Abstract

Mass spectrometry (MS) provides an impressive array of information about the structure, function and interactions of proteins. In recent years, many new developments have been in the field of native MS and these exemplify a new coming of age of this field. In this mini review, we connect the latest methodological and instrumental developments in native MS to the new insights these have enabled. We highlight the prominence of an increasingly common strategy of using hybrid approaches, where multiple MS-based techniques are used in combination, and integrative approaches, where MS is used alongside other techniques such as ion-mobility spectrometry. We also review how the emergence of a native top-down approach, which combines native MS with top-down proteomics into a single experiment, is the pièce de résistance of structural mass spectrometry's coming of age. Finally, we outline key developments that have enabled membrane protein native MS to shift from being extremely challenging to routine, and how this technique is uncovering inaccessible details of membrane protein–lipid interactions.

Introduction

Mass spectrometry (MS) has evolved in recent years to become a pillar for integrative structural biology approaches. Structural MS provides a plethora of information, from protein primary structure and post-translational modifications (PTMs) to higher-order quaternary structure, protein dynamics and interactions. To achieve this breadth of information, different MS approaches have been separately developed with the proteins of interest in either denaturing or native conditions. In the first case, best known as the field of proteomics, the approach can be either peptide-centric (bottom-up) or protein-centric (top-down). Peptide-centric approaches typically analyse peptides derived from proteins in solution, while protein-centric approaches ionise individual protein subunits intact and generate fragments inside the mass spectrometer through gas-phase activation. In the second case, the protein's interactions are maintained in solution and during transfer to the gas phase of the mass spectrometer, hence the name ‘native’ [1]. This approach preserves non-covalent interactions that are the hallmarks of a protein's structure and function and consequently offers access to insights otherwise lost through the other approaches.

We argue that while MS clearly came of age some time ago for structural biology, we are now entering a new age: membrane proteins that used to be almost intractable to study are now amenable to routine analysis, hybrid approaches are becoming the norm, and high-resolution instruments that enable proteomics and native MS analysis simultaneously on the same instrument are offering new experimental strategies.

Many of the latest advances, especially those concerning hybrid approaches are in the sphere of native MS. Therefore, we have chosen to focus on this area in this mini review. We will start with a brief introduction of native MS and hybrid MS-allied approaches, with an emphasis on the insights these give into protein structure. We will then draw attention to the emergence of native top-down MS as a new and highly exciting development in the field, before describing the advances made in native MS for the study of membrane proteins — the final frontier for this cornerstone approach.

Native mass spectrometry is at the heart of structural mass spectrometry

Native MS is the analysis of biomolecules from their ‘native’ state in solution and during transfer to the gas phase of the mass spectrometer [1]. This is possible through the use of soft ionisation techniques, compatible buffers and careful optimisation of instrument parameters to balance adduction and disruption of structure. The advantage of this approach is that non-covalent interactions of proteins, essential for their fold, structure and interactions with other biomolecules, are preserved from solution throughout MS analysis. This unique capacity places native MS at the heart of structural MS, which is inherently interested in the structure and interactions of biomolecules.

Native MS, therefore, enables the identification of complexes, their exact stoichiometry, binding partners and thermodynamics of binding, complex topology, as well as their real-time solution formation [2]. This approach is neatly complementary with classical proteomics-based MS, whose equally important methodologies are being combined in novel hybrid approaches.

Hybrid and integrative approaches for a wider structural and functional picture

By virtue of its strong complementarity, an increasing use of native MS is in hybrid approaches, where various MS-based techniques are used in combination to elucidate a wider picture of protein structure and function. While native MS informs about stoichiometry, co-occurring assemblies and ligand binding, proteomic approaches help to identify and quantify proteins, their different proteoforms, as well as detailed information about their PTMs (Figure 1). Combining both native MS and proteomic approaches can therefore be of great utility to reveal PTM micro-heterogeneities within biological samples. For example, by using high-resolution native MS, a large number of glyco-proteoforms for different proteins purified from human blood serum were recently detected and quantified [3,4]. Then, by combining this approach with peptide-centric proteomics, the heterogeneous glycosylations and their specific locations could be identified, revealing the presence of novel and previously unreported glycosylation sites. Application of such hybrid MS approaches for the assessment of glycosylation occurrence, number and sites in pharmaceutical products could greatly simplify quality control and stability assessment [57].

Overview of the different MS approaches for interrogating the structure and function of proteins.

Figure 1.
Overview of the different MS approaches for interrogating the structure and function of proteins.

Native mass spectrometry preserves and detects non-covalent interactions. Bottom-up and top-down proteomics approaches can identify proteins, PTMs and other modifications, and in the case of top-down approaches reveal proteoform-specific information. Cross-linking proteomics provides information on subunit connectivity, and HDX reveals conformational and dynamic changes in protein structure. Hybrid and integrative approaches combine the individual approaches to enable complete identification and characterisation of multiproteoform complexes.

Figure 1.
Overview of the different MS approaches for interrogating the structure and function of proteins.

Native mass spectrometry preserves and detects non-covalent interactions. Bottom-up and top-down proteomics approaches can identify proteins, PTMs and other modifications, and in the case of top-down approaches reveal proteoform-specific information. Cross-linking proteomics provides information on subunit connectivity, and HDX reveals conformational and dynamic changes in protein structure. Hybrid and integrative approaches combine the individual approaches to enable complete identification and characterisation of multiproteoform complexes.

Some PTMs can be lost using peptide-centric approaches, which means that complementary top-down proteomic approaches that retain those PTMs could be necessary to identify these modifications [810]. Recently, a three-tiered hybrid approach combining native MS, top-down as well as bottom-up proteomics was used to identify the stoichiometry of four different ribosomal particles, to determine the sites of their sequence processing and their PTMs [11]. Hybrid approaches can therefore offer a comprehensive and extremely detailed view into the structure of proteins.

Chemical modifications of proteins in solution prior to proteomic analysis can add another structural dimension to hybrid MS-based approaches. For instance, combining cross-linking [12] with native MS enables the identification of interacting proteins while specifying protein–protein interaction sites and can be used to probe local conformational changes that occur within protein complexes [1317]. Similarly, the use of hydrogen–deuterium exchange (HDX) to label backbone amides gives insights into protein secondary structure, conformational changes as well as ligand-binding sites [1825]. Notably, many of these structural MS applications would not have been possible without the development of large-scale analysis software for data interpretation [26,27].

