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The two-dimensional ion trap. The four quadrupolar rods of the 2D ion trap are segmented thrice, with each set of segments bearing DC axial trapping voltages to create a potential well to confine ion packets. AC applied to all four rods and all three segments, called the “main RF”, acts as a radially-confining force. The linear design and lack of force in the axial dimension allows ions to spread out, offering greater ion storage capacity than the 3D trap.
Source publication
Mass spectrometry (MS) is widely recognized as a powerful analytical tool for molecular research. MS is used by researchers around the globe to identify, quantify, and characterize biomolecules like proteins from any number of biological conditions or sample types. As instrumentation has advanced, and with the coupling of liquid chromatography (LC)...
Contexts in source publication
Context 1
... three dimensional traps, which are used less often, electromagnetic forces act on the ions in the x, y, and z dimensions: x and y are the radial dimensions, and z is the axial dimension (Figure 3). In the more common two dimensional trap, also known as the linear ion trap (LIT), forces act on the ions only in the x and y dimensions; this allows them to spread out axially and increases the ion capacity compared to three dimensional traps ( Figure 4). AC is applied to pairs of electrodes at equal amplitude and opposite sign at a frequency of 1.2 MHz, which is within the RF range. ...
Context 2
... is applied to pairs of electrodes at equal amplitude and opposite sign at a frequency of 1.2 MHz, which is within the RF range. This AC is referred to as the "main RF" and serves to confine the ions radially, like ink in a pen is confined radially within a plastic tube ( Figure 4). Axially, the ions are confined by the creation of a potential well generated by DC offsets; the four ion trap electrodes are cut into three sections and each of these sections has their own DC applied to them ( Figure 4). ...
Context 3
... AC is referred to as the "main RF" and serves to confine the ions radially, like ink in a pen is confined radially within a plastic tube ( Figure 4). Axially, the ions are confined by the creation of a potential well generated by DC offsets; the four ion trap electrodes are cut into three sections and each of these sections has their own DC applied to them ( Figure 4). Since it is more common and has an increased ion storage capacity, the two dimensional trap will be the subject of the remaining discussion on ion trap functionality. ...
Context 4
... ion trap scanning employs "resonance ejection," a process which depends on the application of an additional AC to the exit rods within the trap. The exit rods are the two quadrupolar rods that contain slits cut through the rods for ions to pass out ( Figure 4). The exit rod AC is applied in equal amplitude but opposite phase to each rod. ...
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Citations
... In this case, the dynamics are fully determined by several parameters: a, q and the damping rate γ (see below). Moreover, the trap geometry and field strength are also determined from the values of these parameters [4,18,19]. Motivated by these researches, in this work, we extended the single particle Mathieu equation to the many-body Mathieu equation, and study its dynamics based on classical equations. This work is organized in the following way. ...
Recently, large-scale trapped ion systems have been realized in experiments for quantum simulation and quantum computation. They are the simplest systems for dynamical stability and parametric resonance. In this model, the Mathieu equation plays the most fundamental role for us to understand the stability and instability of a single ion. In this work, we investigate the dynamics of trapped ions with the Coulomb interaction based on the Hamiltonian equation. We show that the many-body interaction will not influence the phase diagram for instability. Then, the dynamics of this model in the large damping limit will also be analytically calculated using few trapped ions. Furthermore, we find that in the presence of modulation, synchronization dynamics can be observed, showing an exchange of velocities between distant ions on the left side and on the right side of the trap. These dynamics resemble to that of the exchange of velocities in Newton's cradle for the collision of balls at the same time. These dynamics are independent of their initial conditions and the number of ions. As a unique feature of the interacting Mathieu equation, we hope this behavior, which leads to a quasi-periodic solution, can be measured in current experimental systems. Finally, we have also discussed the effect of anharmonic trapping potential, showing the desynchronization during the collision process. It is hopped that the dynamics in this many-body Mathieu equation with damping may find applications in quantum simulations. This model may also find interesting applications in dynamics systems as a pure mathematical problem, which may be beyond the results in the Floquet theorem.
... Overall, the mass resolving power in OrbiTrap™ MS (m/Δm > 240 000) is typically higher than the highest available mass resolving power in ToF MS (m/Δm > 30 000), resulting in more accurate mass calibration and signal assignment. 22,26,27 C. Method-specific characteristics ...
... © Author(s) 202326 July 2023 20:24:55 ...
