Ultrahigh-resolution differential ion mobility spectrometry using extended separation times

Ion mobility spectrometry (IMS), and particularly differential IMS or field asymmetric waveform IMS (FAIMS), is emerging as a versatile tool for separation and identification of gas-phase ions, especially in conjunction with mass spectrometry. For over two decades since its inception, the utility of FAIMS was constrained by resolving power (R) of less than ～20. Stronger electric fields and optimized gas mixtures have recently raised achievable R to ～200, but further progress with such approaches is impeded by electrical breakdown. However, the resolving power of planar FAIMS devices using any gas and field intensity scales as the square root of separation time (t). Here, we extended t from the previous maximum of 0.2 s up to 4-fold by reducing the carrier gas flow and increased the resolving power by up to 2-fold as predicted, to >300 for multiply charged peptides. The resulting resolution gain has enabled separation of previously "co-eluting" peptide isomers, including folding conformers and localization variants of modified peptides. More broadly, a peak capacity of ～200 has been reached in tryptic digest separations.     

Silicon microfabricated column with microfabricated differential mobility spectrometer for GC analysis of volatile organic compounds

A 3.0-m-long, 150-microm-wide, 240-microm-deep channel etched in a 3.2-cm-square silicon chip, covered with a Pyrex wafer, and coated with a dimethyl polysiloxane stationary phase is used for the GC separation of volatile organic compounds. The column, which generates approximately 5500 theoretical plates, is temperature-programmed in a conventional convection oven. The column is connected through a heated transfer line to a microfabricated differential mobility spectrometer. The spectrometer incorporates a 63Ni source for atmospheric-pressure chemical ionization of the analytes. Nitrogen or air transport gas (flow 300 cm(3)/min) drives the analyte ions through the cell. The spectrometer operates with an asymmetric radio frequency (RF) electric field between a pair of electrodes in the detector cell. During each radio frequency cycle, the ion mobility alternates between a high-field and a low-field value (differential mobility). Ions oscillate between the electrodes, and only ions with an appropriate differential mobility reach a pair of biased collectors at the downstream end of the cell. A compensation voltage applied to one of the RF electrodes is scanned to allow ions with different differential mobilities to pass through the cell without being annihilated at the RF electrodes. A unique feature of the device is that both positive and negative ions are detected from a single experiment. The combined microfabricated column and detector is evaluated for the analysis of volatile organic compounds with a variety of functionalities.     

Characterization of gas-phase molecular interactions on differential mobility ion behavior utilizing an electrospray ionization-differential mobility-mass spectrometer system

Differential mobility spectrometry (DMS) is a rapidly advancing technology for gas-phase ion separation. The interfacing of DMS with mass spectrometry (MS) offers potential advantages over the use of mass spectrometry alone. Such advantages include improvements to mass spectral signal/noise ratios, orthogonal/complementary ion separation to mass spectrometry, enhanced ion and complexation structural analysis, and potential for rapid analyte quantitation. The introduction of a new ESI-DMS-MS system and its utilization to aid in the understanding of DMS separation theory is described. A current contribution to DMS separation theory is one of an association/dissociation process between ions/molecules in the gas phase during the differential mobility separation. A model study was designed to investigate the molecular dynamics and chemical factors influencing the theorized association/dissociation process, and the mechanisms by which these gas-phase interactions affect an ion's DM behavior. Five piperidine analogues were selected as model analytes, and three alcohol drift gas dopants/modifiers were used to interrogate the analyte ions in the gas phase. Two proposed DMS separation mechanisms, introduced as Core and Fa?ade, corresponding to strong and weak attractions between ions/molecules in the gas phase, are detailed. The proposed mechanisms provide explanation for the observed changes in analyte separation by the various drift gas modifiers. Molecular modeling of the proposed mechanisms provides supportive data and demonstrates the potential for predictive optimization of analyte separation based on drift gas modifier effects.     

Quantifying ligand adsorption to nanoparticles using tandem differential mobility mass analysis

Although electrospray-differential mobility analyzers (ES-DMA) have been previously employed to characterize ligand binding to nanoparticles, absolute quantification of surface coverage can be inaccurate at times because of ligand conformational effects. In this Letter, we report a quantitative technique by in-flight coupling of a particle mass analyzer (APM) with ES-DMA, thus enabling a direct quantitative analysis of mass independent of particle size, material, morphology and conformation. We demonstrate the utility of ES-DMA-APM by studying two model complex systems (gold nanoparticle-bovine serum albumin and polystyrene bead-antibody) as a function of concentration and pH. Our results obtained with ES-DMA-APM are in excellent agreement with prior work. We anticipate that this will enhance the capabilities of online quantitative characterization of ligand binding to nanoparticles.     