In addition to MS-based hybrid approaches, integrative approaches that combine MS with other techniques are also continuing to develop in combination with native MS. Ion mobility (IM), for instance, reveals the overall shape of protein complexes analysed by native MS and offers an orthogonal level of separation for complex samples [2830]. This powerful approach uncovers conformational changes that might occur within proteins [31,32] and is also used to assess the stabilising effects of various ligands by generating collision-induced unfolding plots [3336]. The coupling of IM with MS allows different proteoforms or bound states to be independently assessed, which is more difficult or impossible by other techniques. Recently, exploiting its ability to resolve subtly different structural forms, IM–MS has been used to monitor in-solution sequential unfolding of proteins [37]. Native IM–MS can also be coupled to other hybrid MS approaches, for example, HDX [38,39] or top-down proteomics [40], giving an additional level of structural and functional information. However, and similarly to hybrid approaches, this is only feasible due to the parallel development of integrative modelling [29,4143].

The emergence of native top-down

Many outstanding technological and methodological developments have given rise to the ability of native MS and proteomics to yield incredible insights into nearly all levels of protein structural orders. However, the ‘missing brick’ in this MS-based repertoire was the ability to reveal the primary structure information and identify unknown bound ligands within the context of a native MS experiment of a protein complex. In essence, this is the ability to perform top-down experimental approaches but from a native rather than denatured state (Figure 2). The limitation previously restricting the possibility of this native top-down approach was largely instrumental, and has been overcome by recent developments that enable multi-stage MS on native protein complexes.

Schematic of native mass spectrometry and native top-down mass spectrometry experiments.

Figure 2.
Schematic of native mass spectrometry and native top-down mass spectrometry experiments.

Protein or protein–ligand complexes are analysed from native-like conditions in solution with non-covalent interactions maintained in transfer to the gas phase of the mass spectrometer. In the classical native MS configuration (top), the complex of interest is selected after the ionisation step then subsequently dissociated, during the activation step, into single chains or sub-complexes that are afterwards detected to identify their average mass. Alternatively, in the native top-down instrument configuration (bottom), an additional activation step is added after the ionisation, which will enable the selection of single chains that are later fragmented to obtain primary sequence information or to identify bound ligands. The additional activation step in native top-down instrument configuration could be ‘turned off’ to give a classical native MS pipeline when needed.

Figure 2.
Schematic of native mass spectrometry and native top-down mass spectrometry experiments.

Protein or protein–ligand complexes are analysed from native-like conditions in solution with non-covalent interactions maintained in transfer to the gas phase of the mass spectrometer. In the classical native MS configuration (top), the complex of interest is selected after the ionisation step then subsequently dissociated, during the activation step, into single chains or sub-complexes that are afterwards detected to identify their average mass. Alternatively, in the native top-down instrument configuration (bottom), an additional activation step is added after the ionisation, which will enable the selection of single chains that are later fragmented to obtain primary sequence information or to identify bound ligands. The additional activation step in native top-down instrument configuration could be ‘turned off’ to give a classical native MS pipeline when needed.

Using the new extended mass range Orbitrap platform [44], multi-stage MS was made possible by adding a front-end collisional activation step to disassemble complexes that could then be isolated for further fragmentation with higher-energy collisional dissociation (HCD) [45]. Similarly, in-source activation was also developed for a multi-stage MS approach using ion-mobility Q-ToF instruments [46,47], the latter being historically popular for native MS. In addition, an integrated approach was developed for use on a Fourier-transform ion-cyclotron resonance (FT-ICR) platform. This platform has the advantage of multiple activation methods, which allows for a high sequence coverage, and identification of labile PTMs, as well as interfacial and surface residues [4852]. These developments now enable the identification, in a single experiment, of PTMs and sequence polymorphism as well as the characterisation of ligand binding within protein complexes.

Proteomics from native complexes

Protein assemblies can be very heterogeneous, and these variations can be related to different functional states arising in response to different cellular conditions. This heterogeneity is often difficult to assess using classical structural approaches that often require homogeneous sample or measure ensemble averages. Top-down and bottom-up proteomics can identify sequence polymorphisms and PTMs; however, these approaches cannot directly relate the various modifications to a specific protein complex. Therefore, an advantage of high-resolution mass spectrometers capable of multi-stage MS is the identification, in a single experiment, of distinct proteoforms and PTMs within protein complexes. This advantage was recently demonstrated by the identification of two mutually exclusive phosphorylation sites within the yeast homo-tetrameric fructose-1,6-biphosphatase 1 (FBP1) that are sensitive to variation in growth conditions [53].

The various activation methods already developed and used in top-down proteomics have been translated into native top-down applications. For instance, the integration of ultraviolet photodissociation (UVPD) in the HCD cell [54] has been found to offer higher sequence coverage compared with HCD alone as well as an improved retention of labile PTMs. This approach has been applied to the homodimeric branched-chain amino acid transferase 2, which was dissociated in source, and selected monomers activated either by HCD or by 293 nm photons, yielding an improved sequence coverage for the higher-energy fragmentation by UVPD and enabling the identification of a single amino acid mutation within the enzyme. Alternatively, electron-based activation methods — such as ECD and ETD — can be used to help maintain and thus detect labile PTMs. ECD was recently applied in combination with native MS to identify various isoforms of tau protein and to map its phosphorylation sites [55]. In addition, electron-based activation methods can be of great structural use in native top-down experiments since these methods generate fragment ions correlating to the exposed surface of the studied native proteins [48].

These new methods have also been applied for the untargeted identification of protein complexes from cell lysates [56]. In this research, 125 endogenous complexes were directly identified from mouse heart and human cancer cell lysates. This would not have been possible without the development of powerful data analysis software [56] and sample separation methods [57,58]. Increasing the scale of this untargeted identification, a recent study coupled two liquid-phase separation techniques to native top-down, size-exclusion chromatography and capillary zone electrophoresis, to analyse E. coli cell lysates [59]. This strategy identified numerous protein complexes and proteoforms, half of which had not previously been reported. These new approaches are of high interest and have a strong potential to revolutionise interactomics studies.

Identifying ligands and their binding sites

The development of native top-down approaches offers the unique opportunity to identify directly small molecule ligands bound to protein complexes. This will remove any ambiguity that could be present when ligand identification is made using denaturing methods, in which direct evidence of the interaction is lacking. To date, only this approach has been used to identify lipids bound to membrane proteins, as we discuss later.

