Low Intensity Ion Research Articles

Selected Ion Monitoring for Orbitrap-Based Metabolomics.

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage.

Mass-spectra of new heterocycles: XXIV. Electron impact and chemical ionization study of <i>N</i>-[3-alkoxyand 3-(1<i>H</i>-pyrrol-1-yl)-2-thienyl]imidothiocarbamates

The behavior of a wide range of previously unknown N -(2-thienyl)imidothiocarbamates synthesized in a single preparative step from heterosubstituted allenes (methoxy-, 1-ethoxyethoxy- and 1 H -pyrrol-1-ylallenes) and aliphatic, cycloaliphatic, and aromatic isothiocyanates was studied under conditions of electron (70 eV) and chemical (reagent gas - methane) ionization. Under the electron impact, the studied compounds form an unstable molecular ion, the main direction of fragmentation of which is associated with the breaking of the C-N bond in the imidoformamide fragment with charge localization at the imine nitrogen atom. A similar decay channel of a molecular ion is also observed in the chemical ionization mass spectra of the studied compounds. In this case, characteristic, but low-intensity ions in the electron ionization spectra of N -(3-methoxy-2-thienyl)imidothiocarbamates become dominant in the chemical ionization spectra. In the chemical ionization spectra of N -[3-(1 H -pyrrol-1-yl)-2-thienyl]imidothiocarbamates, the maximum intensity peak belongs to the [ M - SMe]+ ion. For N -[3-(1-ethoxyethoxy)-2-thienyl]imidothiocarbamate, the peak of the ion formed upon successive elimination of ethoxyethene and methanethiol molecules from the [ M + H]+ ion has the maximum intensity.

Cyclic Dimers of 4-n-Propyloxybenzoic Acid with Hydrogen Bonds in the Gaseous State.

A comprehensive study of saturated vapors of 4-n-propyloxybenzoic acid (POBA) by gas electron diffraction (GED) and mass spectrometric (MS) methods supplemented by quantum chemical (QC) calculations was carried out for the first time. An attempt was made to detect dimeric forms of the acid in the gaseous state. It has been established that at the temperature of GED experiment, vapor over a solid sample contains up to 20 mol.% of cyclic dimers with two O-H...O hydrogen bonds. The main geometrical parameters of gaseous monomers and dimers of POBA are obtained. The distance r(O…O) = 2.574(12) Å in the cyclic fragment of the gaseous dimer is close to that in the crystal structure (2.611 Å). In the mass spectrum of the POBA recorded the ions of low intensity with a mass exceeding the molecular mass of the monomer were detected. The presence of ions, whose elemental composition corresponds to the dissociative ionization of the dimer, confirms the results of the GED experiment on the presence of POBA dimers in the gas state. The results of GED studies of acetic acid, benzoic acid, and POBA were compared. It is shown that the COOH fragment saves its geometric structure in monomers, as well as the COOH...HOOC fragment with two hydrogen bonds in dimers of different acids. The intermolecular interaction energy in considered acid dimers was estimated using QC calculations (B97D/6-311++G **). The significant value of last (>84 kJ/mol) is the reason for the noticeable presence of dimers in the gas phase.

GC–MS and GC–IR of regioisomeric 4-N-bromodimethoxybenzyl derivatives of 3-trifluoromethylphenylpiperazine

The seven regioisomeric N-bromodimethoxybenzyl derivatives of 3-TFMPP were synthesized via reductive amination of the seven commercially available bromodimethoxybenzaldehydes. The capillary GC elution profiles for these compounds generally follow the degree of methoxy group substituent crowding on the aromatic ring. The electron ionization mass spectra show a series of major fragment ions common to all seven regioisomeric compounds. The base peak in the EI mass spectra for many of the seven regioisomers occurs at m/z 229 and is the result of contributions from two isobaric fragments, the trifluoromethylphenylpiperazine cation as well as the 79Br bromodimethoxybenzyl cation. Several low intensity ions are related to the specific regioisomeric substitution patterns for the bromodimethoxybenzyl moieties and provide some differentiation for this set of seven compounds. These unique ions allow the seven compounds to be divided into sub-groups and in some cases allow specific isomer identification from only the EI-MS data. The 950 cm−1 to 550 cm−1 lower portion of the fingerprint region in the vapor phase infrared spectra can be used to identify each of the bromodimethoxybenzyl regioisomers after EI-MS fragmentation patterns provide focus on the individual structural sub-groups of compounds in this study.