Preparative linear ion trap mass spectrometer for separation and collection of purified proteins and peptides in arrays using ion soft landing

A preparative mass spectrometer for microarray fabrication is reported. The instrument includes an atmospheric pressure ionization source, a linear ion trap mass analyzer, an ion collection surface positioning system, and a surface loading chamber with independent vacuum pumping. It was designed for the production of protein arrays using the ion soft-landing technique to collect ions on a surface after separation by mass/charge ratio. Small microarrays have been prepared by isolating and soft landing individual protein or peptide ions after electrospray ionization of mixtures. The composition and purity of the separated materials has been confirmed using independent external mass spectrometric analysis of rinse solutions of the collected spots, either by the new method of electrosonic spray ionization MS or by nanospray ionization MS. The ability to retain bioactivity in the mass-selected and collected biomolecules has been demonstrated in particular cases. The reported instrument has also been characterized as an analytical mass spectrometer.     

3D-printing of a complete modular ion mobility spectrometer

Three-dimensional printing (3D-printing) is an asset for rapid prototyping. Therefore, this technology is applied in amateur, fundamental as well as in applied research communities. Moreover, the fused deposition modeling even allows a cheap and fast 3D-printing of functional filaments such as conductive or ferro-magnetic materials. Further applicable materials enable the production of electronic circuits, electrodes or even complete analytical sensors.Here, a 3D-printed stand-alone drift tube ion mobility spectrometer (IMS) completely manufactured in one process is presented. The ionization chamber, the Bradbury-Nielsen gate, the partly conductive drift tube, and the detector including an aperture grid and a Faraday plate were printed by dual extrusion 3D-printing. Therefore, non-conductive polylactic acid (PLA) was utilized for the housing and conductive PLA was used for the electrodes, the ion gate and the detector. Due to a magnetic quick lock system and a modular design, each part of this innovative ion mobility spectrometer can be exchanged in an instant. All parts were validated individually and as a whole by comparing them to an ion mobility spectrometer produced by computerized numerical control machining consisting of polytetrafluoroethylene (PTFE).To investigate the performance, parameters regarding the resolution, resolving power, signal-to-noise ratio, running-in period and long-term stability were used involving a set of isomeric volatile organic compounds (VOCs). Notably, every single 3D-printed component as well as the completely 3D-printed IMS could keep up with the traditionally produced ones. Furthermore, the signal intensity was comparable to the signal intensity of the PTFE-IMS in exemplary optimization steps. The resolution, resolving power and signal-to-noise ratio could be improved by the variation of the Bradbury-Nielsen gate design, thus demonstrating the potential of the 3D-printing for design optimization and rapid prototyping of analytical instrumentation.     

Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer

The quantitative analysis of complex biological samples has emerged as a key research area in the field of proteomics. Although quantitative proteomic experiments remain challenging, these strategies have been greatly facilitated by the development of newer high-performance mass spectrometers. In this work, we have evaluated the use of the LTQ-Orbitrap, a hybrid mass spectrometer in which a linear ion trap is coupled to an Orbitrap mass analyzer, for quantitative analyses. By analyzing a range of yeast protein standards, we found that the high mass accuracy, high resolution, large ion capacity, and large dynamic range of the LTQ-Orbitrap led to as much as a 4-5-fold improvement in the number and quality of the peptide ratio measurements compared to similar analyses done on the LTQ. We also successfully quantified protein expression differences that occur in metabolically labeled rat synapses during brain development to further demonstrate the suitability of the LTQ-Orbitrap for the comparative analysis of complex tissue samples.     

A fast data collection and analysis system for a magnetic spectrometer

The data collection and pre-processing system used in LEAR experiment PS183 is described.     

Capillary electrochromatography for separation of peptides driven with electrophoretic mobility on monolithic column.

