Kevin Giles

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.

Evidence for Macromolecular Protein Rings in the Absence of Bulk Water

We have examined the architecture of a protein complex in the absence of bulk water. By determining collision cross sections of assemblies of the trp RNA binding protein, TRAP, we established that the 11-membered ring topology of the complex can be maintained within a mass spectrometer. We also found that the binding of tryptophan enhances the stability of the ring structure and that addition of a specific RNA molecule increases the size of the complex and prevents structural collapse. These results provide definitive evidence that protein quaternary structure can be maintained in the absence of bulk water and highlight the potential of ion mobility separation for defining shapes of heterogeneous macromolecular assemblies.

Enhancements in travelling wave ion mobility resolution

The use of ion mobility separation to determine the collision cross-section of a gas-phase ion can provide valuable structural information. The introduction of travelling-wave ion mobility within a quadrupole/time-of-flight mass spectrometer has afforded routine collision cross-section measurements to be performed on a range of ionic species differing in gas-phase size/structure and molecular weight at physiologically relevant concentrations. Herein we discuss the technical advances in the second-generation travelling-wave ion mobility separator, which result in up to a four-fold increase in mobility resolution. This improvement is demonstrated using two reverse peptides (mw 490 Da), small ruthenium-containing anticancer drugs (mw 427 Da), a cisplatin-modified protein (mw 8776 Da) and the noncovalent tetradecameric chaperone complex GroEL (mw 802 kDa). What is also shown are that the collision cross-sections determined using the second-generation mobility separator correlate well with the previous generation and theoretically derived values.

Kinetic energy, temperature, and derived rotational temperature dependences for the reactions of Kr+(2P3/2) and Ar+ with HCl

Rate constants for the reactions of Kr+(2P3/2) with HCl and DCl and of Ar+ with HCl have been measured as a function of reactant ion/reactant neutral average center‐of‐mass kinetic energy (〈KEc.m.〉 ) at several temperatures. The measurements were made using helium as the carrier gas. From these data we have derived the dependences of the rate constants on the rotational temperature of H(D)Cl. Rate constants for the reaction of Kr+(2P1/2) with HCl have also been measured as a function of temperature. The rate constants for all of the reactions were found to decrease with increasing temperature. The rate constants were also found to decrease with increasing 〈KEc.m.〉 at low 〈KEc.m.〉 but then to increase at higher 〈KEc.m.〉 . A significant rotational temperature dependence of the rate constant was derived for the reaction of Kr+(2P3/2) with H(D)Cl. The analogous derivation for Ar+ reacting with HCl showed the rate constant for this reaction to be independent of the rotational temperature of HCl within experime...

HIGH THROUGHPUT LIQUID CHROMATOGRAPHY/MASS SPECTROMETRIC ANALYSES USING A NOVEL MULTIPLEXED ELECTROSPRAY INTERFACE

A novel four- channel multiplexed electrospray liquid chromatography interface is described. This device has been used to analyse both single components and mixtures by liquid chromatography/mass spectrometry (LC/MS) as well as synthetic samples prepared by automated procedures. These data provided unambiguous molecular weight assignments to both major components and synthetic by-products in these samples. In this work particular attention has also been paid to the elimination of interchannel crosstalk. Copyright 1999 John Wiley & Sons, Ltd.

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.

Evidence for Structural Variants of a- and b-Type Peptide Fragment Ions Using Combined Ion Mobility/Mass Spectrometry

Tandem mass spectrometry (MS/MS) of peptides plays a key role in the field of proteomics, and an understanding of the fragmentation mechanisms involved is vital for data interpretation. Not all the fragment ions observed by low-energy collision-induced dissociation of protonated peptides are readily explained by the generally accepted structures for a- and b-ions. The possibility of a macrocyclic structure for b-type ions has been recently proposed. In this study, we have undertaken investigations of linear protonated YAGFL-NH2, N-acetylated-YAGFL-NH2, and cyclo-(YAGFL) peptides and their fragments using a combination of ion mobility (IM) separation and mass spectrometry. The use of IM in this work both gives insight into relative structural forms of the ion species and crucial separation of isobaric species. Our study provides compelling evidence for the formation of a stable macrocyclic structure for the b5 ion generated by fragmentation of protonated linear YAGFL-NH2. Additionally we demonstrate that the a4 ion fragment of protonated YAGFL-NH2 has at least two structures; one of which is attributable to a macrocyclic structure on the basis of its subsequent fragmentation. More generally, this work emphasizes the value of combined IM-MS/MS in probing the detailed fragmentation mechanisms of peptide ions, and illustrates the use of combined ion mobility/collisional activation/mass spectrometry analysis in achieving an effective enhancement of the resolution of the mobility separator.

