Sixty years of research on bracken fern (Pteridium spp.) toxins: Environmental exposure, health risks and recommendations for bracken fern control.

Bracken fern (Pteridium spp.) is a highly problematic plant worldwide due to its toxicity in combination with invasive properties on former farmland, in deforested areas and on disturbed natural habitats. The carcinogenic potential of bracken ferns has caused scientific and public concern for six decades. Its genotoxic effects are linked to illudane-type glycosides (ITGs), their aglycons and derivatives. Ptaquiloside is considered the dominating ITG, but with significant contributions from other ITGs. The present review aims to compile evidence regarding environmental pollution by bracken fern ITGs, in the context of their human and animal health implications. The ITG content in bracken fern exhibits substantial spatial, temporal, and chemotaxonomic variation. Consumption of bracken fern as food is linked to human gastric cancer but also causes urinary bladder cancers in bovines browsing on bracken. Genotoxic metabolites are found in milk and meat from bracken fed animals. ITG exposure may also take place via contaminated water with recent data pointing to concentrations at microgram/L-level following rain events. Airborne ITG-exposure from spores and dust has also been documented. ITGs may synergize with major biological and environmental carcinogens like papillomaviruses and Helicobacter pylori to induce cancer, revealing novel instances of chemical and biological co-carcinogenesis. Thus, the emerging landscape from six decades of bracken research points towards a global environmental problem with increasingly complex health implications.

Characterizing lignins from various sources and treatment processes after optimized sample preparation techniques and analysis via ESI-HRMS and custom mass defect software tools.

Sample preparation of complex, natural mixtures such as lignin prior to mass spectrometry analysis, however minimal, is a critical step in ensuring accurate and interference-free results. Modern shotgun-MS techniques, where samples are directly injected into a high-resolution mass spectrometer (HRMS) with no prior separation, usually still require basic sample pretreatment such as filtration and appropriate solvents for full dissolution and compatibility with atmospheric pressure ionization interfaces. In this study, sample preparation protocols have been established for a unique sample set consisting of a wide variety of degraded lignin samples from numerous sources and treatment processes. The samples were analyzed via electrospray (ESI)-HRMS in negative and positive ionization modes. The resulting information-rich HRMS datasets were then transformed into the mass defect space with custom R scripts as well as the open-source Constellation software as an effective way to visualize changes between the samples due to the sample preparation and ionization conditions as well as a starting point for comprehensive characterization of these varied sample sets. Optimized conditions for the four investigated lignins are proposed for ESI-HRMS analysis for the first time, giving an excellent starting point for future studies seeking to better characterize and understand these complex mixtures.

Enhancing Biomolecule Analysis and 2DMS Experiments by Implementation of (Activated Ion) 193 nm UVPD on a FT-ICR Mass Spectrometer.

Ultraviolet photodissociation is a fast, photon-mediated fragmentation method that yields high sequence coverage and informative cleavages of biomolecules. In this work, 193 nm UVPD was coupled with a 12 Tesla FT-ICR mass spectrometer and 10.6 µm infrared multi-photon dissociation to provide gentle slow-heating of UV-irradiated ions. No internal instrument hardware modifications were required. Adjusting the timing of laser pulses to the ion motion within the ICR cell provided consistent fragmentation yield shot-to-shot and may also be used to monitor ion positions within the ICR cell. Single-pulse UVPD of the native-like 5+ charge state of ubiquitin resulted in 86.6% cleavage coverage. Additionally, IR activation post UVPD doubled the overall fragmentation yield and boosted the intensity of UVPD-specific x-type fragments up to 4-fold. This increased yield effect was also observed for the 6+ charge state of ubiquitin, albeit less pronounced. This indicates that gentle slow-heating serves to sever tethered fragments originating from non-covalently linked compact structures and makes activation post UVPD an attractive option to boost fragmentation efficiency for top-down studies. Lastly, UVPD was implemented and optimized as a fragmentation method for 2DMS, a data-independent acquisition method. UVPD-2DMS was demonstrated to be a viable method using BSA digest peptides as a model system.

