Nanoflow LC/IMS-MS and LC/IMS-CID/MS of protein mixtures

Electrospray Ionization Ion Mobility Mass Spectrometry

Electrospray ionization ion mobility mass spectrometry (ESI-IMS-MS) is a rapidly progressing analytical technique for the examination of complex compounds in the gas phase. ESI-IMS-MS separates isomers, provides structural information, and quantitatively identifies peptides, lipids, carbohydrates, polymers, and metabolites in biological samples. ESI-IMS-MS has pharmaceutical, environmental, and manufacturing applications quickly characterizing drugs, petroleum products, and metal macromolecules. This review provides the history of ESI-IMS-MS development and applications to date.

Comprehensive analysis of chestnut tannins by reversed phase and hydrophilic interaction chromatography coupled to ion mobility and high resolution mass spectrometry

In this study, we report a methodology based on reversed phase LC (RP-LC) and hydrophilic interaction chromatography (HILIC) separations coupled to ion mobility (IM) and high resolution mass spectrometry (HR-MS) for the detailed analysis of hydrolysable tannins. The application of this approach to the analysis of an industrial chestnut (Castanea sativa, wood chips) tannin extract is demonstrated. A total of 38 molecular species, including a large number or isomers, were identified in this sample based on HR-MS^(E) and UV absorption spectral information as well as retention behaviour in both separation modes. In total, 128 and 90 isomeric species were resolved by RP- and HILIC-LC-IM-TOF-MS, respectively. The combination of low- and high collision energy mass spectral data with complementary chromatographic separations allowed tentative and putative identification of twenty molecular species, comprising 78 isomers, in chestnut for the first time. Ion mobility resolved six new dimeric and trimeric vescalagin conformers with unique arrival (drift) times, including new conformers of roburin A-D which were not separated using either RP-LC or HILIC. HILIC was found to be the preferred separation mode for the analysis of vescalagin derivatives, while RP-LC is preferred for the analysis of ellagitannins with a cyclic glucose core. For the complete separation of the galloyl glucose species, comprehensive HILIC × RP-LC separation would be required.

Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses

Ion mobility spectrometry (IMS) is a widely used analytical technique for rapid molecular separations in the gas phase. Though IMS alone is useful, its coupling with mass spectrometry (MS) and front-end separations is extremely beneficial for increasing measurement sensitivity, peak capacity of complex mixtures, and the scope of molecular information available from biological and environmental sample analyses. In fact, multiple disease screening and environmental evaluations have illustrated that the IMS-based multidimensional separations extract information that cannot be acquired with each technique individually. This review highlights three-dimensional separations using IMS-MS in conjunction with a range of front-end techniques, such as gas chromatography, supercritical fluid chromatography, liquid chromatography, solid-phase extractions, capillary electrophoresis, field asymmetric ion mobility spectrometry, and microfluidic devices. The origination, current state, various applications, and future capabilities of these multidimensional approaches are described in detail to provide insight into their uses and benefits.

Top-Down Mass Spectrometry: Proteomics to Proteoforms

This chapter highlights many of the fundamental concepts and technologies in the field of top-down mass spectrometry (TDMS), and provides numerous examples of contributions that TD is making in biology, biophysics, and clinical investigations. TD workflows include variegated steps that may include non-specific or targeted preparative strategies, orthogonal liquid chromatography techniques, analyte ionization, mass analysis, tandem mass spectrometry (MS/MS) and informatics procedures. This diversity of experimental designs has evolved to manage the large dynamic range of protein expression and diverse physiochemical properties of proteins in proteome investigations, tackle proteoform microheterogeneity, as well as determine structure and composition of gas-phase proteins and protein assemblies.