The purpose of this Tutorial is to highlight the suitability of time-of-flight secondary ion mass spectrometry (ToF-SIMS) and OrbiTrap™ SIMS (Orbi-SIMS) in bone research by introducing fundamentals and best practices of bone analysis with these mass spectrometric imaging (MSI) techniques. The Tutorial includes sample preparation, determination of best-suited measurement settings, data acquisition, and data evaluation, as well as a brief overview of SIMS applications in bone research in the current literature. SIMS is a powerful analytical technique that allows simultaneous analysis and visualization of mineralized and nonmineralized bone tissue, bone marrow as well as implanted biomaterials, and interfaces between bone and implants. Compared to histological staining, which is the standard analytical procedure in bone research, SIMS provides chemical imaging of nonstained bone sections that offers insights beyond what is conventionally obtained. The Tutorial highlights the versatility of ToF- and Orbi-SIMS in addressing important questions in bone research. By illustrating the value of these MSI techniques, it demonstrates how they can contribute to advance progress in bone research.
... Current mass spectrometers may also combine quadrupoles with other mass analyzers, using quadrupoles as mass filters that can selectively identify ions of chosen m/z and direct them to the mass analyzer or detector. 36 For example, the ThermoFisher Scientific Q Exactive MS combines both quadrupole and orbitrap mass analyzers. 37 Overall, most modern instrumentation is more than capable of successfully performing sensitive proteomics in skeletal muscle. ...
Acute exercise and chronic exercise training elicit beneficial whole‐body changes in physiology that ultimately depend on profound alterations to the dynamics of tissue‐specific proteins. Since the work accomplished during exercise owes predominantly to skeletal muscle, it has received the majority of interest from exercise scientists that attempt to unravel adaptive mechanisms accounting for salutary metabolic effects and performance improvements that arise from training. Contemporary scientists are also beginning to use mass spectrometry‐based proteomics, which is emerging as a powerful approach to interrogate the muscle protein signature in a more comprehensive manner. Collectively, these technologies facilitate the analysis of skeletal muscle protein dynamics from several viewpoints, including changes to intracellular proteins (expression proteomics), secreted proteins (secretomics), post‐translational modifications as well as fiber‐, cell‐, and organelle‐specific changes. This review aims to highlight recent literature that has leveraged new workflows and advances in mass spectrometry‐based proteomics to further our understanding of training‐related changes in skeletal muscle. We call attention to untapped areas in skeletal muscle proteomics research relating to exercise training and metabolism, as well as basic points of contention when applying mass spectrometry‐based analyses, particularly in the study of human biology. We further encourage researchers to couple the hypothesis‐generating and descriptive nature of omics data with functional analyses that propel our understanding of the complex adaptive responses in skeletal muscle that occur with acute and chronic exercise.
... Once these gas phase ions have been created, they are manipulated and isolated by the use of a voltage gradient, ion optics, and an increasing vacuum. 108 Several common mass analyzers include low resolution (±1 Dal measurements) quadrupoles and ion traps, medium resolution time of flight (ToF), and high resolution Fourier-transform ion cyclotron resonance magnets (FTICR) and orbitraps. Most mass spectrometers also have the ability to fragment ions using collisions of ions with each other as well as with neutral gases (collision induced dissociation (CID) and higher energy collision-induced dissociation (HCD), anion radicals (electron transfer or capture dissociation, ETD/ECD), or the application of UV light (UV photon dissociation). ...
... The set of m/z fragments can then be used to reassemble a larger structure. 108 One of the challenges of utilizing mass spectrometry to assign either glycan (removed from protein) or glycopeptide structures is that differing fragmentation techniques and energies are necessary to create fragments of cross-ring, internal glycan, glycan-peptide, and peptide or protein sequences. 106,109 Ion Mobility Ion mobility is an analytical technique where gas-phase ions are separated as they move through an applied electrical field. ...
Glycosylation has a clear role in cancer initiation and progression, with numerous studies identifying distinct glycan features or specific glycoproteoforms associated with cancer. Common findings include that aggressive cancers tend to have higher expression levels of enzymes that regulate glycosylation as well as glycoproteins with greater levels of complexity, increased branching, and enhanced chain length1. Research in cancer glycoproteomics over the last 50-plus years has mainly focused on technology development used to observe global changes in glycosylation. Efforts have also been made to connect glycans to their protein carriers as well as to delineate the role of these modifications in intracellular signaling and subsequent cell function. This review discusses currently available techniques utilizing mass spectrometry-based technologies used to study glycosylation and highlights areas for future advancement.
... Метод масс-спектрометрии применяется несколько десятилетий в большинстве областей человеческой деятельности, где требуется качественный или количественный анализ вещества [3][4][5], и имеет свои устоявшиеся ниши, как в клинической лабораторной диагностике, так и в сфере фундаментальных или прикладных исследований. Времяпролётная масс-спектрометрия с матрично-активированной лазерной десорбцией/ионизацией (MALDI-ToF МС) нашла наибольшее применение в медицинских учреждениях, прежде всего, как инструмент скрининга большого количества образцов культур микроорганизмов, выделенных из клинического материала (кровь, раневое отделяемое). ...
