comprehensive multi-omics based understanding of schizophrenia pathophysiology.

Identification to species level of live single microalgal cells from plankton samples with matrix-free laser/desorption ionization mass spectrometry

INTRODUCTION

Marine planktonic communities are complex microbial consortia often dominated by microscopic algae. The taxonomic identification of individual phytoplankton cells usually relies on their morphology and demands expert knowledge. Recently, a live single-cell mass spectrometry (LSC-MS) pipeline was developed to generate metabolic profiles of microalgae.

OBJECTIVE

Taxonomic identification of diverse microalgal single cells from collection strains and plankton samples based on the metabolic fingerprints analyzed with matrix-free laser desorption/ionization high-resolution mass spectrometry.

METHODS

Matrix-free atmospheric pressure laser-desorption ionization mass spectrometry was performed to acquire single-cell mass spectra from collection strains and prior identified environmental isolates. The computational identification of microalgal species was performed by spectral pattern matching (SPM). Three similarity scores and a bootstrap-derived confidence score were evaluated in terms of their classification performance. The effects of high and low-mass resolutions on the classification success were evaluated.

RESULTS

Several hundred single-cell mass spectra from nine genera and nine species of marine microalgae were obtained. SPM enabled the identification of single cells at the genus and species level with high accuracies. The receiver operating characteristic (ROC) curves indicated a good performance of the similarity measures but were outperformed by the bootstrap-derived confidence scores.

CONCLUSION

This is the first study to solve taxonomic identification of microalgae based on the metabolic fingerprints of the individual cell using an SPM approach.

Analytical Methodologies for the Determination of Organoarsenicals in Edible Marine Species: A Review

Setting regulatory limits for arsenic in food is complicated, owing to the enormous diversity of arsenic metabolism in humans, lack of knowledge about the toxicity of these chemicals, and lack of accurate arsenic speciation data on foodstuffs. Identification and quantification of the toxic arsenic compounds are imperative to understanding the risk associated with exposure to arsenic from dietary intake, which, in turn, underscores the need for speciation analysis of the food. Arsenic speciation in seafood is challenging, owing to its existence in myriads of chemical forms and oxidation states. Interconversions occurring between chemical forms, matrix complexity, lack of standards and certified reference materials, and lack of widely accepted measurement protocols present additional challenges. This review covers the current analytical techniques for diverse arsenic species. The requirement for high-quality arsenic speciation data that is essential for establishing legislation and setting regulatory limits for arsenic in food is explored.

Enhancing Protein Electrospray Charge States by Multivalent Metal Ions: Mechanistic Insights from MD Simulations and Mass Spectrometry Experiments

The structure and reactivity of electrosprayed protein ions is governed by their net charge. Native proteins in non-denaturing aqueous solutions produce low charge states. More highly charged ions are formed when electrospraying proteins that are unfolded and/or exposed to organic supercharging agents. Numerous studies have explored the electrospray process under these various conditions. One phenomenon that has received surprisingly little attention is the charge enhancement caused by multivalent metal ions such as La³⁺ when electrospraying proteins out of non-denaturing solutions. Here, we conducted mass spectrometry and ion mobility spectrometry experiments, in combination with molecular dynamics (MD) simulations, to uncover the mechanistic basis of this charge enhancement. MD simulations of aqueous ESI droplets reproduced the experimental observation that La³⁺ boosts protein charge states relative to monovalent metals (e.g., Na⁺). The simulations showed that gaseous proteins were released by solvent evaporation to dryness, consistent with the charged residue model. Metal ion ejection kept the shrinking droplets close to the Rayleigh limit until ∼99% of the solvent had left. For droplets charged with Na⁺, metal adduction during the final stage of solvent evaporation produced low protein charge states. Droplets containing La³⁺ showed a very different behavior. The trivalent nature of La³⁺ favored adduction to the protein at a very early stage, when most of the solvent had not evaporated yet. This irreversible binding via multidentate contacts suppressed La³⁺ ejection from the vanishing droplets, such that the resulting gaseous proteins carried significantly more charge. Our results illustrate that MD simulations are suitable for uncovering intricate aspects of electrospray mechanisms, paving the way toward an atomistic understanding of mass spectrometry based analytical workflows.