Analytical strategies for studying stem cell metabolism

Owing to their capacity for self-renewal and pluripotency, stem cells possess untold potential for revolutionizing the field of regenerative medicine through the development of novel therapeutic strategies for treating cancer, diabetes, cardiovascular and neurodegenerative diseases. Central to developing these strategies is improving our understanding of biological mechanisms responsible for governing stem cell fate and self-renewal. Increasing attention is being given to the significance of metabolism, through the production of energy and generation of small molecules, as a critical regulator of stem cell functioning. Rapid advances in the field of metabolomics now allow for in-depth profiling of stem cells both in vitro and in vivo, providing a systems perspective on key metabolic and molecular pathways which influence stem cell biology. Understanding the analytical platforms and techniques that are currently used to study stem cell metabolomics, as well as how new insights can be derived from this knowledge, will accelerate new research in the field and improve future efforts to expand our understanding of the interplay between metabolism and stem cell biology.

Mobility-resolved ion selection in uniform drift field ion mobility spectrometry/mass spectrometry: dynamic switching in structures for lossless ion manipulations

A Structures for Lossless Ion Manipulations (SLIM) module that allows ion mobility separations and the switching of ions between alternative drift paths is described. The SLIM switch component has a "Tee" configuration and allows the efficient switching of ions between a linear path and a 90-degree bend. By controlling switching times, ions can be efficiently directed to an alternative channel as a function of their mobilities. In the initial evaluation the switch is used in a static mode and shown compatible with high performance ion mobility separations at 4 Torr. In the dynamic mode, we show that mobility-selected ions can be switched into the alternative channel, and that various ion species can be independently selected based on their mobilities for time-of-flight mass spectrometer (TOF MS) IMS detection and mass analysis. This development also provides the basis of, for example, the selection of specific mobilities for storage and accumulation, and the key component of modules for the assembly of SLIM devices enabling much more complex sequences of ion manipulations.

Size-to-charge dispersion of collision-induced dissociation product ions for enhancement of structural information and product ion identification

Ion mobility is used to disperse product ions formed by collision-induced dissociation (CID) on the basis of charge state and size-to-charge ratio. We previously described an approach for combining CID with ion mobility mass spectrometry (IM-MS) for dispersing fragment ions along charge state specific trend lines (Zinnel, N. F.; Pai, P. J.; Russell, D. H. Anal. Chem. 2012, 84, 3390; Sowell, R. A.; Koeniger, S. L.; Valentine, S. J.; Moon, M. H.; Clemmer, D. E. J. Am. Soc. Mass Spectrom. 2004, 15, 1341; McLean, J. A.; Ruotolo, B. T.; Gillig, K. J.; Russell, D. H. Int. J. Mass Spectrom. 2005, 240, 301), and this approach was used to assign metal ion binding sites for human metallothionein protein MT-2a (Chen, S. H.; Russell, W. K.; Russell, D. H. Anal. Chem. 2013, 85, 3229). Here, we use this approach to distinguish b-type N-terminal fragment ions from both internal fragment ions and y-type C-terminal fragment ions. We also show that in some cases specific secondary structural elements, viz., extended coils or helices, can be obtained for the y-type fragment ions series. The advantage of this approach is that product ion identity can be correlated to gas-phase ion structure, which provides rapid identification of the onset and termination of extended coil structure in peptides.

Advancing the high throughput identification of liver fibrosis protein signatures using multiplexed ion mobility spectrometry

Rapid diagnosis of disease states using less invasive, safer, and more clinically acceptable approaches than presently employed is a crucial direction for the field of medicine. While MS-based proteomics approaches have attempted to meet these objectives, challenges such as the enormous dynamic range of protein concentrations in clinically relevant biofluid samples coupled with the need to address human biodiversity have slowed their employment. Herein, we report on the use of a new instrumental platform that addresses these challenges by coupling technical advances in rapid gas phase multiplexed ion mobility spectrometry separations with liquid chromatography and MS to dramatically increase measurement sensitivity and throughput, further enabling future high throughput MS-based clinical applications. An initial application of the liquid chromatography--ion mobility spectrometry-MS platform analyzing blood serum samples from 60 postliver transplant patients with recurrent fibrosis progression and 60 nontransplant patients illustrates its potential utility for disease characterization.