Denoising of Mass Spectrometry Images via Inverse Maximum Signal Factors Analysis.

Improving signal-to-noise and, thereby, image contrast is one of the key challenges needed to expand the useful applications of mass spectrometry imaging (MSI). Both instrumental and data analysis approaches are of importance. Univariate denoising techniques have been used to improve contrast in MSI images with varying levels of success. Additionally, various multivariate analysis (MVA) methods have proven to be effective for improving image contrast. However, the distribution of important but low intensity ions can be obscured in the MVA analysis, leading to a loss of chemically specific information. In this work we propose inverse maximum signal factors (MSF) denoising as an alternative approach to both denoising and multivariate analysis for MSI imaging. This approach differs from the standard MVA techniques in that the output is denoised images for each original mass peak rather than the frequently difficult to interpret scores and loadings. Five tests have been developed to optimize and validate the resulting denoised images. The algorithm has been tested on a range of simulated data with different levels of noise, correlated noise, varying numbers of underlying components, and nonlinear effects. In the simulations, an excellent correlation between the true images and the denoised images was observed for peaks with an original signal-to-noise ratio as low as 0.1, as long as there was sufficient intensity in the sum of the selected peaks. The power of the approach was then demonstrated on two time-of-flight secondary ion mass spectrometry (ToF-SIMS) images that contained largely uncorrelated noise and a laser post-ionization matrix-assisted laser desorption/ionization mass spectrometry (MALDI-2-MS) image that contained strongly correlated noise. The improvements in signal-to-noise increased with decreasing intensity of the original peaks. A signal-to-noise improvement of as much as two orders of magnitude was achieved for very low intensity peaks. MSF denoising is a powerful addition to the suite of image processing techniques available for studying mass spectrometry images.

Improving Signal to Noise Ratios in Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations (SLIM) using a High Dynamic Range Analog-to-Digital Converter.

Signal digitization is a commonly overlooked part of ion mobility-mass spectrometry (IMS-MS) workflows, yet it greatly affects signal-to-noise ratio and MS resolution measurements. Here, we report on the integration of a 2 GS/s, 14-bit ADC with structures for lossless ion manipulations (SLIM-IMS-MS) and compare the performance to a commonly used 8-bit ADC. The 14-bit ADC provided a reduction in the digitized noise by a factor of ∼6, owing largely to the use of smaller bit sizes. The low baseline allowed threshold voltage levels to be set very close to the MCP baseline voltage, allowing for as much signal to be acquired as possible without overloading or excessive digitization of MCP baseline noise. Analyses of Agilent tuning mixture ions and a mixture of heavy labeled phosphopeptides showed that the 14-bit ADC provided a ∼1.5-2× signal-to-noise (S/N) increase for high intensity ions, such as the Agilent tuning mixture ions and the 2+ and 3+ charge states of many phosphopeptide constituents. However, signal enhancements were as much as 10-fold for low intensity ions, and the 14-bit ADC enabled discernible signal intensities otherwise lost using an 8-bit digitizer. Additionally, the 14-bit ADC required ∼14-fold fewer mass spectra to be averaged to produce a mass spectrum with a similar S/N as the 8-bit ADC, demonstrating ∼10× higher measurement throughput. The high resolution, low baseline, and fast speed of the new 14-bit ADC enables high performance digitization of MS, IMS-MS, and SLIM-IMS-MS spectra and provides a much better picture of analyte profiles in complex mixtures.