The difficult task of identifying ligand-binding sites within protein complexes can be uncovered by structural MS through careful choice of the activation technique used during native top-down. For instance, ECD cleaves polypeptide backbone bonds while preserving non-covalently bound ligands. Taking advantage of this action, the binding sites of manganese and cobalt to the intrinsically disordered protein α-synuclein were identified [60], and the binding site of a molecular tweezer assembly modulator to tau protein was determined [55]. Electron-ionisation dissociation (EID) can also be used to probe ligand-binding sites [61]. This fast activation method [62] gives higher sequence coverage compared with ECD and offers the advantage of dissociating folded gas-phase protein ions, yielding structural information for protein complexes that might be inaccessible by ECD. Another highly advantageous fast activation technique, UVPD, was recently used to determine ligand-binding sites in native top-down [54,6366]. This activation method can generate higher sequence coverage, as mentioned above, while retaining non-covalent interactions, as well as identify ligand-binding sites challenging to identify by ECD or EID.

Advances in structural mass spectrometry of membrane proteins

Until recently, the study of soluble proteins by native MS has been easier and more successful than for membrane proteins. The key difference that makes membrane proteins challenging is that they start their journey in the instrument encapsulated in a membrane mimetic. This imposes an additional requirement; the membrane mimetic needs to be removed after ionisation and before detection (Figure 3). Most commonly, this mimetic has been detergent micelles, although some success has been made using different systems [6771].

Schematic of important processes in native MS of membrane proteins.

Figure 3.
Schematic of important processes in native MS of membrane proteins.

(A) When membrane proteins are introduced to the mass spectrometer, they are commonly encapsulated in a detergent micelle. Collisional activation is required to remove the bound detergent molecules to resolve the charge states. Incomplete detergent removal results in severe reduction in resolution. (B) Detergent removal must occur prior to the quadrupole to enable multi-stage MS approaches for membrane proteins. This assumes a classical instrument design of a quadrupole preceding the main collision cell, and therefore that the amount of available in-source activation needs to be high enough to completely remove the bound detergent molecules. Without in-source activation, no selection in a quadrupole is possible and experiments are limited (top). When in-source activation is applied, then ion selection can take place, enabling multi-stage experiments (bottom).

Figure 3.
Schematic of important processes in native MS of membrane proteins.

(A) When membrane proteins are introduced to the mass spectrometer, they are commonly encapsulated in a detergent micelle. Collisional activation is required to remove the bound detergent molecules to resolve the charge states. Incomplete detergent removal results in severe reduction in resolution. (B) Detergent removal must occur prior to the quadrupole to enable multi-stage MS approaches for membrane proteins. This assumes a classical instrument design of a quadrupole preceding the main collision cell, and therefore that the amount of available in-source activation needs to be high enough to completely remove the bound detergent molecules. Without in-source activation, no selection in a quadrupole is possible and experiments are limited (top). When in-source activation is applied, then ion selection can take place, enabling multi-stage experiments (bottom).

The process of removing the protective membrane mimetic requires application of collisional activation, the levels of which require careful balancing to avoid the unwanted dissociation of interacting proteins/ligands. This selective dissociation became easier with the identification of detergents with relatively volatile properties requiring minimal input of collisional activation [7274]. However, even with these ideal detergents, other parameters need to be carefully controlled, such as the solution-stability of the membrane protein in the favoured detergents [75,76] and the extent of delipidation of the sample as it is extracted from expression-host cell membranes and purified [75,77]. Alternatively, the strategic but very empirical use of micelles of mixed detergent composition is a promising method to balance these factors [74,78]. Notably, and very recently, membrane protein complexes encapsulated in vesicles were detected by native MS, a considerable advance that negates the need in some cases for a mimetic [79].

The other challenge for membrane protein native MS has been related to the instrument design, specifically to the location where the activation required to strip the membrane mimetic takes place. Ideally, this step should be as close to the source region as possible (Figure 3), so that the same repertoire of experiments is achievable as for soluble proteins. Overall, combinations of appropriate solution-preparation of membrane proteins and instrument modifications to increase the levels of in-source activation have worked to reduce this challenge [44,46,72,77,80,81].

Native MS to characterise membrane protein–ligand binding

A particular advantage of native MS is the ability to resolve different bound states of a protein — no longer is the measurement an average of the whole ensemble: the behaviour of the different bound states can be interrogated separately. In a seminal paper for this new age of membrane protein native MS, Laganowsky et al. showed how the folded states of membrane proteins are selectively stabilised by the binding of individual lipid molecules [73,82]. Of particular interest, the lipids identified to have strong stabilising effects were all associated with functional requirements [83], structural conformations and changes in activity of the proteins studied. Methodological improvements have also allowed full thermodynamic parameters of binding to be calculated, showing that there is an entropy–enthalpy compensation for the binding of lipids with different chain lengths, and a potential to differentiate lipid-binding sites based on different thermodynamic parameters of binding [84]. Furthermore, allosteric effects on lipid binding were revealed, with the binding of one lipid affecting the binding of a second [85]. These discoveries led to crystal structures of the ammonia channel bound to lipids [73,85], and the identification of a key residue that controls the allosteric-binding effects. These allosteric effects of lipid binding are not constrained to other lipid molecules; using the ammonia channel as a model system, it was shown that lipids affect the coupling of this membrane protein to its soluble protein partner, GlnK, thus suggesting a role of lipids in regulating nitrogen flux [84]. Few techniques can match the ability of MS to investigate the effects of individual lipid-binding events on membrane protein behaviour, which is why this has become so powerful.

These advancements have led to many exciting new insights into membrane protein–ligand and lipid binding. For instance, off-target drug binding of HIV protease inhibitors to the human zinc metalloprotease ZMPSTE24, an intramembrane protease, was recently detected and the undesirable disease-linked inhibition of the protease observed directly [86]. Antibiotic binding to the flippase MurJ was characterised and shown to be influenced by lipid binding [87]. The functional importance of co-purified lipids was shown for the flippase TmrAB [75], and lipids were also proposed, in part, by native MS to play a role in the structural mechanism of Na+/H+ antiporters, by helping to facilitate conformational changes of the proteins within the membrane [88]. The role of interfacial lipids in stabilising dimeric states of certain membrane proteins has also been revealed by native MS. This behaviour was correlated to the role of lipids in compensating for otherwise weak interfacial strengths between monomers, acting as a metaphorical glue [46]. Lipids were also found to be important for the dimerisation of UapA by similar methods, with the dimeric entity determined to be the functional form of the protein [89]. The development of membrane protein native MS has, therefore, created an unprecedented experimental strategy to explore the effects of individual lipid-binding events.