Ion mobility-mass spectrometry (IM-MS) for top-down proteomics: increased dynamic range affords increased sequence coverage

A general approach that combines mass spectrometry (MS), collision-induced dissociation (CID), ion mobility (IM), and MS for top-down proteomics is described, denoted as MS-CID-IM-MS. Using this approach, CID product ions are dispersed in two dimensions, specifically size-to-charge (IM) and mass-to-charge (MS), and the resulting 2D data display greatly facilitates peptide/protein mass mapping, amino acid sequence analysis, and determination of site-specific protein modifications. Also, this approach alleviates some of the inherent limitations of top-down proteomics, viz. the limitations in dynamic range for fragment ion abundances owing to the number of fragmentation channels available to large ionic systems as well as the resulting spectral congestion. For large peptides such as melittin (2845 Da), CID of the [M + 3H](3+), [M + 4H](4+), and [M + 5H](5+) ions yields amino acid sequence coverage of 42.3%, 38.5%, and 7.7%, respectively, whereas the hybrid MS-CID-IM-MS approach yields amino acid sequence coverages of 84.6%, 65.4%, and 69.2%, respectively. For large biomolecules such as ubiquitin (8565 Da), the amino acid sequence coverage increases from 39% to 76%. The MS-CID-IM-MS top-down approach allows for greater depth of information by allowing the assignment and study of internal fragment ions. Lastly, analysis of the methyl esterification of ubiquitin and single point mutation of human iron sulfur cluster U (HISCU, 14.3 kDa) demonstrates the ability of MS-CID-IM-MS to rapidly identify the presence and sites of modifications.

Travelling wave ion mobility mass spectrometry of 5-aminolaevulinic acid, porphobilinogen and porphyrins

RATIONALE

Human porphyrias, diseases caused by enzyme defects in haem biosynthesis, are characterised by the excessive production, accumulation and excretion of porphyrins and/or 5-aminolaevulinic acid (ALA) and porphobilinogen (PBG). A method for the simultaneous separation, detection and identification of ALA, PBG and porphyrins would greatly facilitate the screening and diagnosis of porphyrias. Such a method would also be invaluable for the biochemical study of the haem, chlorophyll and corrin pathways.

METHODS

An aqueous mixture containing ALA, PBG and type I isomer porphyrins was diluted with acetonitrile and infused (10 μL/min) into a Waters Synapt G2 high-definition mass spectrometer, equipped with a Z-Spray electrospray ionisation (ESI) source. Mass spectra were acquired in positive ionisation mode and the optimised ion mobility spectrometry (IMS) conditions were as follows: IMS wave height (V), 40; IMS wave velocity (m/s), 648; IMS gas flow (mL/min) 90.40; helium gas flow (mL/min), 182.60.

RESULTS

The IMS drift-time increased with increasing ion mass in the order of ALA, PBG, mesoporphyrin, coproporphyrin I, penta-, hexa- and heptacarboxylic acid porphyrin I and uroporphyrin I. The ESI-IMS-MS spectra shows that PBG could form two different positively charged ions by protonation [M+H](+) , m/z 227, or deprotonation [M - H](+) , m/z 225. The protonated PBG (m/z 227) easily eliminated ammonia in source and the fragment ion (m/z 210) was monitored instead. Doubly charged ions of porphyrins having different drift times from the protonated singly charged molecules were observed in high abundance, providing further structural characterisation.

CONCLUSIONS

We have shown, for the first time, an analytical method capable of simultaneously separating haem biosynthetic intermediates and metabolites, for a potential rapid clinical screening method for the porphyrias. IMS-MS allowed the separation of doubly charged porphyrin ions, which will be advantageous for the analysis of natural and synthetic tetrapyrrole compounds, while reducing the misinterpretation of contaminants.

Delineating diseases by IMS-MS profiling of serum N-linked glycans

Altered branching and aberrant expression of N-linked glycans is known to be associated with disease states such as cancer. However, the complexity of determining such variations hinders the development of specific glycomic approaches for assessing disease states. Here, we examine a combination of ion mobility spectrometry (IMS) and mass spectrometry (MS) measurements, with principal component analysis (PCA) for characterizing serum N-linked glycans from 81 individuals: 28 with cirrhosis of the liver, 25 with liver cancer, and 28 apparently healthy. Supervised PCA of combined ion-mobility profiles for several, to as many as 10 different mass-to-charge ratios for glycan ions, improves the delineation of diseased states. This extends an earlier study [J. Proteome Res.2008, 7, 1109-1117] of isomers associated with a single glycan (S(1)H(5)N(4)) in which PCA analysis of the IMS profiles appeared to differentiate the liver cancer group from the other samples. Although performed on a limited number of test subjects, the combination of IMS-MS for different combinations of ions and multivariate PCA analysis shows promise for characterizing disease states.