Rapid assessment of triacylglycerol fatty acyls composition by LC-APPI+-HRMS using monoacylglycerol like fragments intensities

We present a new analytical approach for the analysis of triacylglycerol fatty acyls distribution by normal phase liquid chromatography (NPLC) coupled with APPI+-HRMS. The NPLC method used allows the separation of more than 30 classes of lipids. The energy of the APPI+ source enables the formation of low-intensity ions B fragments ([RC = O+74]+ <3%), characteristic of lipids with a glycerol esterified by one or more fatty acyls. We found the relative intensities of ions B were close to the fatty acyl distribution. To establish the proof of concept, we decided to focus on the triacylglycerols (TGs) class, the major component of plant oils. By either NPLC or FIA, the TGs class appeared as a single peak. In our experimental conditions, ions B are always present in the mass spectra of TGs and each ion B is specific to a fatty acyl group. The Orbitrap mass spectrometer featured high enough resolution and accuracy to identify ions B and distinguish them from other TG fragment ions. A further adjustment of the fatty acyls relative quantities calculation from ions B intensities was computed using weighting coefficients of ions B response. The methodology was developed and validated using plant oils characterized by a GC-FID reference method. NPLC-APPI+-HRMS method offers the advantage of analyzing the fatty acyl composition of complex lipid extracts without the need for sample preparation.

Adduct annotation in liquid chromatography/high-resolution mass spectrometry to enhance compound identification

Annotation and interpretation of full scan electrospray mass spectra of metabolites is complicated by the presence of a wide variety of ions. Not only protonated, deprotonated, and neutral loss ions but also sodium, potassium, and ammonium adducts as well as oligomers are frequently observed. This diversity challenges automatic annotation and is often poorly addressed by current annotation tools. In many cases, annotation is integrated in metabolomics workflows and is based on specific chromatographic peak-picking tools. We introduce mzAdan, a nonchromatography-based multipurpose standalone application that was developed for the annotation and exploration of convolved high-resolution ESI-MS spectra. The tool annotates single or multiple accurate mass spectra using a customizable adduct annotation list and outputs a list of [M+H]+ candidates. MzAdan was first tested with a collection of 408 analytes acquired with flow injection analysis. This resulted in 402 correct [M+H]+ identifications and, with combinations of sodium, ammonium, and potassium adducts and water and ammonia losses within a tolerance of 10 mmu, explained close to 50% of the total ion current. False positives were monitored with mass accuracy and bias as well as chromatographic behavior which led to the identification of adducts with calcium instead of the expected potassium. MzAdan was then integrated in a workflow with XCMS for the untargeted LC-MS data analysis of a 52 metabolite standard mix and a human urine sample. The results were benchmarked against three other annotation tools, CAMERA, findMAIN, and CliqueMS: findMAIN and mzAdan consistently produced higher numbers of [M+H]+ candidates compared with CliqueMS and CAMERA, especially with co-eluting metabolites. Detection of low-intensity ions and correct grouping were found to be essential for annotation performance.Graphical abstract

Characterization of MK-40 Membrane Modified by Layers of Cation Exchange and Anion Exchange Polyelectrolytes.

Coating of ion exchange membranes used in electrodialysis with layers of polyelectrolytes is a proven approach that allows for the increasing of the limiting current, the suppressing of sedimentation, the controlling of the intensity of generation of H+ and OH− ions, and also the improving of monovalent selectivity. However, in the case when two materials with the opposite sign of the charge of fixed groups come in contact, a bipolar boundary is created that can cause undesirable changes in the membrane properties. In this work, we used a MK-40 heterogeneous membrane on the surface of which a layer of polyethyleneimine was applied by adsorption from a solution as a model of heterogeneous membranes modified with oppositely charged polyelectrolyte. It was found that, on one hand, the properties of modified membrane were beneficial for electrodialysis, its limiting current did not decrease and the membrane even acquired a barrier to non-selective electrolyte transport. At the same time, the generation of H+ and OH− ions of low intensity arose, even in underlimiting current modes. It was also shown that despite the presence of a layer of polyethyleneimine, the surface charge of the modified membrane remained negative, which we associate with low protonation of polyethyleneimine at neutral pH.

