Collision cross sections of proteins and their complexes: a calibration framework and database for gas-phase structural biology

Collision cross sections in both helium and nitrogen gases were measured directly using a drift cell with RF ion confinement inserted within a quadrupole/ion mobility/time-of-flight hybrid mass spectrometer (Waters Synapt HDMS, Manchester, U.K.). Collision cross sections for a large set of denatured peptide, denatured protein, native-like protein, and native-like protein complex ions are reported here, forming a database of collision cross sections that spans over 2 orders of magnitude. The average effective density of the native-like ions is 0.6 g cm(-3), which is significantly lower than that for the solvent-excluded regions of proteins and suggests that these ions can retain significant memory of their solution-phase structures rather than collapse to globular structures. Because the measurements are acquired using an instrument that mimics the geometry of the commercial Synapt HDMS instrument, this database enables the determination of highly accurate collision cross sections from traveling-wave ion mobility data through the use of calibration standards with similar masses and mobilities. Errors in traveling-wave collision cross sections determined for native-like protein complexes calibrated using other native-like protein complexes are significantly less than those calibrated using denatured proteins. This database indicates that collision cross sections in both helium and nitrogen gases can be well-correlated for larger biomolecular ions, but non-correlated differences for smaller ions can be more significant. These results enable the generation of more accurate three-dimensional models of protein and other biomolecular complexes using gas-phase structural biology techniques.     

Ion trap/ion mobility/quadrupole/time-of-flight mass spectrometry for peptide mixture analysis

An ion trap/ion mobility/quadrupole/time-of-flight mass spectrometer has been developed for the analysis of peptide mixtures. In this approach, a mixture of peptides is electrosprayed into the gas phase. The mixture of ions that is created is accumulated in an ion trap and periodically injected into a drift tube where ions separate according to differences in gas-phase ion mobilities. Upon exiting the drift tube, ions enter a quadrupole mass filter where a specific mass-to-charge (m/z) ratio can be selected prior to collisional activation in an octopole collision cell. Parent and fragment ions that exit the collision cell are analyzed using a reflectron geometry time-of-flight mass spectrometer. The overall configuration allows different species to be selected according to their mobilities and m/z ratios prior to collision-induced dissociation and final MS analysis. A key parameter in these studies is the pressure of the target gas in the collision cell. Above a critical pressure, the well-defined mobility separation degrades. The approach is demonstrated by examining a mixture of tryptic digest peptides of ubiquitin.     

A tandem ion trap/ion mobility spectrometer

A tandem quadrupole ion trap/ion mobility spectrometer (QIT/IMS) has been constructed for structural analysis based on the gas-phase mobilities of mass-selected ions. The instrument combines the ion accumulation, manipulation, and mass-selection capabilities of a modified ion trap mass spectrometer with gas-phase electrophoretic separation in a custom-built ion mobility drift cell. The quadrupole ion trap may be operated as a conventional mass spectrometer, with ion detection using an off-axis dynode/multiplier arrangement, or as an ion source for the IMS drift cell. In the latter case, pulses of ions are ejected from the trap and transferred to the drift cell where mobility in the presence of helium buffer gas is determined by the collision cross section of the ion. Ions traversing the drift cell are detected by an in-line electron multiplier and the data processed with a multichannel scaler. Preliminary data are presented on instrumental performance characteristics and the application of QIT/ IMS to structural and conformational studies of aromatic ions and protonated amine/crown ether noncovalent complexes generated via ion/molecule reactions in the ion trap.     