Resolving and assigning N-linked glycan structural isomers from ovalbumin by IMS-MS

Ion mobility-mass spectrometry (IMS-MS) and molecular modeling techniques have been used to characterize ovalbumin N-linked glycans. Some glycans from this glycoprotein exist as multiple isomeric forms. The gas-phase separation makes it possible to resolve some isomers before MS analysis. Comparisons of experimental cross sections for selected glycan isomers with values that are calculated for iterative structures generated by molecular modeling techniques allow the assignment of sharp features to specific isomers. We focus here on an example glycan set, each having a m/z value of 1046.52 with formula [H5N4+2Na]2+, where H corresponds to a hexose, and N to a N-acetylglucosamine. This glycan appears to exist as three different isomeric forms that are assignable based on comparisons of measured and calculated cross sections. We estimate the relative ratios of the abundances of the three isomers to be in the range of approximately 1.0:1.35:0.85 to approximately 1.0:1.5:0.80. In total, IMS-MS analysis of ovalbumin N-linked glycans provides evidence for 19 different glycan structures corresponding to high-mannose and hybrid type carbohydrates with a total of 42 distinct features related to isomers and/or conformers.

Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics

Proteomics experiments on complex mixtures have benefited greatly from the advent of fast-scanning ion trap mass spectrometers. However, the complexity and dynamic range of mixtures analyzed using shotgun proteomics is still beyond what can be sampled by data-dependent acquisition. Furthermore, the total liquid chromatography-mass spectrometry (LC-MS) peak capacity is not sufficient to resolve the precursors within these mixtures, let alone acquire tandem mass spectra on all of them. Here we describe the application of a high-field asymmetric waveform ion mobility spectrometry (FAIMS) device as an interface to an ion trap mass spectrometer. The dynamic range and peak capacity of the nanoflow LC-FAIMS-MS analysis was assessed using a complex tryptic digest of S. cerevisiae proteins. By adding this relatively simple device to the front of the mass spectrometer, we obtain an increase in peak capacity >8-fold and an increase in dynamic range of >5-fold, without increasing the length of the LC-MS analysis. Thus, the addition of FAIMS to the front of a table-top mass spectrometer can obtain the peak capacity of multidimensional protein identification technology (MudPIT) while increasing the throughput by a factor of 12.

Improving the efficiency of IMS-IMS by a combing technique

A simple method for increasing the efficiency of multidimensional ion mobility spectrometry (IMS-IMS) measurements (as defined by the number of two-dimensional data sets necessary to sample all of the ions in a complex mixture) is illustrated. In this approach, components from a packet containing a mixture of ions are introduced into the first IMS drift region where they are separated based on differences in mobility. At the exit of this region, narrow distributions of ions having identical mobilities are selected, subjected to gentle activation conditions that are intended to induce conformational changes, and transmitted into a second IMS drift region where the new conformations are separated. Here, we describe a simple timing sequence associated with selection and activation of multiple distributions at the entrance of the second drift region in a systematic fashion that improves the efficiency of two-dimensional IMS-IMS by a factor of approximately 8. The method is illustrated by examination of a mixture of tryptic peptides from human hemoglobin.