Upgrades of the GANDALPH photodetachment detector towards the determination of the electron affinity of astatine

The Gothenburg ANion Detector for Affinity measurements by Laser PHotodetachment (GANDALPH) has recently been built for measurements of electron affinities (EA) of radioisotopes. A first measurement campaign is aimed towards the determination of the EA of astatine, the rarest naturally occurring element on earth. In this work we present several upgrades of GANDALPH which have been implemented in order to facilitate EA measurements of radioisotopes where only low intensity ion beams (<1 pA) can be produced.

Application of 1013 ohm Faraday cup current amplifiers for boron isotopic analyses by solution mode and laser ablation multicollector inductively coupled plasma mass spectrometry.

Boron isotope ratios (δ11 B values) are used as a proxy for seawater paleo-pH, amongst several other applications. The analytical precision can be limited by the detection of low intensity ion beams from limited sample amounts. High-gain amplifiers offer improvements in signal/noise ratio and can be used to increase measurement precision and reduce sample amounts. 1013 ohm amplifier technology has previously been applied to several radiogenic systems, but has thus far not been applied to non-traditional stable isotopes. Here we apply 1013 ohm amplifier technology for the measurement of boron isotope ratios using solution mode MC-ICP-MS and laser ablation mode (LA-)MC-ICP-MS techniques. Precision is shown for reference materials as well as for low-volume foraminifera samples. The baseline uncertainty for a 0.1 pA 10 B+ ion beam is reduced to <0.1 ‰ for a typical measurement period. The external precision is better than 0.2 ‰ (2SD) for δ11 B measurements for solution samples containing as little as 0.8 ng total boron. For in situ microanalyses with LA-MC-ICP-MS, the external precision of 11 B/10 B from an in-house calcite standard was 1 ‰ (2SD) for individual spot analyses, and 0.3 ‰ for the mean of ≥10 replicate spot analyses. 1013 ohm amplifier technology is demonstrated to offer advantages for the determination of δ11 B values by both MC-ICP-MS and LA-MC-ICP-MS for small samples of biogenic carbonates, such as foraminifera shells. 1013 ohm amplifier technology will also be of benefit to other non-traditional stable isotope measurements.

Modified proton transfer reaction mass spectrometry (PTR-MS) operating conditions for in vitro and in vivo analysis of wine aroma.

With proton transfer reaction-mass spectrometry standard operating conditions, analysis of alcoholic beverages is an analytical challenge. Ethanol reacts with the primary ion H3 O+ leading to its depletion and to formation of ethanol-related ions and clusters, resulting in unstable ionization and in significant fragmentation of analytes. Different methods were proposed but generally resulted in lowering the sensitivity and/or complicating the mass spectra. The aim of the present study was to propose a simple, sensitive, and reliable method with fragmentation as low as possible, linearity within a realistic range of volatile organic compounds concentrations, and applicability to in vivo dynamic aroma release (nosespace) studies of wines. For in vitro analyses, a reference flask containing a hydro-alcoholic solution (10% ethanol) was permanently connected to the PTR-MS inlet in order to establish ethanol chemical ionization conditions. A low electric field strength to number density ratio E/N (80 Td) was used in the drift-tube. A stable reagent ion distribution was obtained with the primary protonated ethanol ion C2 H5 OH2+ accounting for more than 80% of the ionized species. The ethanol dimer (C2 H5 OH)2 H+ accounted for only 10%. Fragmentation of some aroma molecules important for white wine flavor (various esters, linalool, cis-rose oxide, 2-methylpropan-1-ol, 3-methylbutan-1-ol, and 2-phenylethanol) was studied from same ethanol content solutions connected alternatively with the reference solution to the instrument inlet. Linear dynamic range and limit of detection (LOD) were determined for ethyl hexanoate. Fragmentation of the protonated analytes was limited to a few ions of low intensity, or to specific fragment ions with no further fragmentation. Association and/or ligand switching reactions from ethanol clusters were only significant for the primary alcohols. Interpretation of the mass spectra was straightforward with easy detection of diagnostic ions. These results made this ethanol ionization method suitable for direct headspace analyses of model wines and to their nosespace analyses.