Revealing the Reactivity of Individual Chemical Entities in Complex Mixtures: the Chemistry Behind Bio-Oil Upgrading.

Bio-oils are precursors for biofuels but are highly corrosive necessitating further upgrading. Furthermore, bio-oil samples are highly complex and represent a broad range of chemistries. They are complex mixtures not simply because of the large number of poly-oxygenated compounds but because each composition can comprise many isomers with multiple functional groups. The use of hyphenated ultrahigh-resolution mass spectrometry affords the ability to separate isomeric species of complex mixtures. Here, we present for the first time, the use of this powerful analytical technique combined with chemical reactivity to gain greater insights into the reactivity of the individual isomeric species of bio-oils. A pyrolysis bio-oils and its esterified bio-oil were analyzed using gas chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry, and in-house software (KairosMS) was used for fast comparison of the hyphenated data sets. The data revealed a total of 10,368 isomers in the pyrolysis bio-oil and an increase to 18,827 isomers after esterification conditions. Furthermore, the comparison of the isomeric distribution before and after esterification provide new light on the reactivities within these complex mixtures; these reactivities would be expected to correspond with carboxylic acid, aldehyde, and ketone functional groups. Using this approach, it was possible to reveal the increased chemical complexity of bio-oils after upgrading and target detection of valuable compounds within the bio-oils. The combination of chemical reactions alongside with in-depth molecular characterization opens a new window for the understanding of the chemistry and reactivity of complex mixtures.

Combining Ultraviolet Photodissociation and Two-Dimensional Mass Spectrometry: A Contemporary Approach for Characterizing Singly Charged Agrochemicals.

Ultraviolet photodissociation (UVPD) has been shown to produce extensive structurally informative data for a variety of chemically diverse compounds. Herein, we demonstrate the performance of the 193 nm UVPD fragmentation technique on structural/moiety characterization of 14 singly charged agrochemicals. Two-dimensional mass spectrometry (2DMS) using infrared multiphoton dissociation (IRMPD) and electron-induced dissociation (EID) have previously been applied to a select range of singly charged pesticides. The ≥80% moiety coverage achieved for the majority of the species by the UVPD and 2D-UVPD methods was on par with and, in some cases, superior to the data obtained by other fragmentation techniques in previous studies, demonstrating that UVPD is viable for these types of species. A three-dimensional (3D) peak picking method was implemented to extract the data from the 2DMS spectrum, overcoming the limitations of the line extraction method used in previous studies, successfully separating precursor specific fragments with milli-Dalton accuracy. Whole spectrum internal calibration combined with 3D peak picking obtained sub-part-per-million (ppm) to part-per-billion (ppb) mass accuracies across the entire 2DMS spectrum.

Advantages of Two-Dimensional Electron-Induced Dissociation and Infrared Multiphoton Dissociation Mass Spectrometry for the Analysis of Agrochemicals.

Analysis of agrochemicals in an environmental matrix is challenging because these samples contain multiple agrochemicals, their metabolites, degradation products, and endogenous compounds. The analysis of such complex samples is achieved using chromatographic separation techniques coupled to mass spectrometry. Herein, we demonstrate a two-dimensional mass spectrometry (2DMS) technique on a 12 T Fourier transform ion cyclotron resonance mass spectrometer that can analyze a mixture of agrochemicals without using chromatography or quadrupole isolation in a single experiment. The resulting 2DMS contour plot contains abundant tandem MS information for each component in the sample and correlates product ions to their corresponding precursor ions. Two different fragmentation methods are employed, infrared multiphoton dissociation (IRMPD) and electron-induced dissociation (EID), with 2DMS to analyze the mixture of singly charged agrochemicals. The product ions of one of the agrochemicals, pirimiphos-methyl, present in the sample was used to internally calibrate the entire 2DMS spectrum, achieving sub part per million (ppm) to part per billion (ppb) mass accuracies for all species analyzed. The work described in this study will show the advantages of the 2DMS approach, by grouping species with common fragments/core structure and mutual functional groups, using precursor lines and neutral loss lines. In addition, the rich spectral information obtained from IRMPD and EID 2DMS contour plots can accurately identify and characterize agrochemicals.