For different types of membrane proteins, the final frontier has been to find ways in which native MS can be used to study G protein-coupled receptors (GPCRs). These are the largest class of proteins in eukaryotes, and are the target for >40% of current drugs, making understanding their functional biology critically important. Using both the resolution afforded by new instrumentation, and approaches to finding volatile detergent combinations that keep proteins stable and functional, this protein class is now tractable. Ligand binding to the human purinergic receptor P2Y1 was detected directly, showing differentiated binding to proteoforms with different phosphorylation [78]. And, most recently, exploiting the aptitude of native MS to investigate lipid interactions, it was demonstrated that GPCRs are sensitive to lipid binding, specifically the physiologically important lipid phosphatidylinositol-4,5-bisphosphate. This lipid stabilises the active states of GPCRs, and enhances the coupling to G-proteins, with which the GPCRs interact to communicate signalling information [90]. The present study has further confirmed that GPCR regulation is complex, but also showcases how native MS now offers a way to uncover and study these effects in considerable detail.

Native top-down MS to identify membrane protein-bound ligands

The native top-down approach developed for soluble proteins was recently translated for the study of membrane proteins using a modified ion-mobility Q-ToF instrument, referred to as a ‘high-energy MS/MS platform’ [46,77]. By adding an in-source activation step, the energy required to strip the detergent micelle is administered in the front-end of the instrument which allows for subsequent ion selection in the quadrupole prior to activation in the collision cell (Figure 3). This makes it possible to directly identify endogenous membrane protein-bound lipids in a single experiment and avoids possible doubts from other approaches, where lipids detected by native MS bound to membrane proteins are identified using a chromatographic or an MS-based approach analysing the total lipid extract present in the sample [75,90,91]. This conventional method poses difficulties as detergent-purified membrane protein samples contain a large number of empty lipo-micelles and isobaric lipid species. Therefore, adding an in-source activation step that strips the detergent micelle makes it possible to select the membrane protein lipid-bound ion in the quadrupole and subsequently fragment it in the collision cell for lipid identification (Figure 3). Using this high-energy MS/MS platform, the additional mass found bound to the homodimeric leucine transporter could be identified as corresponding to two cardiolipin and six phospholipid species, one and three bound per monomer, respectively [46]. In a recent study of three different class A GPCRs, endogenously bound lipids were also identified in a single experiment, revealing a preferential and specific binding to phosphatidylinositol-4,5-bisphosphate [90]. This is an example of how advances in different areas of structural MS, in native and native top-down approaches, can combine to uncover new details of protein structure and function.

Conclusions

By virtue of the above-mentioned breakthroughs and advancements in instrumentation, MS continues to manifest itself as a key tool for integrative structural biology. Its powerful complementary role was recently epitomised by Snijder et al. [92] who, through a combination of native MS, cross-linking and cryo-EM, elucidated the dynamic assembly of the cyanobacterial circadian clock. The field has exciting challenges ahead that will further extend the capabilities of MS to investigate protein structure, function and interactions. For instance, the development of a high-resolution native top-down platform for analysing membrane proteins will offer the same level of discoveries that are now attainable for soluble proteins. Native top-down is now an open playground for integrating approaches such as IM, which has so far only been coupled ‘offline’ in a separate experiment [55,60]. Excitingly, the first step towards an ‘online’ coupling has been very recently made by Poltash et al. [93] who have described the development of a high-resolution native IM–MS using the Orbitrap MS platform. Overall, we expect that MS-based approaches, in parallel with their future developments, will continue to consolidate their powerful role in structural biology. It is clear, therefore, that this new age of MS will be pivotal in discovering the intricacies of protein structure and function.

Abbreviations

     
  • ECD

    electron capture dissociation

  •  
  • ETD

    electron transfer dissociation

  •  
  • FT-ICR

    Fourier-transform ion-cyclotron resonance

  •  
  • GPCR

    G protein-coupled receptor

  •  
  • HCD

    higher-energy collisional dissociation

  •  
  • HDX

    hydrogen-deuterium exchange

  •  
  • IM

    ion mobility

  •  
  • MS

    mass spectrometry

  •  
  • PTM

    post-translational modification

  •  
  • UVPD

    ultraviolet photodissociation

Author Contribution

Both authors contributed equally.

Competing Interests

The Authors declare that there are no competing interests associated with the manuscript.