Separation of isomeric peptides using electrospray ionization/high-resolution ion mobility spectrometry

In this paper, the first examples of baseline separation of isomeric macromolecules by electrospray ionization/ion mobility spectrometry (ESI/IMS) at atmospheric pressure are presented. The behavior of a number of different isomeric peptides in the IMS was investigated using nitrogen as a drift gas. The IMS was coupled to a quadrupole mass spectrometer, which was used for identification and selective detection of the electrosprayed ions. The mobility data were used to determine their average collision cross sections. The gas-phase ions of isomeric peptides were found to have different collision cross sections. In all cases, doubly charged ions exhibited significantly (8-20%) larger collision cross sections than the respective singly charged species. The analysis of mixtures of the isomeric peptides clearly demonstrated the capability of IMS to separate gas-phase peptide ions due to small differences in their conformational structures, which cannot be determined by mass spectrometry. An actual resolving power of 80 was achieved for two doubly charged reversed sequenced pentapeptides. Baseline separation was provided for ions differing by only 2.5% in their measured collision cross sections; partial separation was shown for isomeric ions exhibiting differences as small as 1.1%.     

Electrospray ionization high-field asymmetric waveform ion mobility spectrometry-mass spectrometry

High-field asymmetric waveform ion mobility spectrometry (FAIMS) is a new technique that separates gas-phase ions at atmospheric pressure (760 Torr) and room temperature. A FAIMS instrument acts as an ion filter and can be set to continuously transmit one type of ion. Despite the stringent requirement for a flow of clean, dry gas in the FAIMS analyzer region, a method of coupling electrospray to FAIMS has been developed. The identity of the electrospray ions separated by FAIMS was determined using mass spectrometry (FAIMS-MS). The theory of FAIMS is discussed, and electrospray FAIMS-MS spectra of several compounds in modes P1, P2, N1, and N2 are presented. Ions appearing in P1 and N1 modes tend to have mobilities that increase as a function of increasing electric field strength, whereas ions appearing in P2 and N2 modes tend to have mobilities that decrease. In general, low-mass ions are focused in P1 and N1 modes, whereas larger ions (e.g., proteins) are focused in P2 and N2 modes. Short-chain peptides, (Gly)(n) where n = 1-6, are shown to cross over from P1 mode into P2 mode as the chain length increases. The removal of the low-mass solvent cluster ions, combined with a reduction of the background noise in electrospray FAIMS-MS, results in an improved signal-to-noise ratio for mass spectra of larger ions (e.g., cyctochrome c) when compared with conventional electrospray-MS. Preliminary results also suggest that various charge states of cytochrome c can be distinguished by FAIMS, implying that the ion mobility of these species at high electric field strength is sensitive to the structure of the protein ion. The linearity of response of electrospray FAIMS-MS was investigated using leucine enkephalin and shows the calibration curve to be linear for ～3 orders of magnitude.     

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(2) 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(He) of 89-616 ?(2), and Ω(N(2)) of 151-801 ?(2); 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(2) gas to estimate Ω(He). 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.     

Mass and collision cross-section determination using a low-vacuum mass spectrometer

A simple low-vacuum mass spectrometer (LVMS) operating in the milliTorr pressure range was developed. The instrument resolves masses by time-of-flight measurements and employs a high-gain, fast-response detector that can operate at these pressures. This instrument allows simultaneous determination of mass and collision cross sections of the ions with the bath gas. Here we demonstrate the LVMS's abilities to determine total collision cross sections for the collisions of organic ions with three background gases, He, N(2), and SF(6). As a demonstration of the system capabilities, the unimolecular interconversion of photochemically produced C(7)H(7)(+) to the tropylium ion structure is investigated.     

Resolving structural isomers of monosaccharide methyl glycosides using drift tube and traveling wave ion mobility mass spectrometry

Monosaccharide structural isomers including sixteen methyl-D-glycopyranosides and four methyl-N-acetylhexosamines were subjected to ion mobility measurements by electrospray ion mobility mass spectrometry. Two ion mobility-MS systems were employed: atmospheric pressure drift tube ion mobility time-of-flight mass spectrometry and a Synapt G2 HDMS system which incorporates a low pressure traveling wave ion mobility separator. All the compounds were investigated as [M + Na](+) ions in the positive mode. A majority of the monosaccharide structural isomers exhibited different mobility drift times in either system, depending on differences in their anomeric and stereochemical configurations. In general, drift time patterns (relative drift times of isomers) matched between the two instruments. Higher resolving power was observed using the atmospheric pressure drift tube. Collision cross section values of monosaccharide structural isomers were directly calculated from the atmospheric pressure ion mobility experiments, and a collision cross section calibration curve was made for the traveling wave ion mobility instrument. Overall, it was demonstrated that ion mobility-mass spectrometry using either drift tube or traveling wave ion mobility is a valuable technique for resolving subtle variations in stereochemistry among the sodium adducts of monosaccharide methyl glycosides.     

