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The rapidly increasing adoption of high-resolution accurate-mass methods in analytical laboratories has fueled demand for instruments that combine high performance and reliability with small size and greater ease-of-use. This paper presents the major design principles that are driving the evolution of the hybrid quadrupole-Orbitrap instrument architecture to enable a greater range of applications and users. These principles may be summarized as follows: better usage of physical space and better access for service by means of size reduction of pumping and ion optics; expanded use of technologies from electronics in ion-optical design; flexibility in performance via modularity of design of the hardware and software components; and, harmonization of interfaces with other instruments to facilitate sharing and transferability of analytical workflows. The design of a novel family of hybrid mass spectrometers is described in detail, and performance evaluation is carried out on a wide variety of samples for its three representatives: the Orbitrap Exploris 120, Orbitrap Exploris 240 and Orbitrap Exploris 480 mass spectrometers. The new instrument family is shown to offer compelling potential not only for high-end proteomics and biopharmaceutical applications, but also for screening, trace, targeted and clinical analysis by liquid chromatography/mass spectrometry methods.

The measurement of collision cross sections (CCS) offers supplemental information about sizes and conformations of ions beyond mass analysis alone. We have previously shown that CCSs can be determined directly from the time-domain transient decay of ions in an Orbitrap mass analyzer as ions oscillate around the central electrode and collide with neutral gas, thus removing them from the ion packet. Herein, we develop the soft sphere collision model, thus deviating from prior FT-MS CCS hard sphere model, to determine CCSs as a function of center-of-mass collision energy in the Orbitrap analyzer. With this model, we aim to increase the upper mass limit of CCS measurement for native-like proteins, characterized by low charge states and presumed to be in more compact conformations. We also combine CCS measurements with collision inducing unfolding and MS/MS experiments to monitor protein unfolding and disassembly of protein complexes and measure CCSs of ejected monomers from protein complexes.

Measurement of collision cross section (CCS), a parameter reflecting an ion's size and shape, alongside high-resolution mass analysis extends the depth of molecular analysis by providing structural information beyond molecular mass alone. Although these measurements are most commonly undertaken using a dedicated ion mobility cell coupled to a mass spectrometer, alternative methods have emerged to extract CCSs directly by analysis of the decay rates of either time-domain transient signals or the FWHM of frequency domain peaks in FT mass analyzers. This information is also accessible from FTMS mass spectra obtained in commonly used workflows directly without the explicit access to transient or complex Fourier spectra. Previously, these experiments required isolation of individual charge states of ions prior to CCS analysis, limiting throughput. Here we advance Orbitrap CCS measurements to more users and applications by determining CCSs from commonly available mass spectra files as well as estimating CCS for multiple charge states simultaneously and showcase these methods by the measurement of CCSs of fragment ions produced from collisional activation of proteins.

© 2017 Nature America, Inc., part of Springer Nature. All rights reserved. We report the development of a 3D OrbiSIMS instrument for label-free biomedical imaging. It combines the high spatial resolution of secondary ion mass spectrometry (SIMS; under 200 nm for inorganic species and under 2 μm for biomolecules) with the high mass-resolving power of an Orbitrap (>240,000 at m/z 200). This allows exogenous and endogenous metabolites to be visualized in 3D with subcellular resolution. We imaged the distribution of neurotransmitters - gamma-aminobutyric acid, dopamine and serotonin - with high spectroscopic confidence in the mouse hippocampus. We also putatively annotated and mapped the subcellular localization of 29 sulfoglycosphingolipids and 45 glycerophospholipids, and we confirmed lipid identities with tandem mass spectrometry. We demonstrated single-cell metabolomic profiling using rat alveolar macrophage cells incubated with different concentrations of the drug amiodarone, and we observed that the upregulation of phospholipid species and cholesterol is correlated with the accumulation of amiodarone.