Shot-gun proteomics: why thousands of unidentified signals matter

Mass spectrometry-based proteomics has become a constitutional part of the multi-omics toolbox in yeast research, advancing fundamental knowledge of molecular processes and guiding decisions in strain and product developmental pipelines. Nevertheless, post-translational protein modifications (PTMs) continue to challenge the field of proteomics. PTMs are not directly encoded in the genome; therefore, they require a sensitive analysis of the proteome itself. In yeast, the relevance of post-translational regulators has already been established, such as for phosphorylation, which can directly affect the reaction rates of metabolic enzymes. Whereas, the selective analysis of single modifications has become a broadly employed technique, the sensitive analysis of a comprehensive set of modifications still remains a challenge. At the same time, a large number of fragmentation spectra in a typical shot-gun proteomics experiment remain unidentified. It has been estimated that a good proportion of those unidentified spectra originates from unexpected modifications or natural peptide variants. In this review, recent advancements in microbial proteomics for unrestricted protein modification discovery are reviewed, and recent research integrating this additional layer of information to elucidate protein interaction and regulation in yeast is briefly discussed.

Comprehensive Analysis of Protein Glycation Reveals Its Potential Impacts on Protein Degradation and Gene Expression in Human Cells

Glycation as a type of non-enzymatic protein modification is related to aging and chronic diseases, especially diabetes. Global analysis of protein glycation will aid in a better understanding of its formation mechanism and biological significance. In this work, we comprehensively investigated protein glycation in human cells (HEK293T, Jurkat, and MCF7 cells). The current results indicated that this non-enzymatic modification was not random, and protein at the extracellular regions and the nucleus were more frequently glycated. Systematic and site-specific analysis of glycated proteins allowed us to study the effect of the primary sequences and secondary structures of proteins on glycation. Furthermore, nearly every enzyme in the glycolytic pathway was found to be glycated and a possible mechanism was proposed. Many glycation sites were also previously reported as acetylation and ubiquitination sites, which strongly suggested that this non-enzymatic modification may disturb protein degradation and gene expression. The current results will facilitate further studies of protein glycation in biomedical and clinical research.

Recent developments in DNA adduct analysis using liquid chromatography coupled with mass spectrometry

The formation of DNA adducts by genotoxic agents is an early event in cancer development, and it may lead to gene mutations, thereby initiating tumor development. The measurement of DNA adducts can provide critical information about the genotoxic potential of a chemical and its mechanism of carcinogenesis. In recent decades, liquid chromatography coupled with mass spectrometry has become the most important technique for analyzing DNA adducts. The improvements in resolution achievable with new chromatographic separation techniques coupled with the high specificity and sensitivity and wide dynamic range of new mass spectrometry systems have been used for both qualitative and quantitative analyses of DNA adducts. This review discusses the challenges in qualitative and quantitative analyses of DNA adducts by liquid chromatography coupled with mass spectrometry and highlights recent developments towards overcoming the limitations of liquid chromatography coupled with mass spectrometry methods. The key steps and new solutions, such as sample preparation, mass spectrometry fragmentation, and method validation, are summarized. In addition, the fundamental principles and latest advances in DNA adductomic approaches are reviewed.

Application of quadrupole-Orbitrap high-resolution mass spectrometry in rapid screening and identification of synthetic dyes in herbal medicines

In this work, a method combining ultra-high performance liquid chromatography and hybrid quadrupole-Orbitrap high-resolution mass spectrometry (HR-MS) was developed and validated for use in the simultaneous screening, identification, and quantification of 21 synthetic dyes in herbal medicines. To optimize the chromatographic conditions, we used a combined Full mass scan and data-dependent MS/MS (Full MS/dd-MS²) approach in positive and negative ion mode. Under this mode, selected ions with given fragmentation energy were subjected to a dd-MS² scan following a Full MS scan. The selectivity of this method was effectively improved using 70,000 full width at half maximum mass resolution and narrow mass window (typically 5 ppm), and a single injection was sufficient for simultaneous identification and quantification of 21 synthetic dyes within 10 min. The combined method was fully validated and complies with all criteria for selectivity, sensitivity, calibration curve linearity, accuracy, precision, recovery, matrix effect, and stability. All analytes showed excellent linear relationships as all the coefficients of determination (r²) are greater than 0.9978 over wide ranges of concentrations (e.g. 1.0-500 ng/mL for sunset yellow). The validated method was employed to detect synthetic dyes in herbal medicines and was demonstrated to provide a reliable technical basis for drug regulation and public health protection.

