Design and Performance of a Second-Generation Surface-Induced Dissociation Cell for Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of Native Protein Complexes

Abstract

A second-generation (“Gen 2”) device capable of surface-induced dissociation (SID) and collision-induced dissociation (CID) for Fourier transform ion cyclotron resonance mass spectrometry of protein complexes has been designed, simulated, fabricated, and experimentally compared to a first-generation device (“Gen 1”). The primary goals of the redesign were to 1) simplify SID by reducing the number of electrodes, 2) increase CID and SID sensitivity by lengthening the collision cell, and 3) increase the mass range of the device for analysis of larger multimeric proteins, all while maintaining the normal instrument configuration and operation. Compared to Gen 1, Gen 2 exhibits an approximately 10x increase in sensitivity in flythrough mode, 7x increase in CID sensitivity for protonated leucine enkephalin (m/z 556) and 14x increase of CID sensitivity of 53 kDa streptavidin tetramer. It also approximately doubles of the useful mass range (from m/z 8,000 to m/z 15,000) using a rectilinear ion trap with a smaller inscribed radius or triples it (to m/z 22,000) using a hexapole collision cell and yields a 3–10x increase in SID sensitivity. We demonstrate the increased mass range and sensitivity on a variety of model molecules spanning nearly 3 orders of magnitude in absolute mass and present examples where the high resolution of the FT-ICR is advantageous for deconvoluting overlapping SID fragments.

Simple and Minimally Invasive SID Devices for Native Mass Spectrometry

“…In both low and high energy cases, the predominant fragments are trimers, in agreement with the dimer of trimers arrangement of the subunits. 42,45,51 Gen 3 on the EMR is therefore capable of transmitting and fragmenting ions over a wide range of masses and energies yet demonstrates a simpler SID design to increase usability and improve SID automation for data-dependent MS/MS analyses in the future.…”

Simple and Minimally Invasive SID Devices for Native Mass Spectrometry

“…The FT-ICR collision cell was truncated by nearly half to accommodate the SID design, leading to a notable decrease in sensitivity (trapping capacity). 44,46 A second generation of devices ('Gen 2') 46,48 cut the required SID cell volume by nearly half on the Q-IM-TOF and FT-ICR platforms by utilizing tilted surfaces instead of level ones, thus regaining some lost sensitivity on the FT-ICR in particular. 46 Gen 3 takes a minimalistic approach not only to significantly shorten the SID device but also to simplify SID tuning and improve the collection efficiency of protein complexes after surface collision.…”

Simple and Minimally Invasive SID Devices for Native Mass Spectrometry

“…The FT-ICR collision cell was truncated by nearly half to accommodate the SID design, leading to a notable decrease in sensitivity (trapping capacity). 44,46 A second generation of devices ('Gen 2') 46,48 cut the required SID cell volume by nearly half on the Q-IM-TOF and FT-ICR platforms by utilizing tilted surfaces instead of level ones, thus regaining some lost sensitivity on the FT-ICR in particular. 46 Gen 3 takes a minimalistic approach not only to significantly shorten the SID device but also to simplify SID tuning and improve the collection efficiency of protein complexes after surface collision.…”

“…In both low and high energy cases, the predominant fragments are trimers, in agreement with prior results on Synapt, Orbitrap, and FT-ICR platforms. 43,46,55 Gen 3 on the EMR is therefore capable of transmitting and fragmenting ions over a wide range of masses and energies yet demonstrates a simpler SID design to increase usability and improve SID automation for data-dependent MS/MS analyses in the future.…”

“…This design was then translated to Thermo Scientific Extended Mass Range (EMR) Orbitrap 43 and Bruker FT-ICR 44 platforms (also termed 'Gen 1' devices) and subsequently simplified to ~6-lens systems with tilted surfaces as a second generation ('Gen 2') of devices in the Synapt 45 and FT-ICR. 46 The goals of the Gen 2 redesigns were to 1) shorten the SID devices to accommodate easier incorporation into a variety of commercial platforms, 2) to increase SID sensitivity by increasing ion collection after surface scattering, and 3) to simplify tuning by reducing the number of electrodes. Nonetheless, there is still a desire to simplify and minimize SID device design further while also improving sensitivity.…”