Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
🔬 Techniques
🧬 Organisms
✨ Fluorophores
🧪 Sample Preparation
🏭 Microscope Brands
💻 Software Details
🏛️ Research Organizations (ROR)
Affiliated research institutions:
📊 Figures
Figure 1:
Schematic representations of CID and SID of noncovalent protein complexes with corresponding simplified potential energy diagrams shown at the bottom. In CID (left) protein complexes undergo multiple ...
Figure 2:
Charge-reduced species have more native-like SID fragmentation patterns than their normal-charge counterparts. (a) SID spectrum of (charge-reduced) 18+ C-reactive protein (CRP) at 1 keV, (b) CID spect...
Figure 3:
SID can distinguish between tetramers of different arrangements. A) PISA interfacial analysis for C4 tetramer aquaporinZ, and D2 tetramers streptavidin, neutravidin and transthyretin. B) Low energy SI...
Figure 4:
Predicted AE, based on the initial optimized model as shown in equation 1 , shows good correlation to experimental AE. Reproduced with permission from ref 52 .
Figure 5:
SID can distinguish between different arrangements of subunits. A) SID from a sample at 4 u00b0C of a TTR UU/TT tetramer yielding an MS spectrum with equal signal intensity for UU and TT dimers. (B) S...
Figure 6:
Workflow for characterizing the TNH structure by complementary mass spectrometric tools, reproduced with permission from ref 110 . Copyright 2015 American Chemical Society.
Figure 7:
Using data from nMS and SID experiments, along with homology and ab initio models, a structural model for Mnx could be proposed. Reproduced with permission from ref 117 .
Figure 8:
Comparison of (a) CID and (b) SID spectra of 19+ toyocamycin nitrile hydratase heterohexamer (u03b1u03b2u03b3) 2 on a Micromass/Water QTOF II mass spectrometer retrofitted with a Gen 1 SID device. Rep...
Figure 9:
SID cells for Q-IM-TOF platforms. Schematic diagram of (a) Waters Synapt G2 platform with three integrated SID cells with locations noted. Three generations of SID cells have been installed in the G2,...
Figure 10:
SID-IM reveals the connectivity within a heterohexamer. SID-IM of 14+ TNH on a Waters G2-S fitted with a Gen 1 SID device prior to the IM cell. Shown are low- and high-energy spectra at (a) 700 eV and...
Figure 11:
SID-IM-TOF of the 18+ charge state of holoTRAP 11mer (in 200 mM EDDA with 14 equiv of trp) on a Synapt G2. All oligomeric fragments are observed in mobility space, consistent with the cyclic arrangeme...
Figure 12:
SID-IM of the 43+ and 44+ rabbit 20s proteasome at 150 V. A) full MS (top) and isolation (bottom), B and C) IM-MS analysis of SID products, D-J) extracted spectra for the different regions underlined ...
Figure 13:
IM-SID can be used to individually probe different conformations of in-source activated CRP (cone 200 V). Right hand panels show extracted SID spectra (1260 eV) from the highlighted regions in the lef...
Figure 14:
SID cells for Orbitrap platforms. (a) Schematic of a Thermo Scientific Extended Mass Range (EMR) Orbitrap Exactive platform with SID cell taking the place of a transport multipole, (b) the Gen 1 SID c...
Figure 15:
SID distinguishes ligand binding locations in pentamers CRP (with phosphocholine, PC) and CTB (with GM1s). CID spectra of (a) 18+ CRP at 2700 eV and (c) 18+ CTB at 2200 eV and corresponding SID spectr...
Figure 16:
(a) Deconvoluted mass spectrum of DMPC nanodiscs. Waterfall plots showing (b) CID and (c) SID spectra of DMPC nanodiscs with increasing collision energy. Reproduced from ref. 101 with permission from ...
Figure 17:
SID cells for FT-ICR platforms. (a) Schematic of the solariX FT-ICR platform, (b) CAD renderings of three generations of hybrid SID-CID cells (which replace the red collision cell), (c) illustration o...
Figure 18:
Surface-induced dissociation of 211 kDa multicopper oxidase Mnx on an ultrahigh resolution 15 T FT-ICR platform. (a) SID spectrum of Mnx 26+ through 29+ charge states (inset shows precursor ion popula...
Figure 19:
FT-ICR offers unparalleled resolution for quantifying oligomer abundances from SID. (a) Mass spectrum of cholera toxin B charge-reduced with EDDA and (b) SID fragmentation pattern at collision energy ...
Figure 20:
(a) Illustration of SID in an ELIT, (b) native mass spectrum of triose phosphate isomerase, (c) isolation of the 14+ charge state by mirror switching, and (d) SID spectrum of the 14+ charge state to p...
Figure 21:
Illustration of SID-IM-SID. (a) SID spectrum of 19+ tryptophan synthase at a collision energy of 570 eV, (b) SID-IM at a higher energy of 1330 eV, (c) SID-IM-SID at 2280 eV (second stage) of 12+ u03b1...
Figure 22:
Illustration of SID-IM-SID for native TNH heterohexamer. SID-IM-SID spectra of heterotrimer u03b1u03b2u03b3 (a) 8+ and (b) 9+ produced from a first stage of SID of the heterohexamer (u03b1u03b2u03b3) ...
Figure 23:
Illustration of SID-Q-SID on an ultrahigh resolution 15 T FT-ICR. (a) native mass spectrum of HFQ65 homohexamer charge reduced with TEAA, (b) single stage SID spectrum of the entire charge state distr...
Figure 24:
Comparison of CIU and SIU plots for bovine serum albumin (BSA) 15+ and the N-terminal domain of anthrax lethal factor (LF N 10+ ). (A) CIU OF BSA15+, (b) SIU of BSA15+, (c) CIU of LF N 10+ , and (d) S...
Figure 25:
(a) CID and (b) SID spectra of (Cyt c) 2 11+ Reproduced from ref. 46 . Copyright 2006 American Chemical Society.
Figure 26:
SID spectra of protein complexes exhibit symmetric charge partitioning. SID spectra of (a) phosphorylase B dimer 29+ at 110 V, (b) phosphorylase B dimer 21+ at 150 V, (c) glutamate dehydrogenase hexam...
Figure 27:
Monomer orientations during asymmetric dissociation of cytochrome c dimer 10+ at a center-of-mass distance of (a) 6 nm, (b) 9 nm, and (c) 11 nm. The yellow monomer has 8 charges, and the green monomer...
Figure 28:
Comparison of CCSs of subcomplexes produced by (a,c) CID and (b,d) SID of pentamer C-reactive protein and tetramer concanavalin A. While monomer CCSs agree well with crystal structures, the CCSs of la...
Figure images are served from the NIH/NLM PubMed Central Open Access Subset or Europe PMC; copyright remains with the publishers and authors.
💬 Discussion
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