This chapter discusses fundamentals of the Orbitrap™ mass spectrometry—the use of a purely electrostatic ion trap with harmonic properties to store ions and analyze their mass-to-charge distributions. The first section demonstrates principles of ion confinement in the quadro-logarithmic electrostatic field, where the ions perform hundreds of thousands of oscillations without losing their common phase. The discussion covers practical aspects of ion injection into the trap and the image current detection. The subsequent section introduces the reader to the Orbitrap aberration theory, gives a classification of electric field perturbations, and outlines the compensation methods. The next section concerns signal processing methods of the detected transients and covers both the traditional Fourier transform approaches and super-FT resolving methods. The chapter concludes with the overview of historical milestones of the Orbitrap technology and selected applications.

The paper presents main peculiarities of implementation and testing of an algorithm based on the variational approach to the problem of simulating the stationary distributions of ions in the radiofrequency, low-vacuum ion traps with taking into consideration the Coulomb interaction and interaction with buffer gas. A good agreement between the results of numerical modeling and analytical results obtained earlier by other authors for simpler models is attained. The employment of the software that has been developed in the course of this work enables studying the structure of ion ensembles in the radiofrequency ion traps of different types and obtaining the results being of interest for high-resolution mass spectrometry. The algorithm allows a natural generalization to three-dimensional case.

The paper deals with space-charge interactions in the ion population trapped in the Orbitrap[Formula: see text] mass analyzer where the ions perform multiple quasi-harmonic oscillations in the axial direction. The many-particle problem for interacting ions is mathematically complicated and its solution, even numerical, is obstructed by the required precision of one per million to be maintained on a large number [Formula: see text] of oscillation periods. We develop a perturbation method based on the Bogoliubov–Krylov–Mitropolsky theory and derive averaged Hamiltonian equations in perturbations, which describe the evolution of the ions’ oscillation amplitudes and phases in so-called “slow” time. This approach provides a semi-analytical comprehensive model of resonant and nonresonant space-charge effects and allows fast and accurate numerical computation. Practical mitigation strategies for most deteriorating space-charge effects like coalescence and frequency shifts are considered.

A popular method for peptide quantification relies on isobaric labeling such as tandem mass tags (TMT) which enables multiplexed proteome analyses. Quantification is achieved by reporter ions generated by fragmentation in a tandem mass spectrometer. However, with higher degrees of multiplexing, the smaller mass differences between the reporter ions increase the mass resolving power requirements. This contrasts with faster peptide sequencing capabilities enabled by lowered mass resolution on Orbitrap instruments. It is therefore important to determine the mass resolution limits for highly multiplexed quantification when maximizing proteome depth. Here we defined the lower boundaries for resolving TMT reporter ions with 0.0063 Da mass differences using an ultra-high-field Orbitrap mass spectrometer. We found the optimal method depends on the relative ratio between closely spaced reporter ions and that 64 ms transient acquisition time provided sufficient resolving power for separating TMT reporter ions with absolute ratio changes up to 16-fold. Furthermore, a 32 ms transient processed with phase-constrained spectrum deconvolution provides >50% more identifications with >99% quantified, but with a slight loss in quantification precision and accuracy. These findings should guide decisions on what Orbitrap resolution settings to use in future proteomics experiments relying on TMT reporter ion quantification with identical integer masses.

We demonstrate a method for determining the collision cross-sections (CCSs) of protein ions based on the decay rate of the time-domain transient signal from an Orbitrap mass analyzer. Multiply charged ions of ubiquitin, cytochrome c, and myoglobin were generated by electrospray ionization of both denaturing solutions and ones with high salt content to preserve native-like structures. A linear relationship between the pressure in the Orbitrap analyzer and the transient decay rate was established and used to demonstrate that the signal decay is primarily due to ion-neutral collisions for protein ions across the entire working pressure range of the instrument. The CCSs measured in this study were compared with previously published CCS values measured by ion mobility mass spectrometry (IMS), and results from the two methods were found to differ by less than 7% for all charge states known to adopt single gas-phase conformations.