Pseudorandom sequence modifications for ion mobility orthogonal time-of-flight mass spectrometry

Due to the inherently low duty cycle of ion mobility spectrometry (IMS) experiments that sample from continuous ion sources, a range of experimental advances have been developed to maximize ion utilization efficiency. The use of ion trapping and accumulation approaches prior to the ion mobility drift tube has demonstrated significant gains over discrete sampling from continuous sources but have traditionally relied upon a signal averaging (SA) to attain analytically useful signal-to-noise ratios (SNR). Multiplexed (MP) techniques based upon the Hadamard transform offer an alternative experimental approach by which ion utilization efficiency can be elevated from approximately 1 to approximately 50%. Recently, our research group demonstrated a unique multiplexed ion mobility time-of-flight (MP-IMS-TOF) approach that incorporates ion trapping and can extend ion utilization efficiency beyond 50%. However, the spectral reconstruction of the multiplexed signal using this experiment approach requires the use of sample-specific weighting designs. Such general weighting designs have been shown to significantly enhance ion utilization efficiency using this MP technique, but cannot be universally applied. By modifying both the ion trapping and the pseudorandom sequence (PRS) used for the MP experiment, we have eliminated the need for complex weighting matrices. For both simple and complex mixtures, SNR enhancements of up to 13 were routinely observed as compared to the SA-IMS-TOF approach. In addition, this new class of PRS provides a 2-fold enhancement in the number of ion gate pulses per unit time compared to the traditional HT-IMS experiment.

Peak deconvolution in high-field asymmetric waveform ion mobility spectrometry (FAIMS) to characterize macromolecular conformations

Protonated poly(ethylene glycol), produced by electrospray ionization (ESI), with molecular weights ranging from 0.3 to 5 kDa and charge states from 1+ to 7+ were characterized using high-field asymmetric waveform ion mobility spectrometry (FAIMS). Results for all but some of the 3+ and 4+ charge states are consistent with a single gas-phase conformer or family of unresolved conformers for each of these charge states. The FAIMS compensation voltage scans resulted in peaks that could be accurately fit with a single Gaussian for each peak. The peak widths increase linearly with compensation voltage for maximum ion transmission but do not depend on m/z or molecular weight. Fitting parameters obtained from the poly(ethylene glycol) data were used to analyze conformations of oxidized and reduced lysozyme formed from different solutions. For oxidized lysozyme formed from a buffered aqueous solution, a single conformer (or group of unresolved conformers) was observed for the 7+ and 8+ charge states. Two conformers were observed for the 9+ and 10+ charge states formed from more denaturing solutions. Data for the fully reduced form indicate the existence of up to three different conformers for each charge state produced directly by ESI and a general progression from a more extended to a more folded structure with decreasing charge state. These results are consistent with those obtained previously by proton-transfer reactivity and drift tube ion mobility experiments, although more conformers were identified for the fully reduced form of lysozyme using FAIMS.

Design and performance of an atmospheric pressure ion mobility Fourier transform ion cyclotron resonance mass spectrometer

This manuscript presents our initial results and development of a novel hybrid instrument that combines atmospheric pressure ion mobility spectrometry (AP-IMS) with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Our preliminary results obtained from atmospheric pressure mobility separation of peptide mixtures combined with high-resolution FTICR mass analysis are demonstrated. The custom IMS system was constructed in-house and was coupled to the commercial FTICR-MS instrument through a flared inlet capillary interface. Dual-gate ion filtration was adapted to allow concurrent measurement of both mobility and m/z values. The feasibility of mobility separation was demonstrated with baseline separation of the peptides bradykinin and angiotensin II and their measured reduced mobility constants which were consistent with those previously reported. Furthermore, the unique size-to-charge separation mechanism of IMS that allows isomer separation was explored and demonstrated with the partial separation of two isomeric phosphopeptides. We feel the combination of IMS and FTICR-MS holds great potential for accurate mass analysis of mobility-selected ions and these results are the first to demonstrate the feasibility of coupling these two techniques.