It is difficult to overestimate the urgency of the problem of well-timed diagnosis of viral infections. According to the WHO, dozens of outbreaks of viral diseases are recorded annually, both in developing and developed countries. Moreover, the seasonal flu virus alone is capable of infecting up to 20% of the population, even in European countries with a high level of medicine. And the annual number of deaths due to viral infections, according to official statistics, exceeds 600 thousand people around the world. That’s why the provision of a reliable and fairly rapid diagnosis of viruses, along with subsequent therapy, makes a significant contribution to reducing the incidence of mortality. Despite the fact that PCR-based methods currently remain the most common method for identifying viruses in clinical practice, as recent experience shows, in addition to the already known disadvantages, in the event of large outbreaks, such test systems may simply not be in the required amount. In this regard, it is necessary to supplement and improve the existing tools for identification and research of clinically significant viruses. The MALDI-TOF mass spectrometry method combines a degree of accuracy and versatility, sufficient both for the identification of clinical strains isolated from patients, and for the study of the phenotypic properties of viruses in research laboratories and centers. This article presents and summarizes the main data on the existing or potential application of the method of time-of-flight mass spectrometry with matrix-associated laser desorption / ionization for the identification or study of viruses.
... La résolution de l'analyse est directement dépendante du temps d'acquisition du courant induit par les ions. Les trappes orbitales sont des analyseurs fournissant une très haute résolution pour l'identification de protéines intactes ou de peptides en protéomique[137]. ...
... Schémas représentant la structure et le fonctionnement d'une trappe orbitale. D'aprèsSavaryn et al.[137] ...
Les protéines thérapeutiques occupent une place déterminante dans le traitement de pathologies graves tels les cancers, l'hémophilie ou les déficits immunitaires, et constituent souvent l'unique alternative thérapeutique disponible. La chromatographie liquide et la spectrométrie de masse constituent les méthodes de référence pour la caractérisation structurale des protéines. Cette thèse rassemble des travaux portant sur le développement de méthodes de chromatographie liquide couplées à la spectrométrie de masse pour la caractérisation de différents types de protéines thérapeutiques. La première partie des résultats décrit le développement de méthodes de chromatographie liquide de phase inverse couplées à la spectrométrie de masse pour la caractérisation de modifications post-traductionnelles d'anticorps polyclonaux, telles que l'oxydation et la glycation, et permettant l'évaluation de l'intégrité de ponts disulfures d'anticorps monoclonaux. La seconde partie présente le développement de méthodes de spectrométrie de masse native pour la caractérisation des isoformes d'anticorps monoclonaux et de l'albumine, notamment par le couplage de méthodes de chromatographie d'échanges d'ions à la spectrométrie de masse. En dernier lieu, la relation structure/fonction entre une protéine thérapeutique et un récepteur est évaluée par l'étude de l'impact des modifications post-traductionnelles de l'albumine sur son interaction au récepteur néo natal Fc et l'impact de la lysine en position C-terminale d'un anticorps monoclonal sur son interaction aux récepteurs néo natal Fc et FcγRIIIa.
... Generally, the cations generated, also called precursors, are collected in an ion trap, filtered with a quadrupole (Q) mass filter, or directly by ion optics into a high-resolution mass analyzer. These precursor ions are subsequent fragmented, often by collisional or electron-based dissociation, within the same spectrometer for identification and characterization (Savaryn, Toby, & Kelleher, 2016). This point in the analytical process is essential since it will directly influence the identification of proteoforms. ...
... The highest ion transmission efficiency is expected at DC= 0 (only RF-mode), however, in order to reduce noise and enhance sensitivity and speed, the Oct 2 DC voltage is set to a minimum of 1.70 V, according to the manual. For more detailed information, how the applied DC and RF voltage effect stable ion trajectories the reader is referred to the literature [28]. ...
... The difference in ion yields and IR/MR remains constant, the difference being more pronounced for the analyte mixtures of lower m/z (due to Cap Exit, see below). At Oct 2 DC > 2.2 V, the absolute intensities for both analytes decrease since the region of stability become narrower [28], while IR/MR increases. Therefore, an Oct 2 DC voltage of 1.74 V and an Oct RF voltage of 200 Vpp were selected as settings for all mixtures. ...