Ion Isolation in a Linear Ion Trap Using Dual Resonance Frequencies.

Ion isolation in a linear ion trap is demonstrated using dual resonance frequencies, which are applied simultaneously. One frequency is used to eject ions of a broad m/z range higher in m/z than the target ion, and the second frequency is set to eject a range of ions lower in m/z. The combination of the two thus results in ion isolation. Despite the simplicity of the method, even ions of low intensity may be isolated since signal attenuation is less than an order of magnitude in most cases. The performance of dual frequency isolation is demonstrated by isolating individual isotopes of brominated compounds. Graphical Abstract ᅟ.

Design of a compact Faraday cup for low energy, low intensity ion beams

Beam intensity is one of the key parameters in particle accelerators, in particular during machine commissioning, but also during operation for experiments. At low beam energies and low intensities a number of challenges arise in its measurement as commonly used non-invasive devices are no longer sensitive enough. It then becomes necessary to stop the beam in order to measure its absolute intensity. A very compact Faraday cup for determining ion beam currents from a few nanoamperes down to picoamperes for the HIE-ISOLDE post-accelerator at CERN has been designed, built and tested with beam. It has a large aperture diameter of 30mm and a total length of only 16mm, making it one of the most compact designs ever used.In this paper we present the different steps that were involved in the design and optimization of this device, including beam tests with two early prototypes and the final monitor. We also present an analysis of the losses caused by secondary particle emission for different repelling electrode voltages and beam energies. Finally, we show that results obtained from an analytical model for electron loss probability combined with Monte Carlo simulations of particles trajectories provide a very good agreement with experimental data.

Dehydrogenation and dehalogenation of amines in MALDI‐TOF MS investigated by isotopic labeling

Secondary and tertiary amines have been reported to form [M-H](+) that correspond to dehydrogenation in matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). In this investigation, we studied the dehydrogenation of amines in MALDI-TOF MS by isotopic labeling. Aliphatic amines were labeled with deuterium on the methylene of an N-benzyl group, which resulted in the formation of [M-D](+) and [M-H](+) ions by dedeuteration and dehydrogenation, respectively. This method revealed the proton that was removed. The spectra of most tertiary amines with an N-benzyl group showed high-intensity [M-D](+) and [M-H](+) ion peaks, whereas those of secondary amines showed low-intensity ion peaks. Ratios between the peak intensities of [M-D](+) and [M-H](+) greater than 1 suggested chemoselective dehydrogenation at the N-benzyl groups. The presence of an electron donor group on the N-benzyl groups enhanced the selectivity. The dehalogenation of amines with an N-(4-halobenzyl) group was also observed alongside dehydrogenation. The amino ions from dehalogenation can undergo second dehydrogenation. These results provide the first direct evidence about the position at which dehydrogenation of an amine occurs and the first example of dehalogenation of haloaromatic compounds in MALDI-TOF MS. These results should be helpful in the structural identification and elucidation of synthetic and natural molecules.

The beam diagnostic instruments in Beijing radioactive ion-beam facilities isotope separator on-line

The beam diagnostic instruments for Beijing Radioactive Ion-beam Facilities Isotope Separator On-Line are introduced [B. Q. Cui, Z. H. Peng, Y. J. Ma, R. G. Ma, B. Tang, T. Zhang, and W. S. Jiang, Nucl. Instrum. Methods 266, 4113 (2008); T. J. Zhang, X. L. Guan, and B. Q. Cui, in Proceedings of APAC 2004, Gyeongju, Korea, 2004, http://www.jacow.org, p. 267]. For low intensity ion beam [30-300 keV/1 pA-10 μA], the beam profile monitor, the emittance measurement unit, and the analyzing slit will be installed. For the primary proton beam [100 MeV/200 μA], the beam profile scanner will be installed. For identification of the nuclide, a beam identification unit will be installed. The details of prototype of the beam diagnostic units and some experiment results will be described in this article.