Mobility labeling for parallel CID of ion mixtures

An ion mobility/mass spectrometry technique has been developed to record collision-induced dissociation patterns for multiple ions in a parallel fashion. In this approach, a mixture of ions is separated in a drift tube on the basis of differences in mobilities through a buffer gas. As the ions exit the drift tube, they are accelerated into a collision cell and the ensuing fragment ions are dispersed by differences in mass-to-charge (m/z) ratios in a time-of-flight mass spectrometer. Fragment ions that are formed in the collision cell have drift times that are coincident with their antecedent parent ions, allowing the origin of all fragments formed from the mixture of ions to be determined. The approach is demonstrated by examining fragmentation patterns of the [M + H]+ parent and a series of a-, b-, and y-type fragments of [D-Ala2,3]methionine enkephalin.     

Understanding and designing field asymmetric waveform ion mobility spectrometry separations in gas mixtures

Field asymmetric waveform ion mobility spectrometry (FAIMS) has significant potential for post-ionization separations in conjunction with MS analyses. FAIMS fractionates ion mixtures by exploiting the fact that ion mobilities in gases depend on the electric field in a manner specific to each ion. Nearly all previous work has used pure gases, for which FAIMS fundamentals are understood reasonably well; however, unexpected phenomena observed in some gas mixtures (e.g., N(2)/CO(2)) but not in others (N(2)/O(2)) remain unexplained. Here, we introduce and experimentally test a universal model for FAIMS separations in mixtures, derived from formalisms that determine high-field mobilities in heteromolecular gases. Overall, the theoretical findings are consistent with data for N(2)/CO(2) (although quantitative discrepancies remain), while results for N(2)/O(2) fit Blanc's law, in agreement with measurements. Calculations for He/N(2) and He/CO(2) are also consistent with observations and suggest why adding He to the working gas generally enhances FAIMS performance. As predicted, mixtures of gases with extremely disparate molecular masses and collision cross sections, such as He/SF(6), exhibit spectacular non-Blanc effects, which greatly improve the resolution and peak capacity of technique. Understanding FAIMS operation in gas mixtures is expected to enable the rational design of media for both targeted and global analyses.     

Characterizing oligosaccharides using injected-ion mobility/mass spectrometry

Injected-ion mobility/mass spectrometry techniques have been used to measure the reduced ion mobilities for negatively charged raffinose, melezitose and α-, β-, and γ-cyclodextrins formed by electrospray ionization. At low injection energies, the mass spectra are dominated by negatively charged (deprotonated) parent ions. At high injection energies, the mass spectra recorded for the cyclodextrins and raffinose display peaks that result from cross-ring cleavage of individual sugar units. Melezitose dissociates by cleavage of the glycosidic bonds. The ion mobility distributions can be used to distinguish between different isomeric forms of parent and fragment ions having the same mass-to-charge ratios.     

