In pursuit of resolution in time-of-flight mass spectrometry: A historical perspective

Ion Optical Optimization Method for an Ultrahigh Resolution Planar Multireflection Time-of-Flight Mass Analyzer Using the Hill Climbing Algorithm

A novel ion optical optimization method for planar multireflection time-of-flight mass spectrometry (MR-TOFMS) is introduced in this paper. The multiparameters of the gridless mirror model, including geometric and voltage parameters, are automatically optimized using a self-made program created in SIMION 8.1. Combining with the hill climbing algorithm and parallel computing technique, this method substantially enhances optimization efficiency and accuracy. The fitting results demonstrated that the ion optical performance of the gridless mirror reached up to fourth-order isochronicity with respect to the energy spread and third-order isochronicity with respect to the spatial and angular spread. As a result, the gridless mirror model achieved an aberration limit resolution of 1.7 million under realistic ion beam conditions. Due to constraints of periodic lenses, the aberration limit resolution of the planar MR-TOFMS was optimized to 600k. These results indicate that the hill climbing algorithm is an effective method to search the optimal solutions in complex ion optical systems.

Comparison of high-resolution mass spectrometry acquisition methods for the simultaneous quantification and identification of per- and polyfluoroalkyl substances (PFAS)

Simultaneous identification and quantification of per- and polyfluoroalkyl substances (PFAS) were evaluated for three quadrupole time-of-flight mass spectrometry (QTOF) acquisition methods. The acquisition methods investigated were MS-Only, all ion fragmentation (All-Ions), and automated tandem mass spectrometry (Auto-MS/MS). Target analytes were the 25 PFAS of US EPA Method 533 and the acquisition methods were evaluated by analyte response, limit of quantification (LOQ), accuracy, precision, and target-suspect screening identification limit (IL). PFAS LOQs were consistent across acquisition methods, with individual PFAS LOQs within an order of magnitude. The mean and range for MS-Only, All-Ions, and Auto-MS/MS are 1.3 (0.34-5.1), 2.1 (0.49-5.1), and 1.5 (0.20-5.1) pg on column. For fast data processing and tentative identification with lower confidence, MS-Only is recommended; however, this can lead to false-positives. Where high-confidence identification, structural characterisation, and quantification are desired, Auto-MS/MS is recommended; however, cycle time should be considered where many compounds are anticipated to be present. For comprehensive screening workflows and sample archiving, All-Ions is recommended, facilitating both quantification and retrospective analysis. This study validated HRMS acquisition approaches for quantification (based upon precursor data) and exploration of identification workflows for a range of PFAS compounds.

Modeling Known Sources of Mass Calibration Deviations in High Resolution ToF MS

Modern time-of-flight mass spectrometer instruments exhibit excellent mass accuracy in the parts per billion range. At this level, mass calibration methods should consider potential distortions in the basic calibration. Factors which can cause distortions are to be under control. We have analytically modeled and numerically verified the influence of the main causes of mass calibration distortions, including the uncompensated dependence of flight time on the starting position, spatial gradient of the accelerating field, and overshooting at the rising edge of the accelerating pulse. Additionally, the relativity correction has been taken into account.

Advances in high-resolution mass spectrometry techniques for analysis of high mass-to-charge ions

A major challenge in modern mass spectrometry (MS) is achieving high mass resolving power and accuracy for precision analyses in high mass-to-charge (m/z) regions. To advance the capability of MS for increasingly demanding applications, understanding limitations of state-of-the-art techniques and their status in applied sciences is essential. This review summarizes important instruments in high-resolution mass spectrometry (HRMS) and related advances to extend their working range to high m/z regions. It starts with an overview of HRMS techniques that provide adequate performance for macromolecular analysis, including Fourier-transform, time-of-flight (TOF), quadrupole-TOF, and related data-processing techniques. Methodologies and applications of HRMS for characterizing macromolecules in biochemistry and material sciences are summarized, such as top-down proteomics, native MS, drug discovery, structural virology, and polymer analyses.