Electron Capture Dissociation of Trithiocarbonate-Terminated Acrylamide Homo- and Copolymers: A Terminus-Directed Mechanism?

The structure and sequence elucidation of complex homo- and copolymers is key for further understanding polymers, polymer synthesis, and polymer interactions in biological processes. In this contribution, poly(dimethylacrylamide) homo- and dimethylacrylamide/4-acryloylmorpholine block copolymers were synthesized and analyzed by electron capture dissociation (ECD) and Fourier transform ion cyclotron resonance (FT-ICR) tandem mass spectrometry. Double-resonance experiments were carried out, providing a better understanding of the fragmentation process. A novel radical dissociation process is presented, and electron capture caused a specific cleavage at the terminal butyl-trithiocarbonate group, which initiated a free radical dissociation process.

Facile Determination of Phosphorylation Sites in Peptides Using Two-Dimensional Mass Spectrometry.

Detection and characterization of phosphopeptides by infrared multiphoton dissociation two-dimensional mass spectrometry (IRMPD 2DMS) is shown to be particularly effective. A mixture of phosphopeptides was analyzed by 2DMS without any prior separation. 2DMS enables the data independent analysis of the mixture and the correlation of the fragments to their precursor ions. The extraction of neutral loss lines corresponding to the loss of phosphate under IRMPD fragmentation allows the selective identification of phosphopeptides. Resonance of the 10.6 µm infrared radiation with the vibrational modes of the phosphate functional group produced efficient absorption and high cleavage coverage of the phosphopeptides at much lower irradiation fluence than for nonphosphorylated peptides improving discrimination. Additionally, the localization of the phosphate group was determined.

Comparison of Fragmentation Techniques for the Structural Characterization of Singly Charged Agrochemicals.

Investigating the structure of active ingredients, such as agrochemicals and their associated metabolites, is a crucial requisite in the discovery and development of these molecules. In this study, structural characterization by electron-induced dissociation (EID) was compared to collisionally activated dissociation (CAD) on a series of agrochemicals. EID fragmentation produced a greater variety of fragment ions and complementary ion pairs leading to more complete functional group characterization compared to CAD. The results obtained displayed many more cross-ring fragmentation of the pyrimidine ring compared to the pyridine ring. Compounds that consisted of one aromatic heterocyclic moiety (azoxystrobin, fluazifop acid, fluazifop-p-butyl, and pirimiphos-methyl) displayed cross-ring fragmentation while compounds with only aromatic hydrocarbon rings (fenpropidin and S-metolachlor) displayed no cross-ring fragmentation. The advantages of high-resolution accurate mass spectrometry (HRAM MS) are shown with the majority of assignments at ppb range error values and the ability to differentiate ions with the same nominal mass but different elemental composition. This highlights the potential for HRAM MS and EID to be used as a tool for structural characterization of small molecules with a wide variety of functional groups and structural motifs.

Label-Free Nanoimaging of Neuromelanin in the Brain by Soft X-ray Spectromicroscopy.

A hallmark of Parkinson's disease is the death of neuromelanin-pigmented neurons, but the role of neuromelanin is unclear. The in situ characterization of neuromelanin remains dependent on detectable pigmentation, rather than direct quantification of neuromelanin. We show that direct, label-free nanoscale visualization of neuromelanin and associated metal ions in human brain tissue can be achieved using synchrotron scanning transmission x-ray microscopy (STXM), through a characteristic feature in the neuromelanin x-ray absorption spectrum at 287.4 eV that is also present in iron-free and iron-laden synthetic neuromelanin. This is confirmed in consecutive brain sections by correlating STXM neuromelanin imaging with silver nitrate-stained neuromelanin. Analysis suggests that the 1s-σ* (C-S) transition in benzothiazine groups accounts for this feature. This method illustrates the wider potential of STXM as a label-free spectromicroscopy technique applicable to both organic and inorganic materials.