References

References
1
Leney
,
A.C.
and
Heck
,
A.J.R.
(
2017
)
Native mass spectrometry: what is in the name?
J. Am. Soc. Mass Spectrom.
28
,
5
13
2
Heck
,
A.J.R.
(
2008
)
Native mass spectrometry: a bridge between interactomics and structural biology
.
Nat. Methods
5
,
927
3
Yang
,
Y.
,
Liu
,
F.
,
Franc
,
V.
,
Halim
,
L.A.
,
Schellekens
,
H.
and
Heck
,
A.J.R.
(
2016
)
Hybrid mass spectrometry approaches in glycoprotein analysis and their usage in scoring biosimilarity
.
Nat. Commun.
7
,
13397
4
Franc
,
V.
,
Zhu
,
J.
and
Heck
,
A.J.R.
(
2018
)
Comprehensive proteoform characterization of plasma complement component C8αβγ by hybrid mass spectrometry approaches
.
J. Am. Soc. Mass Spectrom.
29
,
1099
1110
5
Yang
,
Y.
,
Wang
,
G.
,
Song
,
T.
,
Lebrilla
,
C.B.
and
Heck
,
A.J.R.
(
2017
)
Resolving the micro-heterogeneity and structural integrity of monoclonal antibodies by hybrid mass spectrometric approaches
.
mAbs
9
,
638
645
6
Tian
,
Y.
and
Ruotolo
,
B.T.
(
2018
)
The growing role of structural mass spectrometry in the discovery and development of therapeutic antibodies
.
Analyst
143
,
2459
2468
.
7
Wohlschlager
,
T.
,
Scheffler
,
K.
,
Forstenlehner
,
I.C.
,
Skala
,
W.
,
Senn
,
S.
,
Damoc
,
E.
et al.  (
2018
)
Native mass spectrometry combined with enzymatic dissection unravels glycoform heterogeneity of biopharmaceuticals
.
Nat. Commun.
9
,
1713
8
Catherman
,
A.D.
,
Skinner
,
O.S.
and
Kelleher
,
N.L.
(
2014
)
Top down proteomics: facts and perspectives
.
Biochem. Biophys. Res. Commun.
445
,
683
693
9
Armirotti
,
A.
and
Damonte
,
G.
(
2010
)
Achievements and perspectives of top-down proteomics
.
Proteomics
10
,
3566
3576
10
Gregorich
,
Z.R.
and
Ge
,
Y.
(
2014
)
Top-down proteomics in health and disease: challenges and opportunities
.
Proteomics
14
,
1195
1210
11
van de Waterbeemd
,
M.
,
Tamara
,
S.
,
Fort
,
K.L.
,
Damoc
,
E.
,
Franc
,
V.
,
Bieri
,
P.
et al.  (
2018
)
Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods
.
Nat. Commun.
9
,
2493
12
Sinz
,
A.
(
2018
)
Cross-linking/mass spectrometry for studying protein structures and protein–protein interactions: where are we now and where should we go from here?
Angew. Chem. Int. Ed. Engl.
57
,
6390
6396
13
Leitner
,
A.
,
Faini
,
M.
,
Stengel
,
F.
and
Aebersold
,
R.
(
2016
)
Cross-linking and mass spectrometry: an integrated technology to understand the structure and function of molecular machines
.
Trends Biochem. Sci.
41
,
20
32
14
Schmidt
,
C.
and
Robinson
,
C.V.
(
2014
)
A comparative cross-linking strategy to probe conformational changes in protein complexes
.
Nat. Protoc.
9
,
2224
2236
15
Wittig
,
S.
,
Haupt
,
C.
,
Hoffmann
,
W.
,
Kostmann
,
S.
,
Pagel
,
K.
and
Schmidt
,
C.
(
2018
)
Oligomerisation of synaptobrevin-2 studied by native mass spectrometry and chemical cross-linking
.
J. Am. Soc. Mass Spectrom.
30
,
149
160
16
Arlt
,
C.
,
Flegler
,
V.
,
Ihling
,
C.H.
,
Schäfer
,
M.
,
Thondorf
,
I.
and
Sinz
,
A.
(
2017
)
An integrated mass spectrometry based approach to probe the structure of the full-length wild-type tetrameric p53 tumor suppressor
.
Angew. Chem. Int. Ed. Engl.
56
,
275
279
17
Hall
,
Z.
,
Schmidt
,
C.
and
Politis
,
A.
(
2016
)
Uncovering the early assembly mechanism for amyloidogenic β2-microglobulin using cross-linking and native mass spectrometry
.
J. Biol. Chem.
291
,
4626
4637
18
Podobnik
,
M.
,
Savory
,
P.
,
Rojko
,
N.
,
Kisovec
,
M.
,
Wood
,
N.
,
Hambley
,
R.
et al.  (
2016
)
Crystal structure of an invertebrate cytolysin pore reveals unique properties and mechanism of assembly
.
Nat. Commun.
7
,
11598
19
Snijder
,
J.
,
Burnley
,
R.J.
,
Wiegard
,
A.
,
Melquiond
,
A.S.
,
Bonvin
,
A.M.
,
Axmann
,
I.M.
et al.  (
2014
)
Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction
.
Proc. Natl Acad. Sci. U.S.A.
111
,
1379
1384
20
Masson
,
G.R.
,
Jenkins
,
M.L.
and
Burke
,
J.E.
(
2017
)
An overview of hydrogen deuterium exchange mass spectrometry (HDX-MS) in drug discovery
.
Expert Opin. Drug Discov.
12
,
981
994
21
Konermann
,
L.
,
Pan
,
J.
and
Liu
,
Y.-H.
(
2011
)
Hydrogen exchange mass spectrometry for studying protein structure and dynamics
.
Chem. Soc. Rev.
40
,
1224
1234
22
Pirrone
,
G.F.
,
Iacob
,
R.E.
and
Engen
,
J.R.
(
2015
)
Applications of hydrogen/deuterium exchange MS from 2012 to 2014
.
Anal. Chem.
87
,
99
118
23
Kielkopf
,
C.S.
,
Ghosh
,
M.
,
Anand
,
G.S.
and
Brown
,
S.H.J.
(
2018
)
HDX-MS reveals orthosteric and allosteric changes in apolipoprotein-D structural dynamics upon binding of progesterone
.
Protein Sci.
28
,
365
374
24
Huang
,
L.
,
So
,
P.-K.
and
Yao
,
Z.-P.
(
2018
)
Protein dynamics revealed by hydrogen deuterium exchange mass spectrometry: correlation between experiments and simulation
.
Rapid Commun. Mass Spectrom.
25
Xiao
,
Y.
,
Li
,
M.
,
Larocque
,
R.
,
Zhang
,
F.
,
Malhotra
,
A.
,
Chen
,
J.
et al.  (
2018
)
Dimerization interface of osteoprotegerin revealed by hydrogen-deuterium exchange mass spectrometry
.
J. Biol. Chem.
293
,
17523
17535
26
Claesen
,
J.
and
Burzykowski
,
T.
(
2017
)
Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry
.
Mass Spectrom. Rev.