Ion detector of time-of-flight mass spectrometer with registration of leading and trailing edges

The accuracy of the ion flight time measurement in the time-of-flight mass spectrometer is critical to achieving high resolution. The pulse amplitude variation of the detector pulses leads to the registration time spread at a given pulse detection threshold. This time spread can be eliminated by determining the position of the pulse apex. To determine the position of the pulse apex, the output of the ion detector is fed simultaneously to the two channels of the time-to-digital converter. In this case, the first channel is set to register the leading edge, and the second channel is set to register the trailing edge of the pulse. Using a simple processing of the received data, the position of the pulse tip is determined. Thus, the dependence of the temporal position of the peak on the pulse amplitude is largely eliminated. Examples are given, and the efficiency of using this algorithm to increase the resolution of time-of-flight mass spectral peak registration is demonstrated.

Two-step particle swarm optimization algorithm for effective deconvolution and resolution enhancement of various overlapping peaks

RATIONALE

The existing particle swarm optimization (PSO) algorithms are only effective in deconvoluting the overlapping peaks in ion mobility spectra with fewer than four component peaks, which limits the applicability of these algorithms.

METHODS

A high-performance two-step particle swarm optimization (TSPSO) algorithm was developed. Compared to the existing PSO algorithms, TSPSO can narrow the search ranges of all coefficients for the overlapping peaks through Gaussian model calculation, and thus can deconvolute various overlapping peaks with high accuracy, even for 30-component overlapping peaks. In addition, the TSPSO could be further applied to enhance the resolution of the spectra by narrowing the peak widths after the peak deconvolution.

RESULTS

Simulated overlapping peaks were first used to evaluate the performance of TSPSO as compared to the dynamic inertia weight particle swarm optimization (DIWPSO) algorithm. The results showed that the profiles of the peaks deconvoluted by using TSPSO were more consistent with the original ones. The fitness values and the standard deviations of the fitness values from TSPSO were also at least an order of magnitude less than those from DIWPSO. By applying TSPSO, the overlapping peaks from both mass spectrometry (MS) and field asymmetric waveform ion mobility spectrometry (FAIMS) spectra can also be well deconvoluted. In addition, the resolutions of the MS and FAIMS spectra can be effectively enhanced after peak deconvolution. The enhanced spectra matched excellently with the experimental ones acquired at high-resolution modes.

CONCLUSIONS

The experiment results convincingly demonstrate that the TSPSO algorithm is capable of both deconvoluting complex overlapping peaks and enhancing the spectrum resolution with high accuracy.

Time-of-flight mass spectrometer for diagnostics of continuous plasma flow

This paper describes a version of the time-of-flight mass spectrometer based on a modified two-field acceleration approach of Wiley and McLaren. The aim of the device is a diagnostic of continuous plasma flow. The acceleration scheme idea, the construction of the spectrometer, and results of testing in plasma flow of Gd and CeO₂ generated by vacuum arc discharge are described. The instrument function of the spectrometer was measured, and its mass resolution was evaluated as ∼20. With the use of the instrument function, how to interpret the registered signal in the case of intersection of mass peaks was suggested. The presented device has a simple construction and relatively low values of applied acceleration voltages, so it has fewer requirements in manufacturability and cost.

Development of a portable time-of-flight mass spectrometer prototype using a cold electron source

Fundamental obstacles toward the development of a portable time-of-flight mass spectrometer (TOF MS) are ionization sources and vacuum systems. To overcome these, a cold electron source (CES) and a pulse valve are introduced in this study to examine the possibility of developing a portable TOF MS. The CES is developed using a microchannel plate electron multiplier radiated by ultraviolet photons from a light-emitting diode. The CES is controlled using short pulses to generate accelerated electrons that ionize a substrate surface. A 10 ns CES pulse produces an electron flux density of 10¹³ to 10¹⁴ m^-2 on the surface, and the short pulse minimizes the ionization time such that the resolution limit associated with a short drift tube is overcome. In addition, the injected 0.05 m³ quantitative sample reduces the vacuum exhaust load, and simultaneously, it is possible to temporarily form layers of the target molecules on the substrate. The possibility of immediate measurement by directly injecting benzene at ambient pressure was verified through repeated measurements; therefore, it is technically possible to use a CES to allow for a highly compact (and portable) TOF MS.

Simultaneous on-line vacuum single- and multi-photon ionization on an orthogonal acceleration time-of-flight mass spectrometer platform

New instrumental development for robust process monitoring with two soft ionization methods working in parallel.

Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives

Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.

