Tutorial and comprehensive computational study of acceptance and transmission of sinusoidal and digital ion guides

Abstract

A quadrupoles acceptance is a measure of its ability to catch ions with certain trajectories. One way to calculate acceptance is the method of ellipses. The method arose partly from a simplification that trajectories could be calculated for an electrode axis independently of others. It has been used to calculate the acceptance and transmission of sine-driven quadrupole mass filters for over 50 years. Although the method is straightforward, it is generally described with little detail or presented as a confusing string of equations. As such, it may not be decipherable by all practitioners. For this reason, the first half of this paper presents a practical explanation of the method of ellipses and the concepts that make it work. Only equations necessary to describe the method are introduced. The tutorial also prepares the reader for the second half, which presents an alternative approach for calculating acceptance based on an array of initial trajectories. The alternative approach is used to compare the acceptance of simplified sinusoidal and digital ion guides. The method of ellipses was applied to validate results of the new approach for calculation of acceptance.

Implementing Digital-Waveform Technology for Extended m/z Range Operation on a Native Dual-Quadrupole FT-IM-Orbitrap Mass Spectrometer

“…Previously, mass selection with DWT has only been experimentally achieved for small, non-native proteins but has been simulated for complexes approaching MDa masses. − , In this work, the mass selection of individual charge states for large protein complexes (>100 kDa) has been effectuated. The overall performance of DWT for isolation of single charge states of C-reactive protein (CRP), membrane protein ammonium transport channel (AmtB), and type 1 chaperonin GroEL is illustrated by data shown in Figure .…”

“…Previously, mass selection with DWT has only been experimentally achieved for small, non-native proteins 28 but has been simulated for complexes approaching MDa masses. [24][25][26][27]31 In this work, the mass selection of individual charge states for large protein complexes (>100 kDa) has been effectuated. The overall performance of DWT for isolation of With the isolation of a single-charge state for these complexes and with support by previous theory, evidence suggests that the (3,1) stability zone (the intersection of the third stability zone along the X-axis and first stability zone on the Y-axis) can be accessed without a significant loss in throughput or sensitivity.…”

“…The ions exiting q are guided to the second chamber by an octupole ion guide constructed from 3.175 mm rods with a 4.75 mm r 0 measuring 47 mm in length and enter a 250 mm hyperbolic quadrupole (Q) that is maintained at 10 –4 –10 –5 Torr. Q is used to mass-select the ions by digital-waveform technology (DWT) as described and developed by the Reilly laboratory. − Both quadrupoles are identical Thermo Fisher 4 mm r 0 hyperbolic rods with pre- and postfilters (Part Number 80100–60109); quadrupole pre- and postfilters were wired directly to the main rods prior to use. All the experiments described below employ the DWT operation of the Q MS. Ions exiting Q enter an octupole ion guide (47 mm) and then transfer to a 55 cm PF-DT maintained at pressures of 1–2 Torr of He.…”

“…The first quadrupole (q) is operated as an ion guide (RF-only mode) and can also be used for mild collisional activation of the ions to remove unwanted adducted species (H 2 O, salts, detergents, and charge reducing reagents). The second quadrupole (Q) is used for mass selection and is operated using digital-waveform technology (DWT) developed in the Reilly laboratory. − The modular design of the instrument allows for the installation of additional ion activation techniques, such as surface-induced dissociation (SID), − electron transfer/capture dissociation (ETD/ECD), and ultraviolet photodissociation (UVPD) , prior to IM-MS characterization. Collectively, the experimental versatility of the (vT)-nESI-qQ-PF-DT-FT-IM-Orbitrap increases our research capabilities for native-mass-spectrometry-guided structural biology.…”

Experimental Validation of the Digital Tandem Mass Filter

“…This overlap is adjustable and defines the tandem mass window width as well as the ability of the mass filter system to transmit ions. In general, wider mass windows yield better ion transmission/sensitivity because they provide better acceptance of the ions through the quadrupole fields as they develop over the fringe region at the ends of the mass filter . The acceptance of a mass filter is defined by the two-dimensional phase plane area of each RF axis that represents a set of initial trajectories that lead to stable motion within the fully developed fields of the mass filter.…”