Isomer Separation and Gas-Phase Configurations of Organoruthenium Anticancer Complexes: Ion Mobility Mass Spectrometry and Modeling

We have used ion mobility-mass spectrometry combined with molecular modeling for the separation and configurational analysis of three low-molecular-weight isomeric organoruthenium anticancer complexes containing ortho-, meta-, or para-terphenyl arene ligands. The isomers were separated using ion mobility based on traveling-wave technology and the experimentally determined collision cross sections were compared to theoretical calculations. Excellent agreement was observed between the experimentally and theoretically derived measurements.

Application of the Mason−Schamp Equation and Ion Mobility Mass Spectrometry To Identify Structurally Related Compounds in Crude Oil

The various components of crude oil were structurally resolved using an atmospheric-pressure solids analysis probe (ASAP) coupled with ion mobility mass spectrometry (IM-MS). An ASAP source was used to broadly fractionate compounds according to their boiling points, thereby simplifying the resulting mass spectra for easier data interpretation. The m/z-mobility plots obtained by IM-MS analysis of crude oil could be used to find the structural relationship between crude oil molecules. That was demonstrated using ion mobility mass spectra from a homologous series of compounds, differing only by the number of alkyl units, found in crude oil. The peaks from this series were linearly aligned in the plot, suggesting a continuous increase of the collisional cross section with an increase of mass values and hence the absence of significant structural differences within the series. In contrast, peaks in a homologous series differing only in the number of pendant hydrogen atoms were not linearly aligned, suggesting a discontinuous increase of the collisional cross section with an increase of mass values and hence significant structural differences due to the addition or removal of hydrogen. Cases in which a slope change was observed at three- or four-peak intervals may be related to the addition of an aromatic ring to existing structures. Overall, ion mobility mass spectrometry demonstrates a useful tool that can be used to elucidate structural relationships between molecules comprising crude oil.

Are liquid chromatography/electrospray tandem quadrupole fragmentation ratios unequivocal confirmation criteria?

Multiple reaction monitoring (MRM) ratios as provided by tandem mass spectrometers are used to confirm positive residue findings (e.g. veterinary drugs or pesticides). The Commission Decision 2002/657/EEC defines tolerance levels for MRM ratios, which are intended to prevent the reporting of false positives. This paper reports findings where blank sample extracts have been spiked by a drug (difloxacin) and the corresponding measured MRM ratios significantly deviated from MRM ratios observed in matrix-free solution. The observation was explained by the formation of two different [M+H](+) analyte ions within the electrospray ionization (ESI) interface. These two ions vary only by the site of analyte protonation. Since they are isobaric, they are equally transmitted through the first quadrupole, but are differently fragmented in the collision chamber. The existence of two isobaric ions was deduced by statistical data and the observation of a doubly charged analyte ion. It was hypothesized that the combined presence of [M+H](+) and [M+2H](2+) implies the existence of two different singly charged ion species differing only by the site of protonation. Low- and high-energy interface-induced fragmentation was performed on the samples. The surviving precursor ion population was mass selected and again fragmented in the collision chamber. Equal product ion spectra would be expected. However, very different product ion spectra were observed for the two interface regimes. This is consistent with the assumption that the two postulated isobaric precursor ions show different stability in the interface. Hence the abundance ratio among the two types of surviving precursor ions will shift and change the resulting product ion spectra. The existence of the postulated singly charged ions with multiple chargeable sites was finally confirmed by successful ion mobility separation.