36
,
649
667
27
Yılmaz
,
Ş.
,
Shiferaw
,
G.A.
,
Rayo
,
J.
,
Economou
,
A.
,
Martens
,
L.
and
Vandermarliere
,
E.
(
2018
)
Cross-linked peptide identification: a computational forest of algorithms
.
Mass Spectrom. Rev.
37
,
738
749
28
Gabelica
,
V.
and
Marklund
,
E.
(
2018
)
Fundamentals of ion mobility spectrometry
.
Curr. Opin. Chem. Biol.
42
,
51
59
29
Eschweiler
,
J.D.
,
Frank
,
A.T.
and
Ruotolo
,
B.T.
(
2017
)
Coming to grips with ambiguity: ion mobility-mass spectrometry for protein quaternary structure assignment
.
J. Am. Soc. Mass Spectrom.
28
,
1991
2000
30
Konijnenberg
,
A.
,
Butterer
,
A.
and
Sobott
,
F.
(
2013
)
Native ion mobility-mass spectrometry and related methods in structural biology
.
Biochim. Biophys. Acta Proteins Proteomics
1834
,
1239
1256
31
Eyers
,
C.E.
,
Vonderach
,
M.
,
Ferries
,
S.
,
Jeacock
,
K.
and
Eyers
,
P.A.
(
2018
)
Understanding protein–drug interactions using ion mobility–mass spectrometry
.
Curr. Opin. Chem. Biol.
42
,
167
176
32
Ben-Nissan
,
G.
and
Sharon
,
M.
(
2018
)
The application of ion-mobility mass spectrometry for structure/function investigation of protein complexes
.
Curr. Opin. Chem. Biol.
42
,
25
33
33
Allison
,
T.M.
,
Reading
,
E.
,
Liko
,
I.
,
Baldwin
,
A.J.
,
Laganowsky
,
A.
and
Robinson
,
C.V.
(
2015
)
Quantifying the stabilizing effects of protein-ligand interactions in the gas phase
.
Nat. Commun.
6
,
8551
34
Dixit
,
S.M.
,
Polasky
,
D.A.
and
Ruotolo
,
B.T.
(
2018
)
Collision induced unfolding of isolated proteins in the gas phase: past, present, and future
.
Curr. Opin. Chem. Biol.
42
,
93
100
35
Watanabe
,
Y.
,
Vasiljevic
,
S.
,
Allen
,
J.D.
,
Seabright
,
G.E.
,
Duyvesteyn
,
H.
,
Doores
,
K.J.
et al.  (
2018
)
Signature of antibody domain-exchange by native mass spectrometry and collision induced unfolding
.
Anal. Chem.
90
,
7325
7331
36
Hernandez-Alba
,
O.
,
Wagner-Rousset
,
E.
,
Beck
,
A.
and
Cianférani
,
S.
(
2018
)
Native mass spectrometry, ion mobility, and collision-induced unfolding for conformational characterization of IgG4 monoclonal antibodies
.
Anal. Chem.
90
,
8865
8872
37
Li
,
G.
,
Zheng
,
S.
,
Chen
,
Y.
,
Hou
,
Z.
and
Huang
,
G.
(
2018
)
Reliable tracking in-solution protein unfolding via ultrafast thermal unfolding/ion mobility-mass spectrometry
.
Anal. Chem.
90
,
7997
8001
38
Beveridge
,
R.
,
Migas
,
L.G.
,
Payne
,
K.A.P.
,
Scrutton
,
N.S.
,
Leys
,
D.
and
Barran
,
P.E.
(
2016
)
Mass spectrometry locates local and allosteric conformational changes that occur on cofactor binding
.
Nat. Commun.
7
,
12163
39
Pacholarz
,
K.J.
,
Burnley
,
R.J.
,
Jowitt
,
T.A.
,
Ordsmith
,
V.
,
Pisco
,
J.P.
,
Porrini
,
M.
et al.  (
2017
)
Hybrid mass spectrometry approaches to determine how L-histidine feedback regulates the enzyzme MtATP-phosphoribosyltransferase
.
Structure
25
,
730
–738.e4
40
Botzanowski
,
T.
,
Erb
,
S.
,
Hernandez-Alba
,
O.
,
Ehkirch
,
A.
,
Colas
,
O.
,
Wagner-Rousset
,
E.
et al.  (
2017
)
Insights from native mass spectrometry approaches for top- and middle- level characterization of site-specific antibody-drug conjugates
.
mAbs
9
,
801
811
41
Politis
,
A.
,
Stengel
,
F.
,
Hall
,
Z.
,
Hernández
,
H.
,
Leitner
,
A.
,
Walzthoeni
,
T.
et al.  (
2014
)
A mass spectrometry-based hybrid method for structural modeling of protein complexes
.
Nat. Methods
11
,
403
406
42
Politis
,
A.
,
Park
,
A.Y.
,
Hall
,
Z.
,
Ruotolo
,
B.T.
and
Robinson
,
C.V.
(
2013
)
Integrative modelling coupled with ion mobility mass spectrometry reveals structural features of the clamp loader in complex with single-stranded DNA binding protein
.
J. Mol. Biol.
425
,
4790
4801
43
Eschweiler
,
J.D.
,
Farrugia
,
M.A.
,
Dixit
,
S.M.
,
Hausinger
,
R.P.
and
Ruotolo
,
B.T.
(
2018
)
A structural model of the urease activation complex derived from ion mobility-mass spectrometry and integrative modeling
.
Structure
26
,
599
606.e3
44
Rose
,
R.J.
,
Damoc
,
E.
,
Denisov
,
E.
,
Makarov
,
A.
and
Heck
,
A.J.
(
2012
)
High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies
.
Nat. Methods
9
,
1084
1086
45
Belov
,
M.E.
,
Damoc
,
E.
,
Denisov
,
E.
,
Compton
,
P.D.
,
Horning
,
S.
,
Makarov
,
A.A.
et al.  (
2013
)
From protein complexes to subunit backbone fragments: a multi-stage approach to native mass spectrometry
.
Anal. Chem.
85
,
11163
11173
46
Gupta
,
K.
,
Donlan
,
J.A.C.
,
Hopper
,
J.T.S.
,
Uzdavinys
,
P.
,
Landreh
,
M.
,
Struwe
,
W.B.
et al.  (
2017
)
The role of interfacial lipids in stabilizing membrane protein oligomers
.
Nature
541
,
421
424
47
Konijnenberg
,
A.
,
Bannwarth
,
L.
,
Yilmaz
,
D.
,
Koçer
,
A.
,
Venien-Bryan
,
C.
and
Sobott
,
F.
(
2015
)
Top-down mass spectrometry of intact membrane protein complexes reveals oligomeric state and sequence information in a single experiment
.
Protein Sci.
24
,
1292
1300
48
Li
,
H.
,
Nguyen
,
H.H.
,
Ogorzalek Loo
,
R.R.
,
Campuzano
,
I.D.G.
and
Loo
,
J.A.
(
2018
)
An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes
.
Nat. Chem.
10
,
139
148
49
Li
,
H.
,
Wongkongkathep
,
P.
,
Van Orden
,
S.L.
,
Ogorzalek Loo
,
R.R.
and
Loo
,
J.A.
(
2014
)
