16 research outputs found
Recommendations for reporting ion mobility mass spectrometry measurements
© 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc
Interpreting the Collision Cross Sections of Native-like Protein Ions: Insights from Cation-to-Anion Proton-Transfer Reactions
The
effects of charge state on structures of native-like cations
of serum albumin, streptavidin, avidin, and alcohol dehydrogenase
were probed using cation-to-anion proton-transfer reactions (CAPTR),
ion mobility, mass spectrometry, and complementary energy-dependent
experiments. The CAPTR products all have collision cross-section (Ω)
values that are within 5.5% of the original precursor cations. The
first CAPTR event for each precursor yields products that have smaller
Ω values and frequently exhibit the greatest magnitude of change
in Ω resulting from a single CAPTR event. To investigate how
the structures of the precursors affect the structures of the products,
ions were activated as a function of energy prior to CAPTR. In each
case, the Ω values of the activated precursors increase with
increasing energy, but the Ω values of the CAPTR products are
smaller than the activated precursors. To investigate the stabilities
of the CAPTR products, the products were activated immediately prior
to ion mobility. These results show that additional structures with
smaller or larger Ω values can be populated and that the structures
and stabilities of these ions depend most strongly on the identity
of the protein and the charge state of the product, rather than the
charge state of the precursor or the number of CAPTR events. Together,
these results indicate that the excess charges initially present on
native-like ions have a modest, but sometimes statistically significant,
effect on their Ω values. Therefore, potential contributions
from charge state should be considered when using experimental Ω
values to elucidate structures in solution
Effects of Drift Gas Selection on the Ambient-Temperature, Ion Mobility Mass Spectrometry Analysis of Amino Acids
Ion mobility (IM)
separates ions based on their response to an
electric field in the presence of a drift gas. Because of its speed
and sensitivity, the integration of IM and mass spectrometry (MS)
offers many potential advantages for the analysis of small molecules.
To determine the effects that drift gas selection has on the information
content of IM separations, absolute collision cross sections (Ω)
with He, N<sub>2</sub>, Ar, CO<sub>2</sub>, and N<sub>2</sub>O were
measured for the 20 common amino acids using low-pressure, ambient-temperature
ion mobility experiments performed in a radio frequency-confining
drift cell. The drift gases were selected to span a range of masses,
geometries, and polarizabilities. The information content of each
separation was quantified using its peak capacity, which depended
on factors contributing to widths of peaks as well as the range of
Ω relative to the average Ω for the analytes. The selectivity
of each separation was quantified by calculating the peak-to-peak
resolution for each pairwise combination of amino acid ions. The number
of pairs that were resolved depended strongly on the peak capacity,
but the identities of the pairs resolved also depended on the drift
gas. Therefore, results using different drift gases are partially
orthogonal and provide complementary chemical information. The temperatures
and pressures used for these experiments are similar to those used
in many IM-MS instruments, therefore, the outcomes of this research
are applicable to optimizing the information content of a wide range
of contemporary and future IM-MS experiments
Effects of Charge State, Charge Distribution, and Structure on the Ion Mobility of Protein Ions in Helium Gas: Results from Trajectory Method Calculations
Collision cross section
(Ω) values of gas-phase ions of proteins
and protein complexes are used to probe the structures of the corresponding
species in solution. Ions of many proteins exhibit increasing Ω-values
with increasing charge state but most Ω-values calculated for
protein ions have used simple collision models that do not explicitly
account for charge. Here we use a combination of ion mobility mass
spectrometry experiments with helium gas and trajectory method calculations
to characterize the extents to which increases in experimental Ω-values
with increasing charge state may be attributed to increased momentum
transfer concomitant with enhanced long-range interactions between
the protein ion and helium atoms. Ubiquitin and C-to-N terminally
linked diubiquitin ions generated from different solution conditions
exhibit more than a 2-fold increase in Ω with increasing charge
state. For native and energy-relaxed models of the proteins and most
methods for distributing charge, Ω-values calculated using the
trajectory method increase by less than 1% over the range of charge
states observed from typical solution conditions used for native mass
spectrometry. However, the calculated Ω-values increase by 10%
to 15% over the full range of charge states observed from all solution
conditions. Therefore, contributions from enhanced ion-induced dipole
interactions with increasing charge state are significant but without
additional structural changes can account for only a fraction of the
increase in Ω observed experimentally. On the basis of these
results, we suggest guidelines for calculating Ω-values in the
context of applications in biophysics and structural biology
Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure
Ion
mobility is emerging as a rapid and sensitive tool for structural
characterization. Collision cross-section (Ω) values determined
using ion mobility are often compared to values calculated for candidate
structures generated through molecular modeling. Several methods exist
for calculating Ω values, but the trajectory method explicitly
includes contributions from long-range, ion–neutral interactions.