High-fat diet fuels prostate cancer progression by rewiring the metabolome and amplifying the MYC program

Systemic metabolic alterations associated with increased consumption of saturated fat and obesity are linked with increased risk of prostate cancer progression and mortality, but the molecular underpinnings of this association are poorly understood. Here, we demonstrate in a murine prostate cancer model, that high-fat diet (HFD) enhances the MYC transcriptional program through metabolic alterations that favour histone H4K20 hypomethylation at the promoter regions of MYC regulated genes, leading to increased cellular proliferation and tumour burden. Saturated fat intake (SFI) is also associated with an enhanced MYC transcriptional signature in prostate cancer patients. The SFI-induced MYC signature independently predicts prostate cancer progression and death. Finally, switching from a high-fat to a low-fat diet, attenuates the MYC transcriptional program in mice. Our findings suggest that in primary prostate cancer, dietary SFI contributes to tumour progression by mimicking MYC over expression, setting the stage for therapeutic approaches involving changes to the diet.

Effects of oxidant and catalyst on the transformation products of rocket fuel 1,1-dimethylhydrazine in water and soil

Existing methods for cleanup of wastewaters and soils polluted with the extremely toxic rocket fuel unsymmetrical dimethylhydrazine (UDMH) are mainly based on the treatment with various oxidative reagents. Until now, the assessment of their effectiveness was based on the residual content of UDMH and did not take into account the possibility of the formation of a large number of potentially dangerous nitrogen-containing transformation products (TPs). In this study, using the recently developed approach based on high-resolution Orbitrap mass spectrometry, the comprehensive characterization of UDMH TPs formed by the action of air oxygen and different oxidants (Fenton's reagent, KMnO₄, HOCl, H₂O₂ in the presence of Cu²⁺ and [Fe (EDTA)]^- catalysts) typically used to detoxify spill sites was performed. The range of the identified molecular formulas of TPs comprised 303 compounds of various classes. Among them, there is a number of major products not previously described in the literature. It was established that none of the investigated oxidative reagents ensures complete conversion of rocket fuel to safe compounds. The hydrogen peroxide based reagents, particularly H₂O₂ + Na [Fe (EDTA)] system currently used in Kazakhstan, give the greatest number of TPs, for many of which a toxicity was not characterized so far. The majority of the compounds found in model solutions was detected in extracts of soil from the crash site of the Proton carrier rocket, which was subjected to the on-site reagent treatment. During successive treatments, along with the decrease in the number of detectable UDMH TPs, their ratios change in favor of amines.

Standard Proteoforms and Their Complexes for Native Mass Spectrometry

Native mass spectrometry (nMS) is a technique growing at the interface of analytical chemistry, structural biology, and proteomics that enables the detection and partial characterization of non-covalent protein assemblies. Currently, the standardization and dissemination of nMS is hampered by technical challenges associated with instrument operation, benchmarking, and optimization over time. Here, we provide a standard operating procedure for acquiring high-quality native mass spectra of 30-300 kDa proteins using an Orbitrap mass spectrometer. By describing reproducible sample preparation, loading, ionization, and nMS analysis, we forward two proteoforms and three complexes as possible standards to advance training and longitudinal assessment of instrument performance. Spectral data for five standards can guide assessment of instrument parameters, data production, and data analysis. By introducing this set of standards and protocols, we aim to help normalize native mass spectrometry practices across labs and provide benchmarks for reproducibility and high-quality data production in the years ahead. Graphical abstract.

Horizontal Cell Biology: Monitoring Global Changes of Protein Interaction States with the Proteome-Wide Cellular Thermal Shift Assay (CETSA)

The cellular thermal shift assay (CETSA) is a biophysical technique allowing direct studies of ligand binding to proteins in cells and tissues. The proteome-wide implementation of CETSA with mass spectrometry detection (MS-CETSA) has now been successfully applied to discover targets for orphan clinical drugs and hits from phenotypic screens, to identify off-targets, and to explain poly-pharmacology and drug toxicity. Highly sensitive multidimensional MS-CETSA implementations can now also access binding of physiological ligands to proteins, such as metabolites, nucleic acids, and other proteins. MS-CETSA can thereby provide comprehensive information on modulations of protein interaction states in cellular processes, including downstream effects of drugs and transitions between different physiological cell states. Such horizontal information on ligandmodulation in cells is largely orthogonal to vertical information on the levels of different proteins and therefore opens novel opportunities to understand operational aspects of cellular proteomes.