Current Progress in Femtosecond Laser Ablation/Ionisation Time-of-Flight Mass Spectrometry

The last decade witnessed considerable progress in the development of laser ablation/ionisation time-of-flight mass spectrometry (LI-TOFMS). The improvement of both the laser ablation ion sources employing femtosecond lasers and the method of ion coupling with the mass analyser led to highly sensitive element and isotope measurements, minimisation of matrix effects, and reduction of various fractionation effects. This improvement of instrumental performance can be attributed to the progress in laser technology and accompanying commercialisation of fs-laser systems, as well as the availability of fast electronics and data acquisition systems. Application of femtosecond laser radiation to ablate the sample causes negligible thermal effects, which in turn allows for improved resolution of chemical surface imaging and depth profiling. Following in the footsteps of its predecessor ns-LIMS, fs-LIMS, which employs fs-laser ablation ion sources, has been developed in the last two decades as an important method of chemical analysis and will continue to improve its performance in subsequent decades. This review discusses the background of fs-laser ablation, overviews the most relevant instrumentation and emphasises their performance figures, and summarizes the studies on several applications, including geochemical, semiconductor, and bio-relevant materials. Improving the chemical analysis is expected by the implementation of laser pulse sequences or pulse shaping methods and shorter laser wavelengths providing current progress in mass resolution achieved in fs-LIMS. In parallel, advancing the methods of data analysis has the potential of making this technique very attractive for 3D chemical analysis with micrometre lateral and sub-micrometre vertical resolution.

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.

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.

Challenges in polysorbate characterization by mass spectrometry

Polysorbates are used in a variety of applications over a wide range of markets. Simple in concept, these products are complex in actual composition. Mass spectrometry and related techniques have been effectively used to characterize these products, from the major components to the minor residual production byproducts and degradation species. In this paper we review the use of MALDI-MS, LC/MS, GC/MS, and SFC/MS in the analysis of these materials. The wealth of information provided by MALDI is presented, using Polysorbate 60 as an example. Limitations are described, with the impact of matrix selection and cationization agent demonstrated. Furthermore, unique challenges of MALDI analysis of Polysorbate 80 are shown. Polysorbates have been extensively analyzed, especially by the biopharmaceutical industry, to better understand the impact of various grades of purity and manufacture on the stability of formulations. Using Polysorbate 80 as an example, we illustrate some of the more advanced techniques used to more fully characterize these complex molecules using high-resolution LC/MS and LC/MS/MS. Finally, the use of other techniques (such as GC/MS and SFC/MS) is briefly reviewed.

Effects of chromatographic conditions and mass spectrometric parameters on the ionization and fragmentation of triterpene saponins of Ilex asprella in liquid chromatography-mass spectrometry analysis

High performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (HPLC-QTOF-MS) is widely used to qualitatively characterize the chemical profiles of herbal medicines, in which the generated adducts and fragments are crucial for confirming molecular ion (deprotonated/protonated ion) and deducing structure of detected components. However, how chromatographic and mass spectrometric (LC-MS) conditions/parameters affect the quantity and intensity of adducts and fragments of detected components is scarcely concerned. In present study, three types of triterpene saponins from the root of Ilex asprella (RIA) were selected as a case study to systematically investigate the effects of LC/MS conditions/parameters on their ionization and fragmentation, so as to obtain higher intensity (higher detection sensitivity) and quantity (rich information) of adducts and fragments for the characterization of components in RIA. It was found that for LC conditions, methanol as organic phase was more benefit for generating more adducts with higher intensity; formic acid as a modifier suppressed the formation of [M-2H]^2-, thus promoted the generation of other types of adducts at lower concentration but inhibited the generation when the concentration exceeded 0.1%. MS parameters affect scarcely the quantity but mainly intensity of adducts, cone voltage, source temperature and desolvation gas flow have relatively higher impacts when compared with other parameters. Collision energy affected both quantity and intensity of fragments. MS parameters at the medium value largely increased the quantity and intensity of adducts and fragments. Three-types of triterpene saponins presented structurally specific ionization and fragmentation due to their amounts of acidic substitutes. A total of 55 components were detected and definitely or tentatively identified in RIA under the optimized LC-MS conditions, among which 35 triterpene saponins were firstly discovered. This is the first report that proposes and validates a systematic approach for assessing the effects of LC/MS conditions/parameters on the ionization and fragmentation of analytes, which could be helpful for the optimization of LC-MS conditions for effective chemical profiling analysis of herbal medicines.