Assessing the peak capacity of IMS-IMS separations of tryptic peptide ions in He at 300 K

Two-dimensional ion mobility spectrometry (IMS-IMS) coupled with mass spectrometry is examined as a means of separating mixtures of tryptic peptides (from myoglobin and hemoglobin). In this study, we utilize two distinct drift regions that are identical in that each contains He buffer gas at 300 K. The two-dimensional advantage is realized by changing the structures of the ions. As ions arrive at the end of the first drift region, those of a specified mobility are selected, exposed to energizing collisions, and then introduced into a second drift region. Upon collisional activation, some ions undergo structural transitions, leading to substantial changes in their mobilities; others undergo only slight (or no) mobility changes. Examination of peak positions and shapes for peptides that are separated in the first IMS dimension indicates experimental peak capacities ranging from approximately 60 to 80; the peak shapes and range of changes in mobility that are observed in the second drift region (after activation) indicate a capacity enhancement ranging from a factor of approximately 7 to 17. Thus, experimental (and theoretical) evaluation of the peak capacity of IMS-IMS operated in this fashion indicates that capacities of approximately 480 to 1360 are accessible for peptides. Molecular modeling techniques are used to simulate the range of structural changes that would be expected for tryptic peptide ions and are consistent with the experimental shifts that are observed.     

Electrospray ionization high-resolution ion mobility spectrometry for the detection of organic compounds, 1. Amino acids

Our aim in this investigation was to demonstrate the potential of the high-resolution electrospray ionization ion mobility spectrometry (ESI-IMS) technique as an analytical separation tool in analyzing biomolecular mixtures to pursue astrobiological objectives of searching for the chemical signatures of life during an in-situ exploration of solar system bodies. Because amino acids represent the basic building blocks of life, we used common amino acids to conduct the first part of our investigation, which is being reported here, to demonstrate the feasibility of using the ESI-IMS technique for detection of the chemical signatures of life. The ion mobilities of common amino acids were determined by electrospray ionization ion mobility spectrometry using three different drift gases (N2, Ar, and CO2). We demonstrated that the selectivity can be vastly improved in ion mobility spectroscopy (IMS) in detecting organic molecules by using different drift gases. When a judicial choice of drift gas is made, a vastly improved separation of two different amino acid ions resulted. It was found that each of the studied amino acids could be uniquely identified from the others, with the exception of alanine and glycine, which were never separable by more then 0.1 ms. This unique identification is a result of the different polarizabilities of the various drift gases. In addition, a better separation was achieved by changing the drift voltage in successive experimental runs without significantly degrading the resolution. We also report the result of our analysis of liquid samples containing mixtures of amino acids.     

Ionization of the glycerin molecule by the electron impact

The paper describes experimental method for and presents the results of studying positive ion yields produced due to direct and dissociative electron-impact ionization of the glycerin molecule. The mass spectra of the glycerin molecule are studied in the range of mass numbers of 10–95 amu at different temperatures. The energy dependences of the ionization efficiency cross sections of the glycerin molecule ions produced by a monoenergetic electron beam are analyzed; using these dependences, the appearance energies of fragment ions are determined. The dynamics of fragment ion formation is investigated in the temperature range of 300–340 K.     

Multiple ionization and capture in relativistic heavy-ion atom collisions

We show that in relativistic heavy-ion collisions the independent electron model can be used to predict cross sections for multiple inner-shell ionization and capture in a single collision. Charge distributions of 82- to 200-MeV/amu Xe and 105- to 955-MeV/amu U ion beams emerging from thin solid targets were used to obtain single- and multiple-electron stripping and capture cross sections. The probabilities of stripping electrons from the K, L, or M shells were calculated using the semiclassical approximation and Dirac hydrogenic wave functions. For capture, a simplified model for electron capture was used. The data generally agree with theory.     

Cis-trans signatures of proline-containing tryptic peptides in the gas phase

High-resolution ion mobility/time-of-flight techniques were used to measure collision cross sections for 968 tryptic digest peptide ions obtained from digestion of common proteins. Here, we report a mobility signature that aids in identifying proline-containing peptides containing 4-10 residues. Of 129 peptides (< or = 10 residues in length) in the database that contain proline residues, 57% show multiple resolved features in the ion mobility distribution for at least one of the [M + H]+ or [M + 2H]2+ ions. These multiple features are attributed to different conformations that arise from populations of cis and trans forms of proline. The number of resolved peaks in the ion mobility distribution appears to be correlated with the peptide ion charge state and the number of proline residues in the peptide.     