Evaluation of Relative Isotopic Abundance Measurements in a Quadrupole Time-of-Flight Mass Spectrometer for Elemental Composition Determination of Natural Products in Traditional Chinese Medicine

The relative isotopic abundance (RIA) measurement errors of a quadrupole time-of-flight (Q-ToF) instrument incorporating analog-to-digital converter detectors were systemically evaluated by stochastically collecting about 200 data in positive ion mass spectrometry (MS) mode. Errors varied with peak intensities at definite spectral acquisition rates but were very close, even if peak intensities changed sharply at different spectral acquisition rates with the same concentration. Intensity thresholds were systematically defined at 1 Hz of spectral acquisition rates. RIA measurement errors were also evaluated using peak area. It seemed that peak area was better adapted for the high-intensity ions while peak intensity was suited for very low-intensity ions. Several known compounds were selected for RIA measurements for product ions in tandem mass spectropmetry (MS/MS) mode. An extract of a representative traditional Chinese medicinal, Paederia scandens was analyzed with high-performance liquid chromatography-electrospray ionization-QToF-MS/MS. The unique elemental compositions of some compounds could not be identified even with exact masses and MS/MS spectra of measured and reference compounds. RIA errors, especially of (M+2)M(-1), provided vital information for determining the elemental composition.

Improvement using chemometrics in ion mobility coupled to mass spectrometry as a tool for mass spectrometry fragmentation studies: Flavonoid aglycone cases

A chemometric method for the treatment of ion mobility coupled to mass spectrometry (IMS/MS) data is proposed as a complementary tool for obtaining experimental evidence for the study of MS fragmentations, which can provide a direct and automatable methodology for characterising ionic series and the hierarchy of all product ions of an MS spectrum.Two MS/MS with ion mobility experiments have been designed: in the first, the intrinsic mobility of each ion is estimated, and in the second experiment, distributions of the ionic intensity of product ions fragmented after IMS separations are recorded. These mobilograms are aligned using the coshift algorithm and mathematically fitted using Classical Least Squares (CLS) to determine the mobility contributions from their precursor ions.Despite some limitations when studying low intensity ions and ions with similar ion mobility, CLS fitting improves the usage of IMS coupled with accurate mass spectrometry as a complementary tool in the study of MS fragmentation mechanisms and more notably, it offers an automatable and efficient alternative to MS3 experiments.

The Thermal and Mass Spectral Fragmentation of N-Butyl Thiolo-, Thiono-, and Dithio-Chloroformate

Thermal decomposition of n-butyl thiolochloroformate at 150°C follows a similar pattern to that reported previously for n-butyl chloroformate, to give butyl chloride which is largely rearranged to the s-butyl isomer. An ion-pair mechanism, involving 1,2- and 1,3-hydride shifts, is proposed. The less stable thiono- and dithio-chloroformates decompose to give lower yields of butyl chlorides (mainly without rearrangement) together with numerous other byproducts, indicating the operation of a more complex combination of reaction pathways. The mass spectra of all three thio compounds exhibit molecular ions; the most prominent fragment ions in their spectra are the n-butyl cation, and the radical cations COS+ • and CS2 + •. Numerous chlorine-containing ions of low intensity are also observed, and their mode of formation is discussed. GRAPHICAL ABSTRACT

Tilt Angle Generation in NLC on Homeotropic Polymer Surface with Ion Beam Irradiation as a Function of Incident Angle

We have studied the tilt angle generation on the homeotropic polyimide (PI) surface using a low intensity ion beam source as a function of incident angle. An excellent LC alignment of nematic liquid crystal (NLC) on the PI surface with ion beam exposure for all incident angles was observed. The tilt angle of NLC on the homeotropic PI surface for all incident angles was from 90 to 88 degree was observed. Also the tilt angle of NLC on the homeotropic PI surface with ion beam exposure of 400 eV had a tendency to increase as ion beam energy incident angle become more instance from 45 degree. Finally, a good LC alignment thermal stability on the homeotropic PI surface with ion beam exposure can be achieved.