ICR MS Research Articles

Chemical and fractional composition of bio-oil obtained from Arthrospira platensis by hydrothermal liquefaction

This work is devoted to the study of chemical and fractional composition of the bio-oil obtained from Arthrospira platensis by hydrothermal liquefaction in the temperature range of 240-330 °C. For bio-oil analysis standard elemental analysis, ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS) and thermogravimetric analysis were used. It was shown that the yield of bio-oil was increased from 12.4% at 240 °C to 37.2% at 330 °C. With temperature increasing the spectrum of compounds found in bio-oil using FT ICR MS narrowes and moves to the region of low-molecular compounds. It was found that among the components containing nitrogen and oxygen, compounds containing 1 and 2 nitrogen atoms, as well as ON and O2N3 classes, dominate in the bio-oil. With the increase in the temperature of the liquefaction process, classes of compounds containing several oxygen atoms ON, O2N3, O3N2, ON2, transforms into the classes N and N2. By thermogravimetric analysis it was shown that the gasoline fraction (with boiling temperatures up to 200 °C) in bio-oil samples obtained from Arthrospira platensis at 240-330 °C was in the range of 20-22%. The fraction of light-boiling components in bio-oil was slightly decreased when the temperature of hydrothermal process was increased.

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra.

Ultrahigh resolution mass spectrometry, such as Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work, we describe software Formularity with a user-friendly interface for CIA function and newly developed search function Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. Tap water and HOC spike in Suwannee River NOM were used to assess HOC identification in complex environmental samples. Strategies for reconciliation of CIA and IPA assignments were discussed. Software and sample databases with documentation are freely available.

Metabolic profile of human coelomic fluid.

Till now there is very limited knowledge on the molecular content of coelomic fluid and cells. This study presents the first attempt to elucidate the metabolic profile of such samples. Samples were collected via coelocentesis from 41 women during the first trimester of gestation. Metabolic content was assessed using four different analytical platforms. For targeted analysis a hydrophilic interaction chromatography ultra high performance LC-MS/MS method was applied. Holistic analysis performed by GC-MS, NMR spectroscopy and ion cyclotron ultra-high resolution MS (FT-ICR-MS) instrumentation. Our observations suggest coelomic fluid and cells as promising biosamples, rich in metabolites with potential use in mammalian system biology studies.

The investigation of the bitumen from ancient Greek amphora using FT ICR MS, H/D exchange and novel spectrum reduction approach.

Recently Russian archeologists have discovered on Taman peninsula an ancient (V B.C.) Greek amphora full of dense bitumen. This is the oldest amphora in the world that contains bitumen. We report the investigation of this bitumen using ultrahigh resolution Fourier transform mass spectrometry. Also we used recently developed in-ESI source Hydrogen/Deuterium exchange approach for the structural characterization of the individual molecules and estimation of the biodegradation of the bitumen. The increase of number of the labile hydrogens compared to the non-degraded oil can serve as an additional evidence of the degradation of bitumen via oxidation. For the facilitation of the spectrum processing we have developed the special iterative spectrum reduction approach. It was observed that molecules that have only oxygen heteroatoms possess two -OH groups what is unusual for the petroleum. Based on this we suggested that the bitumen degraded during its being in amphora for 2500 years. Copyright © 2016 John Wiley & Sons, Ltd.

40 years of Fourier transform ion cyclotron resonance mass spectrometry

This article reviews the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in several respects: (a) a strong static magnetic field serves to convert ion mass-to-charge ratio into cyclotron frequency. Because frequency is the most accurately measurable property, ICR MS inherently offers higher mass resolution and mass accuracy than any other mass analyzer. (b) Coherent excitation followed by induced charge detection yields a time-domain signal whose discrete Fourier transform produces a mass spectrum of ions spanning a wide m/z range simultaneously. By simple analogy to weighing objects with a mechanical balance, that “multiplex” advantage can be shown to be equivalent to “multichannel” detection by an array of individual single-channel detectors. (c) FT-ICR MS performance benefits from near-elimination of magnetic field inhomogeneity by inherent ion cyclotron rotation and ion axial oscillation; inherent nearly quadrupolar electrostatic trapping potential and nearly uniform rf electric field homogeneity near the center of the ICR ion trap (both improved even further by recent ICR cell designs); and theoretically optimal excitation and mass selection produced by stored-waveform inverse Fourier transformation (SWIFT). (d) External ion accumulation allows efficient coupling of atmospheric pressure continuous ionization sources (notably electrospray ionization) with pulsed high-vacuum FT-ICR MS excitation/detection, and injection of externally trapped ions through the “magnetic mirror” into the ICR ion trap has been optimized based on ion trajectory simulations. (e) MS/MS can be performed either inside (e.g., electron capture dissociation, infrared multiphoton dissociation) or outside (e.g., collision-induced dissociation, electron transfer dissociation) the ICR ion trap. (f) Finally, FT-ICR MS instrumentation and experimental event sequences have benefited from striking parallels to prior nuclear magnetic resonance spectroscopy developments. Similarly, non-ICR FT MS development (notably the orbitrap) has benefited from FT-ICR precedents.