MIND: A Double-Linear Model To Accurately Determine Monoisotopic Precursor Mass in High-Resolution Top-Down Proteomics.

Top-down proteomics approaches are becoming ever more popular, due to the advantages offered by knowledge of the intact protein mass in correctly identifying the various proteoforms that potentially arise due to point mutation, alternative splicing, post-translational modifications, etc. Usually, the average mass is used in this context; however, it is known that this can fluctuate significantly due to both natural and technical causes. Ideally, one would prefer to use the monoisotopic precursor mass, but this falls below the detection limit for all but the smallest proteins. Methods that predict the monoisotopic mass based on the average mass are potentially affected by imprecisions associated with the average mass. To address this issue, we have developed a framework based on simple, linear models that allows prediction of the monoisotopic mass based on the exact mass of the most-abundant (aggregated) isotope peak, which is a robust measure of mass, insensitive to the aforementioned natural and technical causes. This linear model was tested experimentally, as well as in silico, and typically predicts monoisotopic masses with an accuracy of only a few parts per million. A confidence measure is associated with the predicted monoisotopic mass to handle the off-by-one-Da prediction error. Furthermore, we introduce a correction function to extract the "true" (i.e., theoretically) most-abundant isotope peak from a spectrum, even if the observed isotope distribution is distorted by noise or poor ion statistics. The method is available online as an R shiny app: https://valkenborg-lab.shinyapps.io/mind/.

A Light-Activated Acyl Carrier Protein "Trap" for Intermediate Capture in Type†II Iterative Polyketide Biocatalysis.

A discrete acyl carrier protein (ACP) bearing a photolabile nonhydrolysable carba(dethia) malonyl pantetheine cofactor was chemoenzymatically prepared and utilised for the trapping of biosynthetic polyketide intermediates following light activation. From the in vitro assembly of the polyketides SEK4 and SEK4b, by the type II actinorhodin "minimal" polyketide synthase (PKS), a range of putative ACP-bound diketides, tetraketides, pentaketides and hexaketides were identified and characterised by FT-ICR-MS, providing direct insights on active site accessibility and substrate processing for this enzyme class.

Two-dimensional mass spectrometry: new perspectives for tandem mass spectrometry.

Fourier transform ion cyclotron resonance mass analysers (FT-ICR MS) can offer the highest resolutions and mass accuracies in mass spectrometry. Mass spectra acquired in an FT-ICR MS can yield accurate elemental compositions of all compounds in a complex sample. Fragmentation caused by ion-neutral, ion-electron, or ion-photon interactions leads to more detailed structural information on compounds. The most often used method to correlate compounds and their fragment ions is to isolate the precursor ions from the sample before fragmentation. Two-dimensional mass spectrometry (2D MS) offers a method to correlate precursor and fragment ions without requiring precursor isolation. 2D MS therefore enables easy access to the fragmentation patterns of all compounds from complex samples. In this article, the principles of FT-ICR MS are reviewed and the 2D MS experiment is explained. Data processing for 2D MS is detailed, and the interpretation of 2D mass spectra is described.

Structural analysis of peptides modified with organo-iridium complexes, opportunities from multi-mode fragmentation.