Revealing ligand binding sites and quantifying subunit variants of noncovalent protein complexes in a single native top-down FTICR MS experiment
.
J. Am. Soc. Mass Spectrom.
25
,
2060
2068
50
Zhang
,
J.
,
Malmirchegini
,
G.R.
,
Clubb
,
R.T.
and
Loo
,
J.A.
(
2015
)
Native top-down mass spectrometry for the structural characterization of human hemoglobin
.
Eur. J. Mass Spectrom.
21
,
221
231
51
Zhang
,
H.
,
Cui
,
W.
,
Wen
,
J.
,
Blankenship
,
R.E.
and
Gross
,
M.L.
(
2011
)
Native electrospray and electron-capture dissociation FTICR mass spectrometry for top-down studies of protein assemblies
.
Anal. Chem.
83
,
5598
5606
52
Li
,
H.
,
Wolff
,
J.J.
,
Van Orden
,
S.L.
and
Loo
,
J.A.
(
2014
)
Native top-down electrospray ionization-mass spectrometry of 158 kDa protein complex by high-resolution Fourier transform ion cyclotron resonance mass spectrometry
.
Anal. Chem.
86
,
317
320
53
Ben-Nissan
,
G.
,
Belov
,
M.E.
,
Morgenstern
,
D.
,
Levin
,
Y.
,
Dym
,
O.
,
Arkind
,
G.
et al.  (
2017
)
Triple-stage mass spectrometry unravels the heterogeneity of an endogenous protein complex
.
Anal. Chem.
89
,
4708
4715
54
Mehaffey
,
M.R.
,
Sanders
,
J.D.
,
Holden
,
D.D.
,
Nilsson
,
C.L.
and
Brodbelt
,
J.S.
(
2018
)
Multistage ultraviolet photodissociation mass spectrometry to characterize single amino acid variants of human mitochondrial BCAT2
.
Anal. Chem.
90
,
9904
9911
55
Nshanian
,
M.
,
Lantz
,
C.
,
Wongkongkathep
,
P.
,
Schrader
,
T.
,
Klärner
,
F.-G.
,
Blümke
,
A.
et al.  (
2018
)
Native top-down mass spectrometry and ion mobility spectrometry of the interaction of tau protein with a molecular tweezer assembly modulator
.
J. Am. Soc. Mass Spectrom.
90
,
9904
9911
56
Skinner
,
O.S.
,
Havugimana
,
P.C.
,
Haverland
,
N.A.
,
Fornelli
,
L.
,
Early
,
B.P.
,
Greer
,
J.B.
et al.  (
2016
)
An informatic framework for decoding protein complexes by top-down mass spectrometry
.
Nat. Methods
13
,
237
240
57
Skinner
,
O.S.
,
Do Vale
,
L.H.F.
,
Catherman
,
A.D.
,
Havugimana
,
P.C.
,
Sousa
,
M.
,
Compton
,
P.D.
et al.  (
2015
)
Native GELFrEE: a new separation technique for biomolecular assemblies
.
Anal. Chem.
87
,
3032
3038
58
Melani
,
R.D.
,
Seckler
,
H.S.
,
Skinner
,
O.S.
,
Do Vale
,
L.H.F.
,
Catherman
,
A.D.
,
Havugimana
,
P.C.
et al.  (
2016
)
CN-GELFrEE – clear native gel-eluted liquid fraction entrapment electrophoresis
.
JoVE
108
,
e53597
59
Shen
,
X.
,
Kou
,
Q.
,
Guo
,
R.
,
Yang
,
Z.
,
Chen
,
D.
,
Liu
,
X.
et al.  (
2018
)
Native proteomics in discovery mode using size-exclusion chromatography–capillary zone electrophoresis–tandem mass spectrometry
.
Anal. Chem.
90
,
10095
9
60
Wongkongkathep
,
P.
,
Han
,
J.Y.
,
Choi
,
T.S.
,
Yin
,
S.
,
Kim
,
H.I.
and
Loo
,
J.A.
(
2018
)
Native top-down mass spectrometry and ion mobility MS for characterizing the cobalt and manganese metal binding of α-synuclein protein
.
J. Am. Soc. Mass Spectrom.
29
,
1870
1880
61
Li
,
H.
,
Sheng
,
Y.
,
McGee
,
W.
,
Cammarata
,
M.
,
Holden
,
D.
and
Loo
,
J.A.
(
2017
)
Structural characterization of native proteins and protein complexes by electron ionization dissociation-mass spectrometry
.
Anal. Chem.
89
,
2731
2738
62
Fung
,
Y.M.E.
,
Adams
,
C.M.
and
Zubarev
,
R.A.
(
2009
)
Electron ionization dissociation of singly and multiply charged peptides
.
J. Am. Chem. Soc.
131
,
9977
9985
63
O'Brien
,
J.P.
,
Li
,
W.
,
Zhang
,
Y.
and
Brodbelt
,
J.S.
(
2014
)
Characterization of native protein complexes using ultraviolet photodissociation mass spectrometry
.
J. Am. Chem. Soc.
136
,
12920
129208
64
Cammarata
,
M.B.
,
Thyer
,
R.
,
Rosenberg
,
J.
,
Ellington
,
A.
and
Brodbelt
,
J.S.
(
2015
)
Structural characterization of dihydrofolate reductase complexes by top-down ultraviolet photodissociation mass spectrometry
.
J. Am. Chem. Soc.
137
,
9128
9135
65
Cammarata
,
M.B.
,
Schardon
,
C.L.
,
Mehaffey
,
M.R.
,
Rosenberg
,
J.
,
Singleton
,
J.
,
Fast
,
W.
et al.  (
2016
)
Impact of G12 mutations on the structure of K-Ras probed by ultraviolet photodissociation mass spectrometry
.
J. Am. Chem. Soc.
138
,
13187
13196
66
Mehaffey
,
M.R.
,
Cammarata
,
M.B.
and
Brodbelt
,
J.S.
(
2018
)
Tracking the catalytic cycle of adenylate kinase by ultraviolet photodissociation mass spectrometry
.
Anal. Chem.
90
,
839
846
67
Hopper
,
J.T.
,
Yu
,
Y.T.
,
Li
,
D.
,
Raymond
,
A.
,
Bostock
,
M.
,
Liko
,
I.
et al.  (
2013
)
Detergent-free mass spectrometry of membrane protein complexes
.
Nat. Methods
10
,
1206
1208
68
Keener
,
J.E.
,
Reid
,
D.J.
,
Evan Zambrano
,
D.
,
Zak
,
C.
and
Marty
,
M.T.
(
2018
)
Characterizing the lipid annulus surrounding membrane proteins with native mass spectrometry of nanodiscs
.
Biophys. J.
114
,
457a
458a
69
Reid
,
D.J.
,
Keener
,
J.E.
,
Wheeler
,
A.P.
,
Zambrano
,
D.E.
,
Diesing
,
J.M.
,
Reinhardt-Szyba
,
M.
et al.  (
2017
)
Engineering nanodisc scaffold proteins for native mass spectrometry
.
Anal. Chem.
89
,
11189
11192
70
Marty
,
M.T.
,
Hoi
,
K.K.
and
Robinson
,
C.V.
(
2016
)
Interfacing membrane mimetics with mass spectrometry
.
Acc. Chem. Res.
49
,
2459
2467
71
Watkinson
,
T.G.
,
Calabrese
,
A.N.
,
Giusti
,
F.
,
Zoonens
,
M.
,
Radford
,
S.E.
and
Ashcroft