Fourier transform ion cyclotron resonance (FT ICR) mass spectrometry: Theory and simulations

Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer offers highest resolving power and mass accuracy among all types of mass spectrometers. Its unique analytical characteristics made FT ICR important tool for proteomics, metabolomics, petroleomics, and investigation of complex mixtures. Signal acquisition in FT ICR MS takes long time (up to minutes). During this time ion-ion interaction considerably affects ion motion and result in decreasing of the resolving power. Understanding of those effects required complicated theory and supercomputer simulations but culminated in the invention of the ion trap with dynamic harmonization which demonstrated the highest resolving power ever achieved. In this review we summarize latest achievements in theory and simulation of FT ICR mass spectrometers.

Thermal Stability of Simvastatin under Different Atmospheres

Simvastatin (SV) is a widely used drug for the treatment of hypercholesterolemia in humans. Nevertheless, serious efforts are still being made to develop new SV formulations with, for example, improved tabletability or bioavailability properties. These efforts frequently involve heating the compound well above ambient temperature or even fusion. In this work, the thermal stability of solid SV under different atmospheres was investigated by using isothermal tests in glass ampules, differential scanning calorimetry, and Calvet-drop microcalorimetry experiments. These tests were combined with analytical data from diffuse reflectance infrared Fourier-transform spectroscopy and liquid chromatography coupled with tandem mass spectrometry or Fourier transform ion cyclotron resonance mass spectrometry (LC–FT–ICR–MS). No decomposition was observed when the sample was kept at a temperature ≤373K under N2or reduced pressure (13.3 Pa) atmospheres. Thermal degradation was, however, observed for temperatures ≥353K in the presence of pure or atmospheric oxygen. The nature of the two main oxidative degradation products was determined through MS/MS experiments and accurate mass measurements of the precursor ions using FT–ICR–MS. The obtained results indicated that the decomposition process involves the oxidation of the hexahydronaphthalene fragment of SV.

FT–ICR–MS analysis of lignin

Fourier transform ion cyclotron resonance mass spectrometry (FT–ICR–MS) of a steam-exploded lignin from wheat straw showed that fragments with a mass higher than 4534 Da cannot be obtained. Furthermore, FT–ICR–MS showed that lignin is not a completely random polymer, but shows some regularity with a difference of 44.026 m/z (C2H4O) between the peaks. The distribution of Kendrick mass defect in the function of Kendrick nominal masses showed the same behaviour. FT–ICR–MS analysis of bagasse lignin (Granit) showed that the largest value of mass found was 4347 Da. The peaks show regularities with a difference of 44.026 m/z between the peaks. The organosolv lignin showed that the polymer with the largest mass value was 3699 Da in FT–ICR–MS. The analysis of the peaks did not show regularity; however, the Kendrick diagram for this lignin showed the same slope as in the other samples, in agreement with the C2H4O regular difference between peaks.

Measuring protein synthesis using metabolic 2H labeling, high-resolution mass spectrometry, and an algorithm

We recently developed a method for estimating protein dynamics in vivo with heavy water ( 2H 2O) using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) [16], and we confirmed that 2H labeling of many hepatic free amino acids rapidly equilibrated with body water. Although this is a reliable method, it required modest sample purification and necessitated the determination of tissue-specific amino acid labeling. Another approach for quantifying protein kinetics is to measure the 2H enrichments of body water (precursor) and protein-bound amino acid or proteolytic peptide (product) and to estimate how many copies of deuterium are incorporated into a product. In the current study, we used nanospray linear trap Fourier transform ion cyclotron resonance mass spectrometry (LTQ FT–ICR MS) to simultaneously measure the isotopic enrichment of peptides and protein-bound amino acids. A mathematical algorithm was developed to aid the data processing. The most notable improvement centers on the fact that the precursor/product labeling ratio can be obtained by measuring the labeling of water and a protein (or peptide) of interest, thereby minimizing the need to measure the amino acid labeling. As a proof of principle, we demonstrate that this approach can detect the effect of nutritional status on albumin synthesis in rats given 2H 2O.