A mode of capillary electrochromatography for separation of ionic compounds driven by electrophoretic mobility on a neutrally hydrophobic monolithic column was developed. The monolithic column was prepared from the in situ copolymerization of lauryl methacrylate and ethylene dimethacrylate to form a C12 hydrophobic stationary phase. It was found that EOF in this hydrophobic monolithic column was very poor, even the pH value of mobile phase at 8.0. The peptides at acidic buffer were separated on the basis of their differences in electrophoretic mobility and hydrophobic interaction with the stationary phase; therefore, different separation selectivity can be obtained in CEC from that in capillary zone electrophoresis (CZE). Separation of peptides has been realized with high column efficiency (up to 150,000 plates/meter) and good reproducibility (migration time with RSD <0.5%), and all of the peptides, including some basic peptides, showed good peak symmetry. Effects of the mobile phase compositions on the retention of peptides at low pH have been investigated in a hydrophobic capillary monolithic column. The significant difference in selectivity of peptides in CZE and CEC has been observed. Some peptide isomers that cannot be separated by CZE have been successfully separated on the capillary monolithic column in this mode with the same buffer used.     

Separation of a set of peptide sequence isomers using differential ion mobility spectrometry

Protein identification in bottom-up proteomics requires disentangling isomers of proteolytic peptides, a major class of which are sequence inversions. Their separation using ion mobility spectrometry (IMS) has been limited to isomeric pairs. Here we demonstrate baseline separation of all seven 8-mer tryptic peptide isomers using differential IMS. Evaluation of peak capacity implies that even larger libraries should be resolved for heavier peptides with higher charge states.     

Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer

We describe an approach to the quantitative analysis of complex protein mixtures using a MALDI quadrupole time-of-flight (MALDI QqTOF) mass spectrometer and isotope coded affinity tag reagents (Gygi, S. P.; et al. Nat. Biotechnol. 1999, 17, 994-9.). Proteins in mixtures are first labeled on cysteinyl residues using an isotope coded affinity tag reagent, the proteins are enzymatically digested, and the labeled peptides are purified using a multidimensional separation procedure, with the last step being the elution of the labeled peptides from a microcapillary reversed-phase liquid chromatography column directly onto a MALDI sample target. After addition of matrix, the sample spots are analyzed using a MALDI QqTOF mass spectrometer, by first obtaining a mass spectrum of the peptides in each sample spot in order to quantify the ratio of abundance of pairs of isotopically tagged peptides, followed by tandem mass spectrometric analysis to ascertain the sequence of selected peptides for protein identification. The effectiveness of this approach is demonstrated in the quantification and identification of peptides from a control mixture of proteins of known relative concentrations and also in the comparative analysis of protein expression in Saccharomyces cerevisiae grown on two different carbon sources.     

Physical characterization of icosahedral virus ultra structure, stability, and integrity using electrospray differential mobility analysis

We present a rapid and quantitative method to physically characterize the structure and stability of viruses. Electrospray differential mobility analysis (ES-DMA) is used to determine the size of capsomers (i.e., hexons) and complete capsids. We demonstrate how to convert the measured mobility size into the icosahedral dimensions of a virus, which for PR772 become 68.4 nm for vertex-to-vertex, 54.4 nm for facet-to-facet, and 58.2 nm for edge-to-edge lengths, in reasonable agreement with dimensions from transmission electron microscopy for other members of the family Tectiviridae (e.g., PRD1). These results indicate ES-DMA's mobility diameter most closely approximates the edge-to-edge length. Using PR772's edge length (36.0 nm) and the size of the major capsid hexon (≈8.4 nm) from ES-DMA with icosahedral geometry, PR772's T = 25 symmetry is confirmed and the number of proteins in the capsid shell is determined. We also demonstrate the use of ES-DMA to monitor the temporal disintegration of PR772, the thermal degradation of PP7, and the appearance of degradation products, essential to viral stability assays. These results lay groundwork essential for the use of ES-DMA for a variety of applications including monitoring of vaccine and gene therapy vector products, confirmation of viral inactivation, and theoretical studies of self-assembling macromolecular structures.     

Improvement in analysis of O2 in N2 by using Ar drift gas in an ion mobility spectrometer

Ion mobility spectrometry (IMS) is capable of providing real-time analysis of several impurities in inert gases. Because of its poor peak resolution, the IMS is susceptible to peak interferences. Previous study has shown that the detection limit and accuracy of O2 measurement in N2 suffers from peak interference. In many applications, the interference can be avoided by selecting a proper drift gas. For N2 analysis, we have demonstrated that the peak interference of O2 can be eliminated by using Ar as a drift gas. The use of Ar changes the chemical reactions that occur inside the drift region and results in different product ions. The peaks of new product ions are well-separated and do not coincide with the peak representing O2.     