Recent implementations of the trajectory method have significantly
reduced its expense and have made applications to proteins far more
tractable. Here, we use ion mobility experiments and trajectory method
calculations to characterize the effects of charge state, charge distribution,
and structure on the ion mobility of proteins in nitrogen gas. These
results show that ion-induced dipole interactions contribute significantly
to the Ω values of these ions with nitrogen gas, even for the
modestly charged ions commonly observed in native mass spectrometry
experiments. Therefore, these interactions contribute significantly
to the values measured in most structural biology and biophysics applications
of ion mobility using nitrogen gas. Comparisons between the reciprocal
mobilities of protein ions in helium gas and in nitrogen gas show
that there are significant, noncorrelated differences between these
values. As a consequence, it is challenging to estimate the errors
associated with interconverting between helium- and nitrogen-based
mobilities without extensive characterization in both gases, even
for ions of proteins with similar sequences. Therefore, we recommend
reporting Ω and mobility values that are based on the predominant
gas present in the separation and applying additional caution when
comparing results from mobility experiments performed using different
gases
Structural Dynamics of Native-Like Ions in the Gas Phase: Results from Tandem Ion Mobility of Cytochrome <i>c</i>
Ion mobility (IM)
is a gas-phase separation technique that is used
to determine the collision cross sections of native-like ions of proteins
and protein complexes, which are in turn used as restraints for modeling
the structures of those analytes in solution. Here, we evaluate the
stability of native-like ions using tandem IM experiments implemented
using structures for lossless ion manipulations (SLIM). In this implementation
of tandem IM, ions undergo a first dimension of IM up to a switch
that is used to selectively transmit ions of a desired mobility. Selected
ions are accumulated in a trap and then released after a delay to
initiate the second dimension of IM. For delays ranging from 16 to
33 231 ms, the collision cross sections of native-like, 7+ cytochrome <i>c</i> ions increase monotonically from 15.1 to 17.1 nm<sup>2</sup>. The largest products formed in these experiments at near-ambient
temperature are still far smaller than those formed in energy-dependent
experiments (∼21 nm<sup>2</sup>). However, the collision cross
section increases by ∼2% between delay times of 16 and 211
ms, which may have implications for other IM experiments on these
time scales. Finally, two subpopulations from the full population
were each mobility selected and analyzed as a function of delay time,
showing that the three populations can be differentiated for at least
1 s. Together, these results suggest that elements of native-like
structure can have long lifetimes at near-ambient temperature in the
gas phase but that gas-phase dynamics should be considered when interpreting
results from IM
Effects of Polarity on the Structures and Charge States of Native-Like Proteins and Protein Complexes in the Gas Phase
Native
mass spectrometry and ion mobility spectrometry were used to investigate
the gas-phase structures of selected cations and anions of proteins
and protein complexes with masses ranging from 6 to 468 kDa. Under
the same solution conditions, the average charge states observed for
all native-like anions were less than those for the corresponding
cations. Using an rf-confining drift cell, similar collision cross
sections were measured in positive and negative ion mode suggesting
that anions and cations have very similar structures. This result
suggests that for protein and protein complex ions within this mass
range, there is no inherent benefit to selecting a specific polarity
for capturing a more native-like structure. For peptides and low-mass
proteins, polarity and charge-state dependent structural changes may
be more significant. The charged-residue model is most often used
to explain the ionization of large macromolecules based on the Rayleigh
limit, which defines the upper limit of charge that a droplet can
hold. Because ions of both polarities have similar structures and
the Rayleigh limit does not depend on polarity, these results cannot
be explained by the charged-residue model alone. Rather, the observed
charge-state distributions are most consistent with charge-carrier
emissions during the final stages of analyte desolvation, with lower
charge-carrier emission energies for anions than the corresponding
cations. These results suggest that the observed charge-state distributions
in most native mass spectrometry experiments are determined by charge-carrier
emission processes; although the Rayleigh limit may determine the
gas-phase charge states of larger species, e.g., virus capsids
Effects of Solution Structure on the Folding of Lysozyme Ions in the Gas Phase
The
fidelity between the structures of proteins in solution and
protein ions in the gas phase is critical to experiments that use
gas-phase measurements to infer structures in solution. Here we generate
ions of lysozyme, a 129-residue protein whose native tertiary structure
contains four internal disulfide bonds, from three solutions that
preserve varying extents of the original native structure. We then
use cation-to-anion proton-transfer reactions (CAPTR) to reduce the
charge states of those ions in the gas phase and ion mobility to probe
their structures. The collision cross section (Ω) distributions
of each CAPTR product depends to varying extents on the original solution,
the charge state of the product, and the charge state of the precursor.