Alkyl amides in two organic-rich anoxic sediments: A possible new abiotic route for N sequestration

Fixed nitrogen (N) plays an integral role in global cycling; while most is recycled to refuel primary productivity, a small fraction escapes to be preserved and stabilised in sediments. Despite decades of research, the functionality and reactivity of this sequestered organic N has been poorly understood. This study was undertaken to shed light on this problem by characterising the bulk sediment organic matter using nuclear magnetic resonance (NMR), followed by molecular level analysis using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT–ICR–MS). We studied two organic-rich anaerobic sediments, one from a freshwater system and another from a marine paralic basin. Mangrove Lake, Bermuda (marine) and Mud Lake, Florida (freshwater) have been shown in past studies to contain high levels of N-containing organic matter. Our resulting multidimensional NMR data suggests the existence of a new type of amide functionality in both these lake sediments, and we investigated this further using FT–ICR–MS and gas chromatography mass spectrometry (GC–MS). FT–ICR–MS confirmed the existence of homologous series of CHNO containing compounds, whose structures are verified using GC–MS as alkyl amides. Model reactions involving naturally occurring esters and ammonia suggest the source of alkyl amides to be amidation of esters with sedimentary ammonia derived from anaerobic degradation of organic matter. This expands upon previous hypotheses for preservation of amide containing compounds that call upon biological/abiological protection of proteins and peptides or the formation of refractory nitrogenous adducts.

Comparative Proteomic Analysis of Proteins Involved in the Tumorigenic Process of Seminal Vesicle Carcinoma in Transgenic Mice

We studied the seminal vesicle secretion (SVS) of transgenic mice by using one-dimensional gel electrophoresis combined with LTQ-FT ICR MS analysis to explore protein expression profiles. Using unique peptide numbers as a cut-off criterion, 79 proteins were identified with high confidence in the SVS proteome. Label-free quantitative analysis was performed by using the IDEAL_Q software program. Furthermore, western blot assays were performed to validate the expression of seminal vesicle proteins. Sulfhydryl oxidase 1, glia-derived nexin, SVS1, SVS3, and SVS6 showed overexpression in SVS during cancer development. With high sequence similarity to human semenogelin, SVS2 is the most abundance protein in SVS and is dramatically decreased during the tumorigenic process. Our results indicate that these protein candidates could serve as potential targets for monitoring seminal vesicle carcinoma. Moreover, this information can provide clues for investigating seminal vesicle secretion-containing seminal plasma for related human diseases.

Crude Oil Polar Chemical Composition Derived from FT−ICR Mass Spectrometry Accounts for Asphaltene Inhibitor Specificity

We examine oil-specific asphaltene inhibitor chemistry of two chemically distinct asphaltene inhibitors. Laboratory and field tests show oil-specific asphaltene inhibitor performance for two geographically distinct crude oils. The crude oils and their corresponding asphaltenes were characterized by total acid number (TAN), elemental analysis, Fourier transform infrared spectroscopy (FTIR), and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT−ICR MS). ESI FT−ICR MS reveals differences in the relative abundance of heteroatom-containing compound classes in the two crude oils and the two asphaltenes. We identify acidic and/or basic species that may be responsible for the observed differences in inhibitor chemistry. Asphaltene inhibitor specificity can be explained by acid−base-type interactions between the inhibitor and polar species in the crude oils or asphaltene fractions. ESI FT−ICR MS provides the first evidence for inhibitor effectiveness related to heteroatom ...

Dual polarity accurate mass calibration for electrospray ionization and matrix-assisted laser desorption/ionization mass spectrometry using maltooligosaccharides

In view of the fact that memory effects associated with instrument calibration hinder the use of many mass-to-charge ( m/ z) ratios and tuning standards, identification of robust, comprehensive, inexpensive, and memory-free calibration standards is of particular interest to the mass spectrometry community. Glucose and its isomers are known to have a residue mass of 162.05282 Da; therefore, both linear and branched forms of polyhexose oligosaccharides possess well-defined masses, making them ideal candidates for mass calibration. Using a wide range of maltooligosaccharides (MOSs) derived from commercially available beers, ions with m/z ratios from approximately 500 to 2500 Da or more have been observed using Fourier transform ion cyclotron resonance mass spectrometry (FT–ICR–MS) and time-of-flight mass spectrometry (TOF–MS). The MOS mixtures were further characterized using infrared multiphoton dissociation (IRMPD) and nano-liquid chromatography/mass spectrometry (nano-LC/MS). In addition to providing well-defined series of positive and negative calibrant ions using either electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI), the MOSs are not encumbered by memory effects and, thus, are well-suited mass calibration and instrument tuning standards for carbohydrate analysis.