Pharmacokinetic and tissue distribution studies of cassane diterpenoids, in rats through an ultra-high-performance liquid chromatography-Q exactive hybrid quadrupole-Orbitrap high-resolution accurate mass spectrometry

Cassane diterpenoids (CA) are considered as the main active constituents of medicinal plants belonging to the Caesalpinia genus. Three cassane derivatives, bonducellpin G (BG), 7-O-acetyl-bonducellpin C (7-O-AC) and caesalmin E (CE), isolated from Caesalpinia minax Hance seeds, showed strong anti-inflammatory activity. In this paper, pharmacokinetics (BG, 7-O-AC, CE) and tissue distribution (7-O-AC, CE) properties were studied for the first time using a reliable, sensitive and rapid UHPLC-Q-Orbitrap HR-MS to develop new anti-inflammatory agents. A novel quantitative method with full scan in positive ion mode was used to determine the contents of compounds. They were separated using acetonitrile-water (0.1% formic acid) as gradient mobile phase. The calibration curve displayed good linearity and the lower limit of quantitation was 0.005-0.02 μg/mL for all analytes. Meanwhile, the absorption, distribution, metabolism, excretion (ADME) property was predicted using PreADMET web. The pharmacokinetic parameters indicated that they were absorbed quickly, eliminated rapidly together with high blood concentration. The results of tissue distribution demonstrated that CE was distributed rapidly and widely among tissues, and stomach was the main tissue site of CE and 7-O-AC, followed by small intestine/liver. This study indicates that the structures and dosages of active CA should be modified to help improve the absorption rate and residence time, and the findings are helpful for the pharmaceutical design of CA derivatives.

Characterization of proteins in cultural heritage using MALDI–TOF and LC–MS/MS mass spectrometric techniques

Identification of proteinaceous materials in artworks is of high interest to restorers-conservators, art historians and archaeologists, because it helps to shed light on the used painting techniques, to attribute unknown artworks, to make conclusions on prehistoric diets, etc. The chapter is devoted to the mass spectrometry instrumentation, evaluation of obtained data and it is showing several examples of the application of matrix-assisted laser desorption/ionization–time-of-flight and liquid chromatography–electrospray ionization–quadrupole–time-of-flight mass spectrometers on cultural heritage samples.

Purification and Proteomics of Influenza Virions

This chapter describes a basic workflow for analyzing the protein composition of influenza virions. In order to obtain suitable material, the chapter describes how to concentrate influenza virions from the growth media of infected cells and to purify them by ultracentrifugation through a density gradient. This approach is also suitable for purifying influenza virions from the allantoic fluid of embryonated chicken eggs. As a small quantity of microvesicles are co-purified with virions, optional steps are included to increase the stringency of purification by enriching material with viral receptor binding and cleaving activity. Material purified in this way can be used for a variety of downstream applications, including proteomics. As a detailed example of this, the chapter also describes a standard workflow for analyzing the protein composition of concentrated virions by liquid chromatography and tandem mass spectrometry.

Identification of Pathogenic Bacteria from Public Libraries via Proteomics Analysis

Hazardous organisms may thrive on surfaces that are often exposed to human contact, including children’s library books. In this study, swab samples were taken from 42 children’s books collected from four public libraries in Texas and California. Samples were then cultivated in brain–heart infusion (BHI) medium and then in Luria broth (LB) medium containing either ampicillin or kanamycin. All 42 samples (100%) were positive for bacterial growth in normal BHI medium. Furthermore, 35 samples (83.3%) and 20 samples (47.6%) in total were positive in LB medium containing ampicillin or kanamycin, respectively. Bacterial populations were then identified in samples using an Orbitrap Fusion™ Tribrid ™ mass spectrometer, a state-of-the-art proteomic analysis tool. Identified bacterial species grown in ampicillin included Bacillus, Acinetobacter, Pseudomonas, Staphylococcus, Enterobacter, Klebsiella, Serratia, Streptococcus, Escherichia, Salmonella, and Enterococcus. In contrast, identified bacteria grown in kanamycin included Staphylococcus, Streptococcus, Enterococcus, and Bacillus. The presences of pathogenic bacteria species were also confirmed. The results of this study warrant follow up studies to assess the potential health risks of identified pathogens. This study demonstrates the utility of proteomics in identifying environmental pathogenic bacteria for specific public health risk evaluations.