Experimental Characterization of Protein Complex Structure, Dynamics, and Assembly

Experimental methods for the characterization of protein complexes have been instrumental in achieving our current understanding of the protein universe and continue to progress with each year that passes. In this chapter, we review some of the most important tools and techniques in the field, covering the important points in X-ray crystallography, cryo-electron microscopy, NMR spectroscopy, and mass spectrometry. Novel developments are making it possible to study large protein complexes at near-atomic resolutions, and we also now have the ability to study the dynamics and assembly pathways of protein complexes across a range of sizes.

Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data

Time of flight secondary ion mass spectrometry (ToF-SIMS) is a powerful surface-sensitive characterization tool allowing the imaging of chemical properties over a wide range of organic and inorganic material systems. This technique allows precise studies of chemical composition with sub-100-nm lateral and nanometer depth spatial resolution. However, comprehensive interpretation of ToF-SIMS results is challenging because of the very large data volume and high dimensionality. Furthermore, investigation of samples with pronounced topographical features is complicated by systematic and measureable shifts in the mass spectrum. In this work we developed an approach for the interpretation of the ToF-SIMS data, based on the advanced data analytics. Along with characterization of the chemical composition, our approach allows extraction of the sample surface morphology from a time of flight registration technique. This approach allows one to perform correlated investigations of surface morphology, biological function, and chemical composition of Arabidopsis roots.

Time-of-flight mass spectrometry: Introduction to the basics

The intention of this tutorial is to introduce into the basic concepts of time-of-flight mass spectrometry, beginning with the most simple single-stage ion source with linear field-free drift region and continuing with two-stage ion sources combined with field-free drift regions and ion reflectors-the so-called reflectrons. Basic formulas are presented and discussed with the focus on understanding the physical relations of geometric and electric parameters, initial distribution of ionic parameters, ion flight times, and ion flight time incertitude. This tutorial is aimed to help the applicant to identify sources of flight time broadening which limit good mass resolution and sources of ion losses which limit sensitivity; it is aimed to stimulate creativity for new experimental approaches by discussing a choice of instrumental options and to encourage those who toy with the idea to build an own time-of-flight mass spectrometer. Large parts of mathematics are shifted into a separate chapter in order not to overburden the text with too many mathematical deviations. Rather, thumb-rule formulas are supplied for first estimations of geometry and potentials when designing a home-built instrument, planning experiments, or searching for sources of flight time broadening. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:86-109, 2017.

Exploration of metabolite signatures using high-throughput mass spectrometry coupled with multivariate data analysis

Disease impacts important metabolic pathways and the alteration of metabolites may serve as a potential biomarker for early-stage diagnosis.

Distance-of-Flight Mass Spectrometry: What, Why, and How?

Distance-of-flight mass spectrometry (DOFMS) separates ions of different mass-to-charge (m/z) by the distance they travel in a given time after acceleration. Like time-of-flight mass spectrometry (TOFMS), separation and mass assignment are based on ion velocity. However, DOFMS is not a variant of TOFMS; different methods of ion focusing and detection are used. In DOFMS, ions are driven orthogonally, at the detection time, onto an array of detectors parallel to the flight path. Through the independent detection of each m/z, DOFMS can provide both wider dynamic range and increased throughput for m/z of interest compared with conventional TOFMS. The iso-mass focusing and detection of ions is achieved by constant-momentum acceleration (CMA) and a linear-field ion mirror. Improved energy focus (including turn-around) is achieved in DOFMS, but the initial spatial dispersion of ions remains unchanged upon detection. Therefore, the point-source nature of surface ionization techniques could put them at an advantage for DOFMS. To date, three types of position-sensitive detectors have been used for DOFMS: a microchannel plate with a phosphorescent screen, a focal plane camera, and an IonCCD array; advances in detector technology will likely improve DOFMS figures-of-merit. In addition, the combination of CMA with TOF detection has provided improved resolution and duty factor over a narrow m/z range (compared with conventional, single-pass TOFMS). The unique characteristics of DOFMS can enable the intact collection of large biomolecules, clusters, and organisms. DOFMS might also play a key role in achieving the long-sought goal of simultaneous MS/MS. Graphical Abstract ᅟ.