Free‐flow electrophoresis for top‐down proteomics by Fourier transform ion cyclotron resonance mass spectrometry

High-efficiency prefractionation of complex protein mixtures is critical for top-down proteomics, i.e., the analysis of intact proteins by MS. Free-flow electrophoresis (FFE) can be used for IEF to separate proteins within a pH gradient according to their pIs. In an FFE system, this separation is performed entirely in the liquid phase, without the need for particulate chromatographic media, gels, or membranes. Herein, we demonstrated the compatibility of IEF-FFE with ESI-Fourier transform ICR MS (ESI-FTICR-MS) for top-down experiments. We demonstrated that IEF-FFE of intact proteins were highly reproducible between FFE instruments, between laboratories, and between analyses. Applying native (0.2% hydroxypropylmethyl cellulose) IEF-FFE to an enzyme resulted in no decrease in enzyme activity; applying either native or denaturing (8 M urea) IEF-FFE to a four-protein mixture with different pIs resulted in isolation of each protein into separate fractions in a 96-well plate. After desalting, each protein was sequenced by top-down MS/MS. As an application of this technique, chicken erythrocyte histone H2A-IV and its major modified forms were enriched by IEF-FFE. Top-down analysis revealed Lys-5 to be a major acetylation site, in addition to N-terminal acetylation.

Characterization of Acidic Species in Athabasca Bitumen and Bitumen Heavy Vacuum Gas Oil by Negative-Ion ESI FT−ICR MS with and without Acid−Ion Exchange Resin Prefractionation

Because acids in petroleum materials are known to corrode processing equipment, highly acidic oils are sold at a discount [on the basis of their total acid number (TAN)]. Here, we identify the acidic species in raw Canadian bitumen (Athabasca oil sands) and its distilled heavy vacuum gas oil (HVGO) as well as acid-only and acid-free fractions isolated by use of an ion-exchange resin (acid−IER) and negative-ion electrospray ionization Fourier transform ion cyclotron resonance (ESI FT−ICR MS) mass spectrometry. The ultrahigh mass resolving power ( m/Δ m 50% > 400 000) and high mass accuracy (better than 500 ppb) of FT−ICR MS, along with Kendrick mass sorting, enable the assignment of a unique elemental composition to each peak in the mass spectrum. Acidic species are characterized by class (N n O o S s heteroatom content), type [number of rings plus double bonds to carbon or double-bond equivalent (DBE)], and carbon number distribution. We conclude that the analytical capability of FT−ICR MS and the selecti...

Limitations of Size-Exclusion Chromatography in Analyzing Petroleum Asphaltenes: A Proof by Atomic Force Microscopy

The analysis of a Maya asphaltene using size-exclusion chromatography (SEC) and 1-methyl-2-pyrrolidinone (NMP), tetrahydrofuran (THF), and toluene as the eluent (separately used) showed radically different chromatograms. The SEC of fossil fuel hydrocarbons, e.g., asphaltenes, using NMP has shown a two-peak structure, which has been the source of debate, whether the peak excluded from the column porosity (appearing at the shorter retention times) contained asphaltenic aggregates or very large molecular masses of thousands of mass units. The SEC of asphaltenes using THF and toluene showed retained peaks at the longer retention times. In this work, atomic force microscopy (AFM), a technique capable of reliable and accurate detection of the interaction forces between various molecules and in different media, was exploited to investigate the interaction forces between polystyrene (PS) particles (SEC column packing) and asphaltenes in air and in NMP. AFM showed a strong interaction between the PS particles and asphaltenes, the outcome of which can be the aggregation of asphaltenes in the SEC columns. The use of solvents, such as toluene, NMP, and THF, which either damage the column packing or do not dissolve asphaltenes completely, the interaction between asphaltenes, and the SEC column packing and aggregation of asphaltenes in the SEC columns are the major limitations of SEC in analyzing asphaltenes. Furthermore, PSs, currently used to calibrate SEC columns, are significantly different from asphaltenes in their structure and solubility behavior. In addition, the quantitative results of the SEC are considerably different from the reports from other techniques, e.g., LD, MALDI, FT−ICR MS, and molecular diffusivity methods. Thus, SEC results cannot be used quantitatively to determine mass distributions of asphaltenes.