Serum proteome profiles identifies parathyroid hormone physiologic response

Parathyroid hormone (amino acids 1-34) (PTH) regulates bone and calcium homeostasis. The magnitude of the effects of PTH on bone varies in osteoporosis patients. We employed ProteinChip technology to generate protein profiles from sera of mice treated once daily with PTH or vehicle for 3 or 11 days. Data analyses on selected arrays indicated significant increases in serum proteins or peptides in PTH-treated groups, compared to vehicle-controls. The magnitude of change increased with duration of treatment. Anion-exchange fractionation of sera prior to profiling on array surfaces increased the number of proteins detected that were regulated by PTH. The optimized purification conditions developed "on-chip" for subsets of proteins, reflected corresponding behavior with process-compatible chromatographic resins under elution chromatography. We have identified and evaluated subsets of serum proteins regulated by PTH treatment, using a combination of ProteinChip technology, column chromatography, PAGE and LC-MS/MS. Our data demonstrate the feasibility of using a panel of serum proteins to detect PTH responsiveness in humans.

Influence of cation adduction on the separation characteristics of flavonoid diglycoside isomers using dual gate-ion mobility-quadrupole ion trap mass spectrometry

An electrospray ionization-dual gate-ion mobility-quadrupole ion trap mass spectrometer was used to evaluate the separation characteristics of isomeric flavonoid diglycosides adducted with sodium, potassium, and silver. This instrumental configuration allows ions to be selectively accumulated within the ion trap on the basis of their gas phase conformation prior to mass analysis. For the metal cations examined, silver produced the most compact adducts with flavonoid diglycosides. Listed in order of increasing size, the trend of flavonoid diglycoside ion-neutral cross sections adducted with Na+, K+, and Ag+ was narirutin < naringin < hesperidin < neohesperidin < rutin. To examine the separation contribution of the carbohydrate group, hesperetin, the aglycone of hesperidin, and neohesperin were compared to quercetin, the aglycone of rutin. Separation of the flavonoid diglycosides indicated that quercetin-derived diglycosides drifted longer than their hesperetin-derived isomers. Combined with the observed collision assisted dissociation (CAD) data, these findings suggest that carbohydrate moiety plays a significant role in both the separation and metal chelating characteristics of flavonoid diglycosides.

Mass Analysis of Mobility-Selected Ion Populations Using Dual Gate, Ion Mobility, Quadrupole Ion Trap Mass Spectrometry

An electrospray ionization, dual gate, ion mobility, quadrupole ion trap mass spectrometer (ESI-DG-IM-QIT-MS) was constructed and evaluated for its ability to select mobility-filtered ions prior to mass analysis. While modification of the common signal-averaged ion mobility experiment was required, no modifications to the QIT were necessary. The dual gate scanning mode of operation was used to acquire mobility spectra, whereas the single mobility monitoring experiment selectively filtered ions for concentration and subsequent fragmentation within the QIT. Ion mobility separation of positively charged peptides and negatively charged carbohydrates, followed by MS fragmentation, was demonstrated. For a 1-min acquisition time, it was possible to obtain complete de novo sequence information for the examined peptides. Fragmentation of the negative carbohydrate chlorine adducts yielded ions characteristic of cross-ring and glycosidic bond cleavage. Previous unions of atmospheric pressure ion mobility and mass spectrometry have been limited in their ability to reproducibly obtain MSn data for mobility separation ions. The union of high-pressure ion mobility with quadrupole ion trap mass spectrometry presents the unique opportunity to obtain more detailed information regarding the chemistries of gas-phase ions.

Development of Field Modulation in a Split-Field Drift Tube for High-Throughput Multidimensional Separations

A field modulation approach for high-throughput ion mobility/time-of-flight analyses of complex mixtures has been developed using a split-field drift tube. In this approach, complex mixtures of peptides, such as those that arise from tryptic digestion of protein mixtures, are separated by nanocolumn liquid chromatography, ionized by electrospray ionization, and analyzed by ion mobility/time-of-flight techniques. The split-field drift tube allows parent ions to be separated based on differences in their low-field mobilities through the first-field region before entering the second region. For increased throughput, the magnitude of the field in the second region can be modulated throughout an LC separation in order to favor transmission of different types of ions: parent ions at low fields; fragments from primarily [M+3H]3+ peptides at moderate fields; or, fragmentation of [M+3H]3+ and [M+2H]2+ species at higher fields. We demonstrate the approach with two examples: a mixture of tryptic peptides from digestion of hemoglobin; and a complex mixture of tryptic peptides from digestion of human plasma.