Selective detection of alkanolamine vapors by ion mobility spectrometry with ketone reagent gases

The ion mobility (IMS) spectra of the alkanolamines, monoethanolamine (MEA), 3-amino-1-propanol (PRA), 4-amino-1-butanol (BUA), and 5-amino-1-pentanol (PEA) with acetone and 4-heptanone reagent gases have been measured using a hand-held spectrometer. Monomer and dimer peak patterns were observed for all the alkanolamines with acetone reagent gas. Drift times of monomer and dimer ion clusters for each alkanolamine increased linearly in order of size of alkyl group. Ammonia, Freon 22, and F76 diesel vapors, having similar or coincident mobilities, caused severe interference. Replacement of acetone with 4-heptanone reagent gas resulted in good separation by the altering drift times of product ions. The limit of detection was 0.005 ppm having a linear range of 0.005-0.7 ppm, and signal saturation occurred above 0.88 ppm. Detection was reversible, with a response time of 4 min and a slower recovery time of > 60 min, at vapor levels of 0.7 ppm and ambient nozzle and drift-region temperatures. In contrast to acetone chemistry, single-peak patterns were observed for the alkanolamines with the 4-heptanone reagent. Further, drift times unexpectedly remained stagnant with increasing alkyl-group size. From atmospheric pressure chemical ionization (APcI) tandem mass spectral identifications and collision induced studies, dynamic changes in product-ion equilibria in the IMS drift region compensated by differences in collision cross sections were suggested as the governing causes of the unusual mobility effect.     

Electrospray ionization high-resolution ion mobility spectrometry-mass spectrometry

A hybrid atmospheric pressure ion mobility spectrometer is described which exhibits resolving power approaching the diffusion limit for singly and multiply charged ions (over 200 for the most favorable case). Using an electrospray ionization source and a downstream quadrupole mass spectrometer with electron multiplier as detector, this ESI-IMS-MS instrument demonstrates the potential of IMS for rapid analytical separations with a resolving power similar to liquid chromatography. The first measurements of gas-phase mobility spectra of mass-identified multiply charged ions migrating at atmospheric pressure are reported. These spectra confirm that collision cross sections are strongly affected by charge state. Baseline separations of multiply charged states of cytochrome c and ubiquitin demonstrate the improved resolving power of this instrument compared with previous atmospheric pressure ion mobility spectrometers. The effects of electric potential, initial pulse duration, ion-molecule reactions, ion desolvation, Coulombic repulsion, electric field homogeneity, ion collection, and charge on the resolving power of this ion mobility spectrometer are discussed.     

Monitoring structural changes of proteins in an ion trap over approximately 10-200 ms: unfolding transitions in cytochrome c ions.

A new technique for studying the time dependence of conformational changes of gas-phase protein ions is described. In this approach, a short pulse of electrosprayed protein ions is introduced into an ion trap and stored. After a defined time period, the distribution of ions is ejected from the trap into an ion mobility/time-of-flight mass spectrometer. Combined measurements of mobilities and flight times in the mass spectrometer provide information about the abundances of different conformer types and charge-state distributions. By varying the storage time in the trap, it is possible to monitor changes in ion conformation that occur over extended time periods (approximately 10-200 ms). The method is demonstrated by examining changes in cytochrome c ion conformations for the +7 to +10 charge states.     

Ion mobility spectrometer with radial collisional focusing

An ion mobility spectrometer that has its mobility cell as a 20-segment quadrupole and functionally the q2 of a triple-quadrupole mass spectrometer has been assembled and tested. The combination of high cell pressure (maximum of 4 Torr of helium) and low axial field (20-160 V per 20.2 cm) results in negligible internal excitation of the ions despite applications of rf and axial fields. The presence of collisional focusing ensures efficient ion transmission and good sensitivity. Collision cross sections of atomic, cluster, peptide, and protein ions were measured and found comparable to literature and calculated cross sections.