The hydroxyethyl substitution along and among the polymer chains of respective cellulose ethers (HEC and HEMC) can be analyzed by ESI-IT-MS after permethylation of the free OH-groups, partial hydrolysis, and m ABA labeling. This method requires the correct quantification of the molar ratios of the constituents belonging to a particular degree of polymerization (DP) with respect to their numbers of MeOEt and Me groups without any discrimination along the MS analysis pathway. The influence of the chemistry on the ionization and the impact of the voltages controlling the ion transport (Cap Exit, Octopoles) and the ion storage efficiency (Trap Drive, TD) on a relative quantification were studied using binary equimolar mixtures of cellobiose with increasing number of methoxyethyl and decreasing number of methyl groups (Δ m/z 88, 2× MeOEt). No suppression effects were observed in concentration-dependent measurements. Choice of Cap Exit is especially crucial for low m/z with less MeOEt residues. An equation describing the relationship between Oct 2 DC, m/z , and TD max (TD at maximum intensity) was established from the experimental data and applied to calculate TD max for higher DPs (larger COS). Optimized conditions allowed to determine the correct molar ratio of binary mixtures. Measurements of overlapping m/z segments and subsequent interrelation of the data gave complete substitution profiles for MeOEt/Me celluloses in accordance with reference data. The study generally makes aware of potential erroneous quantification in ESI-IT-MS analysis using internal standards of similar chemistry or in relative quantification of analytes, even for those with related structures.
Graphical abstract
... It suggests a higher fragmentation ability of the IT where the resonance energies applied, and maybe more importantly the time spent in resonance in the IT, are sufficient to break up stable aromatic structures 19 . Moreover, the pressure in the space where the CID takes place is also much higher in the ITQ (40 mtorr) than in QqQs (1.5 mtorr), which could lead to more collisions happening. ...
Rationale
Multiple Reaction Monitoring (MRM) is a sensitive and selective detection mode for target trace-level analysis. However, it requires the fragmentation of labile bonds which are not present in molecules such as Polycyclic Aromatic Hydrocarbons (PAHs) and their heterocyclic derivatives (PANHs, PASHs).
Methods
We present the application of an alternative MS/MS mode called “pseudo-MRM” for the GC-MS/MS analysis of Polycyclic Aromatic Compounds (PACs). This mode is based on the monitoring of transitions with no mass loss between the parent and the product ion. Pseudo-MRM peak areas were compared with those of classic MRM on three different mass spectrometers: two Triple Quadrupoles and an Ion Trap.
Results
For all non-polar PACs studied here (PAHs, PANHs and PASHs), the pseudo-MRM transition was always the most intense. The classic MRM transitions exhibited peak areas 2 to 5 times lower. On the contrary, for the functionalized PACs (oxygenated and nitrated PAHs), classic MRM was favored over pseudo-MRM.
These observations were confirmed on two Triple Quadrupoles (QqQs), and the real-world applicability of pseudo-MRM on QqQs was validated by the successful analysis of Diesel PM. However, a comparison with an Ion Trap showed that pseudo-MRM was never favored on the Ion Trap, which caused fragmentation of non-polar PACs in MS/MS.
Conclusions
The results of this study show an important gain in sensitivity when using pseudo-MRM instead of MRM for non-polar PACs on Triple Quadrupole instruments. The selectivity of MRM is preserved in pseudo-MRM by applying non-zero collision energies to which only these non-polar PACs are resistant, not the isobaric interferences. No interference issue was observed when analyzing Diesel PM, a complex matrix, with our pseudo-MRM method. Therefore, we advise for a broader use of this MS/MS mode for trace-level determination of non-polar PAHs.
... In fact, the MS7 spectrum ( Figure 3) was found to contain a dominant fragment ion at m/z 444.07, which differs by approximately 0.11 Dalton from its theoretical m/z value. Because of the low resolution of ion trap mass spectroscopy (ITMS), the ion m/z values had a relatively high mass error, which differs from the MS1 and MS2 analyses performed via Fourier transform mass spectrometry (FTMS) [37,38]. As shown in Figure 3, the characteristic fragment ion at m/z 444.07 was produced by m/z 647.93 (theoretical m/z: 648.28) via the loss of Man as a 'by' ion (the green circle). ...
Bisecting N-acetylglucosamine (GlcNAc), a GlcNAc linked to the core β-mannose residue via a β1,4 linkage, is a special type of N-glycosylated modification that has been reported to be involved in various biological processes, such as cell adhesion and fetal development. This N-glycan structure was found to be abundant in human trophoblasts; it was postulated to be resistant to natural killer cell-mediated cytotoxicity, enabling a mother to nourish a fetus without rejection. In this study, we hypothesized that the human amniotic membrane, which serves as the last barrier for the fetus, may also express bisected type glycans. To test this hypothesis, glycomic analysis of the human amniotic membrane was performed, and bisected N-glycans were detected. Further, our proteomic data, which had been previously employed to explore human missing proteins, were analyzed and the presence of bisecting GlcNAc peptides was confirmed. A total of 41 glycoproteins with 43 glycopeptides were found to possess a bisecting GlcNAc, and 25 of these glycoproteins were reported to exhibit this type of modification for the first time. These results provide insights for implementing bisecting GlcNAc modification in the human amniotic membrane, and can be beneficial to functional studies on glycoproteins with bisecting GlcNAc modifications and functional studies on immune suppression in human placenta (raw data: https://db.cngb.org/search/project/CNP0001701/).