Analysis of a nuclease activity of catalytic domain of Thermus thermophilus MutS2 by high-accuracy mass spectrometry

Electrospray ionization with Fourier-transform ion cyclotron resonance mass spectrometry (ESI–FT ICR MS) is a powerful tool for analyzing the precise structural features of biopolymers, including oligonucleotides. Here, we described the detailed characterization of a newly discovered nuclease activity of the C-terminal domain of Thermus thermophilus MutS2 (ttMutS2). Using this method, the length, nucleotide content and nature of the 5′- and 3′-termini of the product oligonucleotides were accurately identified. It is revealed that the C-terminal domain of ttMutS2 incised the phosphate backbone of oligodeoxynucleotides non-sequence-specifically at the 3′ side of the phosphates. The simultaneous identification of the innumerable fragments was achieved by the extremely high-accuracy of ESI–FT ICR MS.

Emerging Technologies for Identification of Disinfection Byproducts: GC/FT−ICR MS Characterization of Solvent Artifacts

Water samples from a local water treatment plant were analyzed, using gas chromatography Fourier transform ion cyclotron resonance mass spectrometry (GC/FT-ICR MS), to identify potential disinfection byproducts (DBPs). Both liquid-liquid extraction (LLE) and solid-phase microextraction (SPME) techniques were used for sample preparation prior to GC/MS analyses. Based on the averaged mass measurement accuracy (MMA) of better than five parts-per-million (<5 ppm), multiple solvent artifacts were identified. It is shown that solventless SPME can be utilized to reduce potential interferences from solvent stabilizers. Six DBPs were detected and their molecular compositions were assigned at a high level of confidence. At the ppb concentration ranges and in the broadband mass spectral detection mode, internally calibrated mass spectra provided concurrent high resolution (resolving power M/deltaM50% > 30,000 at m/z values -110) and MMA of better than one part-per-million (MMA < 1 ppm). The use of thermochemical data, such as proton affinities, as a complementary tool to enhance analytical resolution is also demonstrated.

Serum glycan analysis in metastatic breast cancer

11504 Background: There is a need for a reliable breast cancer biomarker that can predict a patient’s response to therapy. Serum glycans, or oligosaccharides, are of particular interest as over half of all proteins are glycosylated and alterations in glycosylation influence growth, adhesion, metastasis and immune surveillance of tumor, among other important functions. Serum glycans can be analyzed by high resolution mass spectrometry. Methods: Sera from patients with known metastatic breast cancer and age-matched healthy controls without medical problems were prospectively analyzed by mass spectroscopy. Women over the age of 18, who were not pregnant or breastfeeding, and who were without other active cancers were eligible. Samples were de-identified for laboratory personnel who analyzed sera by matrix-assisted laser desoprtion/ionization (MALDI) and Fourier transform ion-cyclotron resonance mass sepctrometry (FT ICR MS). Glycans were also profiled by chromatographic separation using a microchip nanoLC (Agilent) with a time-of-flight (TOF) mass analyzers. Results: Sera from 25 patients with metastatic breast cancer and 25 controls were evaluated. The mass profiles were obtained corresponding to both N-linked oligosaccharides (N-glycans) and O-linked oligosaccharides (O-glycans). Distinct variations in glycosylation were observed among sera analyzed from patients with metastatic breast cancer compared to controls. Specific glycan masses were analyzed and found to correspond to N-glycans. The chromatographic glycan profile showed individual glycans that were distinct for the cancer patients. Conclusions: Analysis of serum gylcans by mass spectrometry represents a new paradigm of cancer biomarker studies, focusing on post-translational modifications of proteins, rather than protein expression. Further refinement of this technology may be clinically useful in monitoring response to therapy in metastatic breast cancer. No significant financial relationships to disclose.

Compositional Characterization of Bitumen/Water Emulsion Films by Negative- and Positive-Ion Electrospray Ionization and Field Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

By means of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT−ICR MS) and automated field desorption/ionization (FD) FT−ICR MS, we identify nonvolatile nonpolar, polar acidic, and basic water-in-bitumen emulsion film stabilizers. Highly condensed aromatic basic, nonpolar, and acidic asphaltene multilayered films stabilize emulsions near or at critical bitumen concentration for asphaltene flocculation. Solvent diluent added beyond the critical dilution concentration precipitates highly condensed acidic, all basic, and most neutral species from the oil/water interface. The most abundant classes in high bitumen concentration emulsion films include neutral pure hydrocarbons and S, acidic O2 and O2S, and basic N and NS heteroatom classes. Highly abundant low bitumen concentration emulsion film stabilizers include acidic O2, O4, and O3S classes.