A variational approach is proposed for simulation of equilibrium ion distributions in radiofrequency low-vacuum ion traps with allowance for the Coulomb interaction and collisions of ions with the buffer gas molecules. A unimodal thermodynamic functional (potential) is introduced, the Euler equation for which is equivalent to the Poisson equation for Coulomb field and the Boltzmann distribution for ion density. The original problem is thus reduced to minimization of this thermodynamic potential in a functional space. By using the potential theory and Fourier analysis, the infinite-dimensional minimization problem is further reduced to a relevant finite-dimensional quadratic programming problem, which is numerically solved by means of the conjugate gradient method. Special emphasis is given to the physical grounds underlying the numerical method proposed. Examples of 2D and 3D calculations are presented and discussed.

The multireflection ion traps with isochronous properties offer a lot of opportunities for time-of-flight mass spectrometry by elongation of the ion path, thus preserving the compact dimensions of an instrument. We have built and tested a two-mirror linear trap that provides at least 80,000 mass-resolving power. Although the mass resolution appears promising, there are substantial limitations that arise from Coulomb interactions of the trapped ions. Among these, the mutual repulsion of ions with same or close mass-to-charge ratios appears dominant, resulting in counterintuitive motion synchronization. The self-bunching and coalescence effects are also examined by numerical simulation.

A variational 3D approach to the problem of simulating stationary distributions of ions in the radiofrequency low-vacuum ion traps with regard to Coulomb interaction and collisions of ions with buffer gas molecules is proposed. The software developed in the course of this work is employed to study the structure of stationary ion ensembles in the radiofrequency ion traps of various types. The effect of high-frequency and constant voltages, space-charge density, and buffer gas temperature on the formation of stationary distributions in the radiofrequency ion traps and their limiting capacitance is investigated. It is shown that the use of electrodes with a constant voltage in the presence of high enough ion density allows pre-filtering of ions directly in a high-frequency trap-accumulator.

A popular method for peptide quantification relies on isobaric labeling such as tandem mass tags (TMT), which enables multiplexed proteome analyses. Quantification is achieved by reporter ions generated by fragmentation in a tandem mass spectrometer. However, with higher degrees of multiplexing, the smaller mass differences between the reporter ions increase the mass resolving power requirements. This contrasts with faster peptide sequencing capabilities enabled by lowered mass resolution on Orbitrap instruments. It is therefore important to determine the mass resolution limits for highly multiplexed quantification when maximizing proteome depth. Here, we defined the lower boundaries for resolving TMT reporter ions with 0.0063 Da mass differences using an ultra-high-field Orbitrap mass spectrometer. We found the optimal method depends on the relative ratio between closely spaced reporter ions and that 64 ms transient acquisition time provided sufficient resolving power for separating TMT reporter ions with absolute ratio changes up to 16-fold. Furthermore, a 32 ms transient processed with phase-constrained spectrum deconvolution provides >50% more identifications with >99% quantified but with a slight loss in quantification precision and accuracy. These findings should guide decisions on what Orbitrap resolution settings to use in future proteomics experiments, relying on isobaric TMT reporter ion quantification.

The rapidly increasing adoption of high-resolution accurate-mass methods in analytical laboratories has fueled demand for instruments that combine high performance and reliability with small size and greater ease-of-use. This paper presents the major design principles that are driving the evolution of the hybrid quadrupole-Orbitrap instrument architecture to enable a greater range of applications and users. These principles may be summarized as follows: better usage of physical space and better access for service by means of size reduction of pumping and ion optics; expanded use of technologies from electronics in ion-optical design; flexibility in performance via modularity of design of the hardware and software components; and, harmonization of interfaces with other instruments to facilitate sharing and transferability of analytical workflows. The design of a novel family of hybrid mass spectrometers is described in detail, and performance evaluation is carried out on a wide variety of samples for its three representatives: the Orbitrap Exploris 120, Orbitrap Exploris 240 and Orbitrap Exploris 480 mass spectrometers.The new instrument family is shown to offer compelling potential not only for high-end proteomics and biopharmaceutical applications, but also for screening, trace, targeted and clinical analysis by liquid chromatography/mass spectrometry methods.