,
A.E.
(
2015
)
Systematic analysis of the use of amphipathic polymers for studies of outer membrane proteins using mass spectrometry
.
Int. J. Mass Spectrom.
391
,
54
61
72
Laganowsky
,
A.
,
Reading
,
E.
,
Hopper
,
J.T.
and
Robinson
,
C.V.
(
2013
)
Mass spectrometry of intact membrane protein complexes
.
Nat. Protoc.
8
,
639
651
73
Laganowsky
,
A.
,
Reading
,
E.
,
Allison
,
T.M.
,
Ulmschneider
,
M.B.
,
Degiacomi
,
M.T.
,
Baldwin
,
A.J.
et al.  (
2014
)
Membrane proteins bind lipids selectively to modulate their structure and function
.
Nature
510
,
172
175
74
Reading
,
E.
,
Liko
,
I.
,
Allison
,
T.M.
,
Benesch
,
J.L.P.
,
Laganowsky
,
A.
and
Robinson
,
C.V.
(
2015
)
The role of the detergent micelle in preserving the structure of membrane proteins in the gas phase
.
Angew. Chem. Int. Ed.
54
,
4577
4581
75
Bechara
,
C.
,
Nöll
,
A.
,
Morgner
,
N.
,
Degiacomi
,
M.T.
,
Tampé
,
R.
and
Robinson
,
C.V.
(
2015
)
A subset of annular lipids is linked to the flippase activity of an ABC transporter
.
Nat. Chem.
7
,
255
262
76
Reading
,
E.
,
Walton Troy
,
A.
,
Liko
,
I.
,
Marty Michael
,
T.
,
Laganowsky
,
A.
,
Rees Douglas
,
C.
et al.  (
2015
)
The effect of detergent, temperature, and lipid on the oligomeric state of MscL constructs: insights from mass spectrometry
.
Chem. Biol.
22
,
593
603
77
Gupta
,
K.
,
Li
,
J.
,
Liko
,
I.
,
Gault
,
J.
,
Bechara
,
C.
,
Wu
,
D.
et al.  (
2018
)
Identifying key membrane protein lipid interactions using mass spectrometry
.
Nat. Protoc.
13
,
1106
1120
78
Yen
,
H.-Y.
,
Hopper
,
J.T.S.
,
Liko
,
I.
,
Allison
,
T.M.
,
Zhu
,
Y.
,
Wang
,
D.
et al.  (
2017
)
Ligand binding to a G protein–coupled receptor captured in a mass spectrometer
.
Sci. Adv.
3
,
e1701016
79
Chorev
,
D.S.
,
Baker
,
L.A.
,
Wu
,
D.
,
Beilsten-Edmands
,
V.
,
Rouse
,
S.L.
,
Zeev-Ben-Mordehai
,
T.
et al.  (
2018
)
Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry
.
Science
362
,
829
834
80
Gault
,
J.
,
Donlan
,
J.A.C.
,
Liko
,
I.
,
Hopper
,
J.T.S.
,
Gupta
,
K.
,
Housden
,
N.G.
et al.  (
2016
)
High-resolution mass spectrometry of small molecules bound to membrane proteins
.
Nat. Methods
13
,
333
336
81
Fort
,
K.L.
,
van de Waterbeemd
,
M.
,
Boll
,
D.
,
Reinhardt-Szyba
,
M.
,
Belov
,
M.E.
,
Sasaki
,
E.
et al.  (
2018
)
Expanding the structural analysis capabilities on an Orbitrap-based mass spectrometer for large macromolecular complexes
.
Analyst
143
,
100
105
82
Liu
,
Y.
,
Cong
,
X.
,
Liu
,
W.
and
Laganowsky
,
A.
(
2017
)
Characterization of membrane protein–lipid interactions by mass spectrometry ion mobility mass spectrometry
.
J. Am. Soc. Mass Spectrom.
28
,
579
586
83
Mirandela
,
G.D.
,
Tamburrino
,
G.
,
Hoskisson
,
P.A.
,
Zachariae
,
U.
and
Javelle
,
A.
(
2018
)
The lipid environment determines the activity of the E. coli ammonium transporter, AmtB
.
FASEB J.
115
,
100
105
84
Cong
,
X.
,
Liu
,
Y.
,
Liu
,
W.
,
Liang
,
X.
and
Laganowsky
,
A.
(
2017
)
Allosteric modulation of protein–protein interactions by individual lipid binding events
.
Nat. Commun.
8
,
2203
85
Patrick
,
J.W.
,
Boone
,
C.D.
,
Liu
,
W.
,
Conover
,
G.M.
,
Liu
,
Y.
,
Cong
,
X.
et al.  (
2018
)
Allostery revealed within lipid binding events to membrane proteins
.
Proc. Natl Acad. Sci. U.S.A.
115
,
2976
2981
86
Mehmood
,
S.
,
Marcoux
,
J.
,
Gault
,
J.
,
Quigley
,
A.
,
Michaelis
,
S.
,
Young
,
S.G.
et al.  (
2016
)
Mass spectrometry captures off-target drug binding and provides mechanistic insights into the human metalloprotease ZMPSTE24
.
Nat. Chem.
8
,
1152
1158
87
Bolla
,
J.R.
,
Sauer
,
J.B.
,
Wu
,
D.
,
Mehmood
,
S.
,
Allison
,
T.M.
and
Robinson
,
C.V.
(
2018
)
Direct observation of the influence of cardiolipin and antibiotics on lipid II binding to MurJ
.
Nat. Chem.
10
,
363
371
88
Landreh
,
M.
,
Marklund
,
E.G.
Uzdavinys
,
P.
,
Degiacomi
,
M.T.
,
Coincon
,
M.
,
Gault
,
J.
et al.  (
2017
)
Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters
.
Nat. Commun.
8
,
13993
89
Pyle
,
E.
,
Kalli
,
A.C.
,
Amillis
,
S.
,
Hall
,
Z.
,
Lau
,
A.M.
,
Hanyaloglu
,
A.C.
et al.  (
2018
)
Structural lipids enable the formation of functional oligomers of the eukaryotic purine symporter UapA
.
Cell Chem. Biol.
25
,
840
848.e4
90
Yen
,
H.-Y.
,
Hoi
,
K.K.
,
Liko
,
I.
,
Hedger
,
G.
,
Horrell
,
M.R.
,
Song
,
W.
et al.  (
2018
)
Ptdins(4,5)P2 stabilizes active states of GPCRs and enhances selectivity of G-protein coupling
.
Nature
559
,
423
427
91
Zhou
,
M.
,
Morgner
,
N.
,
Barrera
,
N.P.
,
Politis
,
A.
,
Isaacson
,
S.C.
,
Matak-Vinkovic
,
D.
et al.  (
2011
)
Mass spectrometry of intact V-type ATPases reveals bound lipids and the effects of nucleotide binding
.
Science
334
,
380
385
92
Snijder
J
,
Schuller
JM
,
Wiegard
A
,
Lössl
P
,
Schmelling
N
,
Axmann
IM
, et al. .
Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state
.
Science
2017
;
355
:
1181
1184
.
93
Poltash
,
M.L.
,
McCabe
,
J.W.
,
Shirzadeh
,
M.
,
Laganowsky
,
A.
,
Clowers
,
B.H.
and
Russell
,
D.H.
(
2018
)
Fourier transform-ion mobility-orbitrap mass spectrometer: a next-generation instrument for native mass spectrometry
.
Anal. Chem.
90
,
10472
10472