Metabolomics and Isotope Tracing

Great strides have been made over the past decade toward comprehensive study of metabolism. Mass spectrometry (MS) has played a central role by enabling measurement of many metabolites simultaneously. Tracking metabolite labeling from stable isotope tracers can in addition reveal pathway activities. Here, we describe the basics of metabolite measurement by MS, including sample preparation, metabolomic analysis, and data interpretation. In addition, drawing on examples of successful experiments, we highlight the ways in which metabolomics and isotope tracing can illuminate biology.

ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments

BACKGROUND

The investigation of intracellular metabolism is the mainstay in the biotechnology and physiology settings. Intracellular metabolic rates are commonly evaluated using labeling pattern of the identified metabolites obtained from stable isotope labeling experiments. The labeling pattern or mass distribution vector describes the fractional abundances of all isotopologs with different masses as a result of isotopic labeling, which are typically resolved using mass spectrometry. Because naturally occurring isotopes and isotopic impurity also contribute to measured signals, the measured patterns must be corrected to obtain the labeling patterns. Since contaminant isotopologs with the same nominal mass can be resolved using modern mass spectrometers with high mass resolution, the correction process should be resolution dependent.

RESULTS

Here we present a software tool, ElemCor, to perform correction of such data in a resolution-dependent manner. The tool is based on mass difference theory (MDT) and information from unlabeled samples (ULS) to account for resolution effects. MDT is a mathematical theory and only requires chemical formulae to perform correction. ULS is semi-empirical and requires additional measurement of isotopologs from unlabeled samples. We validate both methods and show their improvement in accuracy and comprehensiveness over existing methods using simulated data and experimental data from Saccharomyces cerevisiae. The tool is available at https://github.com/4dsoftware/elemcor .

CONCLUSIONS

We present a software tool based on two methods, MDT and ULS, to correct LC-MS data from isotopic labeling experiments for natural abundance and isotopic impurity. We recommend MDT for low-mass compounds for cost efficiency in experiments, and ULS for high-mass compounds with relatively large spectral inaccuracy that can be tracked by unlabeled standards.

Small alkyl amines as ion-pair reagents for the separation of positional isomers of impurities in phosphate diester oligonucleotides

In an effort to improve separation of impurities in oligonucleotide drugs, alkyl amines of different length and carbon content were evaluated as reagents in ion pair-reversed phase (IP-RP) HPLC with mass spectrometric detection. A range of columns was tested in combination with different buffers, ion-pair modifiers and varying pH adjustments. For phosphorothioate oligonucleotides, larger amines, like tributyl and hexyl amine provided the best chromatography, as small amines tended to broaden peaks due to the separation of diastereoisomers. For phosphate diester oligonucleotides, the best separations were obtained using small alkyl amines, like propyl-, isopropyl- and diethylamine. Conditions optimized for oligonucleotide sequence and type of impurity enabled full separation of the individual components of composite impurities, such as n-1, N³-(2-cyanoethyl)thymine (CNET), deaminated and 3-(2-oxopropyl)imidazopyrimidinone (OPC) impurities. The addition of long-chain alkyl acids like hexanoic acid to the IP buffer resulted in further improvements in peak separation.

Rapid analysis of pyridinoline and deoxypyridinoline in biological samples by liquid chromatography with mass spectrometry and a silica hydride column

Pyridinoline and deoxypyridinoline crosslinks are biomarkers found in urine for collagen degradation in bone turnover. For the first time, a rapid, sensitive, and ion-pairing free method is described for the analysis of pyridinoline and deoxypyridinoline using ultra-high performance liquid chromatography with Cogent Diamond Hydride column and detection by Q Exactive hybrid quadrupole-orbitrap high resolution accurate mass spectrometry. The separation was achieved using both isocratic and gradient conditions and run time <5 min under isocratic conditions of 20% acetonitrile in water containing 0.1% formic acid. Pyridoxine was used as an internal standard and relative standard deviation of the retention times of both pyridinoline and deoxypyridinoline were <1%. The limit of detection was 0.082 ± 0.023 μM for pyridinoline and 0.118 ± 0.052 μM for deoxypyridinoline. The limit of quantitation was 0.245 ± 0.070 μM for pyridinoline and 0.354 ± 0.157 μM for deoxypyridinoline. The method was validated by the detection and quantitation of both pyridinoline and deoxypyridinoline in skin and urine samples.