For example, the Ω distributions of the 6+ ions depend strongly
on the original solutions conditions and to a lesser extent on the
charge state of the precursor. Energy-dependent experiments suggest
that very different structures are accessible to disulfide-reduced
and disulfide-intact ions, but similar Ω distributions are formed
at high energy for disulfide-intact ions from denaturing and from
aqueous conditions. The Ω distributions of the 3+ ions are all
similar but exhibit subtle differences that depend more strongly on
the original solutions conditions than other factors. More generally,
these results suggest that specific CAPTR products may be especially
sensitive to specific elements of structure in solution
Analysis of Native-Like Ions Using Structures for Lossless Ion Manipulations
Ion mobility separation of native-like
protein and protein complex
ions expands the structural information available through native mass
spectrometry analysis. Here, we implement Structures for Lossless
Ion Manipulations (SLIM) for the analysis of native-like ions. SLIM
has been shown previously to operate with near lossless transmission
of ions up to 3000 Da in mass. Here for the first time, SLIM was used
to separate native-like protein and protein complex ions ranging in
mass from 12 to 145 kDa. The resulting arrival-time distributions
were monomodal and were used to determine collision cross section
values that are within 3% of those determined from radio-frequency-confining
drift cell measurements. These results are consistent with the retention
of native-like ion structures throughout these experiments. The apparent
resolving powers of native-like ions measured using SLIM are as high
as 42, which is the highest value reported directly from experimental
data for the native-like ion of a protein complex. Interestingly,
the apparent resolving power depends strongly on the identity of the
analyte, suggesting that the arrival-time distributions of these ions
may have contributions from an ensemble of structures in the gas phase
that is unique to each analyte. These results suggest that the broad
range of emerging SLIM technologies may all be adaptable to the analysis
of native-like ions, which will enable future applications in the
areas of structural biology, biophysics, and biopharmaceutical characterization
Ion Mobility Mass Spectrometry of Peptide Ions: Effects of Drift Gas and Calibration Strategies
One difficulty in using ion mobility (IM) mass spectrometry
(MS) to improve the specificity of peptide ion assignments is that
IM separations are performed using a range of pressures, gas compositions,
temperatures, and modes of separation, which makes it challenging
to rapidly extract accurate shape parameters. We report collision
cross section values (Ω) in both He and N<sub>2</sub> gases
for 113 peptide ions determined directly from drift times measured
in a low-pressure, ambient temperature drift cell with radio-frequency
(rf) ion confinement. These peptide ions have masses ranging from
231 to 2969 Da, Ω<sub>He</sub> of 89–616 Å<sup>2</sup>, and Ω<sub>N<sub>2</sub></sub> of 151–801 Å<sup>2</sup>; thus, they are ideal for calibrating results from proteomics
experiments. These results were used to quantify the errors associated
with traveling-wave Ω measurements of peptide ions and the errors
concomitant with using drift times measured in N<sub>2</sub> gas to
estimate Ω<sub>He</sub>. More broadly, these results enable
the rapid and accurate determination of calibrated Ω for peptide
ions, which could be used as an additional parameter to increase the
specificity of assignments in proteomics experiments