Species-specific bacteria identification using differential mobility spectrometry and bioinformatics pattern recognition

As bacteria grow and proliferate, they release a variety of volatile compounds that can be profiled and used for speciation, providing an approach amenable to disease diagnosis through quick analysis of clinical cultures as well as patient breath analysis. As a practical alternative to mass spectrometry detection and whole cell pyrolysis approaches, we have developed methodology that involves detection via a sensitive, micromachined differential mobility spectrometer (microDMx), for sampling headspace gases produced by bacteria growing in liquid culture. We have applied pattern discovery/recognition algorithms (ProteomeQuest) to analyze headspace gas spectra generated by microDMx to reliably discern multiple species of bacteria in vitro: Escherichia coli, Bacillus subtilis, Bacillus thuringiensis, and Mycobacterium smegmatis. The overall accuracy for identifying volatile profiles of a species within the 95% confidence interval for the two highest accuracy models evolved was between 70.4 and 89.3% based upon the coordinated expression of between 5 and 11 features. These encouraging in vitro results suggest that the microDMx technology, coupled with bioinformatics data analysis, has potential for diagnosis of bacterial infections.     

Preparation, separation, and conformational analysis of differentially sulfated heparin octasaccharide isomers using ion mobility mass spectrometry

Heparin is a linear sulfated polysaccharide widely used in medicine because of its anticoagulant properties. The various sulfation and/or acetylation patterns on heparin impart different degrees of conformational change around the glycosidic bonds and subsequently alter its function as an anticoagulant, anticancer, or antiviral drug. Characterization of these structures is important for eventual elucidation of its function but presents itself as an analytical challenge due to the inherent heterogeneity of the carbohydrates. Heparin octasaccharide structural isomers of various sulfation patterns were investigated using ion mobility mass spectrometry (IMMS). In addition to distinguishing the isomers, we report the preparation and tandem mass spectrometry analysis for multiple sulfated or acetylated oligosaccharides. Herein, our data indicate that heparin octasaccharide isomers were separated on the basis of their structural conformations in the ion mobility cell. Subsequent to this separation, isomers were further distinguished using product ions resulting from tandem mass spectrometry. Overall, IMMS analysis was used to successfully characterize and separate individual isomers and subsequently measure their conformations.     

Fuzzy rule-building expert system classification of fuel using solid-phase microextraction two-way gas chromatography differential mobility spectrometric data

Gas chromatography/differential mobility spectrometry (GC/DMS) has been investigated for characterization of fuels. Neat fuel samples were sampled using solid-phase microextraction (SPME) and analyzed using a micromachined differential mobility spectrometer with a photoionization source interfaced to a gas chromatograph. The coupling of DMS to GC offers an additional order of information in that two-way data are obtained with respect to compensation voltages and retention time. A fuzzy rule-building expert system (FuRES) was used as a multivariate classifier for the two-way gas chromatograms of fuels, including rocket (RP-1, RG-1), diesel, and jet (JP-4, JP-5, JP-7, JP-TS, JetA-3639, Jet A-3688, Jet A-3690, Jet A-3694, and Jet A-generic) fuels. The GC-DMS with SPME was able to produce characteristic profiles of the fuels and a classification rate of 95 +/- 0.3% obtained with a FuRES model. The classification system also had perfect classification for each fuel sample when applied one month later.     

Ultrasensitive identification of localization variants of modified peptides using ion mobility spectrometry

Localization of the modification sites on peptides is challenging, particularly when multiple modifications or mixtures of localization isomers (variants) are involved. Such variants commonly coelute in liquid chromatography and may be undistinguishable in tandem mass spectrometry (MS/MS) for lack of unique fragments. Here, we have resolved the variants of singly and doubly phosphorylated peptides employing drift tube ion mobility spectrometry (IMS) coupled to time-of-flight mass spectrometry. Even with a moderate IMS resolving power of ～80-100, substantial separation was achieved for both 2+ and 3+ ions normally generated by electrospray ionization, including for the variants indistinguishable by MS/MS. Variants often exhibit a distribution of 3-D conformers, which can be adjusted for optimum IMS separation by prior field heating of ions in a funnel trap. The peak assignments were confirmed using MS/MS after IMS separation, but known species could be identified using just the ion mobility "tag". Avoiding the MS/MS step lowers the detection limit of localization variants to <100 amol, an order of magnitude better than that provided by electron transfer dissociation in an Orbitrap MS.     

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%.     

A new Zeeman electrothermal atomic-absorption spectrometer: technology and analysis

The technical parameters and analytical characteristics of a new Zeeman atomic-absorption spectrometer (the Quant Z) are presented. The characteristic masses and the limits of the detection of certain elements of the new instrument are compared with those of similar instruments.