The most widely used anticancer drugs are platinum complexes, but complexes of other transition metals also show promise and may widen the spectrum of activity, reduce side-effects, and overcome resistance. The latter include organo-iridium(iii) 'piano-stool' complexes. To understand their mechanism of action, it is important to discover how they bind to biomolecules and how binding is affected by functionalisation of the ligands bound to iridium. We have characterised, by MS and MS/MS techniques, unusual adducts from reactions between 3 novel iridium(iii) anti-cancer complexes each possessing reactive sites both at the metal (coordination by substitution of a labile chlorido ligand) and on the ligand (covalent bond formation involving imine formation by one or two aldehyde functions). Peptide modification by the metal complex had a drastic effect on both Collisonally Activated Dissociation (CAD) and Electron Capture Dissociation (ECD) MS/MS behaviour, tuning requirements, and fragmentation channels. CAD MS/MS was effective only when studying the covalent condensation products. ECD MS/MS, although hindered by electron-quenching at the Iridium complex site, was suitable for studying many of the species observed, locating the modification sites, and often identifying them to within a single amino acid residue.

Top-Down Deep Sequencing of Ubiquitin Using Two-Dimensional Mass Spectrometry.

Two-dimensional mass spectrometry (2DMS) allows data independent fragmentation of all ions in a sample and correlation of fragment ions to their precursors without isolation prior to fragmentation. Developments in computer capabilities and implementations in Fourier transform ion cyclotron resonance (FTICR) MS over the past decade have allowed the technique to become a useful analytical tool for bottom-up proteomics (BUP) and, more recently, in top-down protein analysis (TDP). In this work, a new method of TDP is developed using 2D FTICR MS, called MS/2D FTICR MS or MS/2DMS. In MS/2DMS, an entire protein is initially fragmented in a hexapole collision cell, e.g., with collisionally activated dissociation (CAD). The primary fragments are then sent to the ICR cell, where 2DMS is performed with infrared multiphoton dissociation (IRMPD) or electron-capture dissociation (ECD). The resulting 2D mass spectra retain information equivalent to a set of TDP MS3 experiments on the selected protein. Up to n - 1 fragmentation steps can be added to the process, as long as an ion of interest can be unambiguously fragmented before the ICR cell, leading to an MS n/2DMS experiment whose output is a 2D mass spectrum retaining information equivalent to MS n. MS/2DMS and MS/MS/2DMS are used in this work for the structural analysis of ubiquitin (Ubi), noting several unique features which aid fragment identification. The use of CAD-MS/IRMPD-2DMS, CAD-MS/ECD-2DMS, and MS2/2DMS using, respectively, in-source dissociation (ISD), CAD, and ECD-2DMS led to 97% cleavage coverage for Ubi.

Coupling Electron Capture Dissociation and the Modified Kendrick Mass Defect for Sequencing of a Poly(2-ethyl-2-oxazoline) Polymer.

With increasing focus on the structural elucidation of polymers, advanced tandem mass spectrometry techniques will play a crucial role in the characterization of these compounds. In this contribution, synthesis and analysis of methyl-initiated and xanthate-terminated poly(2-ethyl-2-oxazoline) using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) was achieved. Electron capture dissociation (ECD) produced full end group characterization as well as backbone fragmentation including complete sequence coverage of the polymer. A method of fragment ion characterization is also presented with the use of the high-resolution-modified Kendrick mass defect plots as a means of grouping fragments from the same fragmentation pathways together. This type of data processing is applicable to all tandem mass spectrometry techniques for polymer analysis but is made more effective with high mass accuracy methods. ECD FT-ICR MS demonstrates its promising role as a structural characterization technique for polyoxazoline species.

Can Two-Dimensional IR-ECD Mass Spectrometry Improve Peptide de Novo Sequencing?

Two-dimensional mass spectrometry (2D MS) correlates precursor and fragment ions without ion isolation in a Fourier transform ion cyclotron resonance mass spectrometer (FTICR MS) for tandem mass spectrometry. Infrared activated electron capture dissociation (IR-ECD), using a hollow cathode configuration, generally yields more information for peptide sequencing in tandem mass spectrometry than ECD (electron capture dissociation) alone. The effects of the fragmentation zone on the 2D mass spectrum are investigated as well as the structural information that can be derived from it. The enhanced structural information gathered from the 2D mass spectrum is discussed in terms of how de novo peptide sequencing can be performed with increased confidence. 2D IR-ECD MS is shown to sequence peptides, to distinguish between leucine and isoleucine residues through the production of w ions as well as between C-terminal ( b/ c) and N-terminal ( y/ z) fragments through the use of higher harmonics, and to assign and locate peptide modifications.

Polymer Analysis in the Second Dimension: Preliminary Studies for the Characterization of Polymers with 2D MS.

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FTICR MS or 2D MS) allows direct correlation between precursor and fragment ions without isolation prior to fragmentation. The method has been optimized for the analysis of complex mixtures and used so far for the analysis of small molecules and peptides obtained by tryptic digestion of proteins and entire proteins. In this work, a 2D MS method is developed to characterize complex mixtures of polymers using infrared multiphoton decay (IRMPD) and electron capture dissociation (ECD) as fragmentation techniques, and D-α-tocopheryl polyethylene glycol 1000 succinate (TPGS), Polysorbate 80, and poly(methyl methacrylate) (PMMA) as analytes. The use of 2D MS allowed generation of fragment m/z values for all the compounds in the mixture at once and allowed tandem mass spectrometry of species very close in m/z that would have been difficult to isolate with a quadrupole for standard MS/MS. Furthermore, the use of unique features of 2D MS such as the extraction of neutral-loss lines allowed the successful assignment of peaks from low abundant species that would have been more difficult with standard MS/MS. For all the samples, the amount of information obtained with 2D MS was comparable with what obtained with multiple 1D MS/MS experiments targeted on each individual component within each mixture but required a single experiment of about 20-40 min.

Two-dimensional mass spectrometry in a linear ion trap, an in silico model.

RATIONALE: Two-dimensional mass spectrometry (2D MS) is a technique that correlates precursor and product ions in a sample without requiring prior ion isolation. Until now, this technique has only been implemented on Fourier transform ion cyclotron resonance mass spectrometers. By coupling 2D MS techniques in linear ion traps (LITs) with a mass analyser with a fast duty cycle (e.g. time-of-flight), data-independent tandem mass spectrometry techniques can be compatible on a liquid chromatography (LC) or gas chromatography (GC) timescale. METHODS: The feasibility of 2D MS in a LIT is explored using SIMION ion trajectory calculations. RESULTS: By applying stored waveform inverse Fourier transform techniques for radial excitation on a LIT, the sizes of ion clouds were found to be modulated according to the ions' resonant frequencies in the LIT. By simulating a laser-based fragmentation at the centre of the LIT after the radius modulation step, product ion abundances were found to be modulated according to the resonant frequency of their precursor. CONCLUSIONS: A 2D mass spectrum could be obtained using the results from the simulation. This in silico model shows the feasibility of 2D MS on a LIT. 2D MS in a LIT allows for tandem mass spectrometry without ion isolation. Copyright © 2017 John Wiley & Sons, Ltd.

Automatic assignment of metal-containing peptides in proteomic LC-MS and MS/MS data sets.

Transition metal-containing proteins and enzymes are critical for the maintenance of cellular function and metal-based (metallo)drugs are commonly used for the treatment of many diseases, such as cancer. Detection and characterisation of metallodrug targets is crucial for improving drug-design and therapeutic efficacy. Due to the unique isotopic ratios of many metal species, and the complexity of proteomic samples, standard MS data analysis of these species is unsuitable for accurate assignment. Herein a new method for differentiating metal-containing species within complex LCMS data is presented based upon the Smart Numerical Annotation Procedure (SNAP). SNAP-LC accounts for the change in isotopic envelopes for analytes containing non-standard species, such as metals, and will accurately identify, record, and display the particular spectra within extended LCMS runs that contain target species, and produce accurate lists of matched peaks, greatly assisting the identification and assignment of modified species and tailored to the metals of interest. Analysis of metallated species obtained from tryptic digests of common blood proteins after reactions with three candidate metallodrugs is presented as proof-of-concept examples and demonstrates the effectiveness of SNAP-LC for the fast and accurate elucidation of metallodrug targets.