Biomedical subjects

Keqi Tang

Publications and source records attributed to Keqi Tang.

At least 19 recordsLinked to original sources

PubMed2007

MicroSPE-nanoLC-ESI-MS/MS using 10-microm-i.d. silica-based monolithic columns for proteomics.

Silica-based monolithic capillary columns (25 cm x 10 microm i.d.) with integrated nanoESI emitters have been developed to provide high-quality and robust microSPE-nanoLC-ESI-MS analyses. The integrated nanoESI emitter adds no dead volume to the LC separation, allowing stable electrospray operation at flow rates of approximately 10 nL/min. In an initial application with a linear ion trap MS, we identified 5510 unique peptides that covered 1443 distinct Shewanella oneidensis proteins from a 300-ng tryptic digest sample in a single 4-h LC-MS/MS analysis. The use of an integrated monolithic ESI emitter provided enhanced resistance to clogging and provided good run-to-run reproducibility.

Chromatography, Liquid↗

PubMed2006

Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry.

We have developed a new procedure for fabricating fused-silica emitters for electrospray ionization-mass spectrometry (ESI-MS) in which the end of a bare fused-silica capillary is immersed into aqueous hydrofluoric acid, and water is pumped through the capillary to prevent etching of the interior. Surface tension causes the etchant to climb the capillary exterior, and the etch rate in the resulting meniscus decreases as a function of distance from the bulk solution. Etching continues until the silica touching the hydrofluoric acid reservoir is completely removed, essentially stopping the etch process. The resulting emitters have no internal taper, making them much less prone to clogging compared to, e.g., pulled emitters. The high aspect ratios and extremely thin walls at the orifice facilitate very low flow rate operation; stable ESI-MS signals were obtained for model analytes from 5-microm-diameter emitters at a flow rate of 5 nL/min with a high degree of interemitter reproducibility. In extensive evaluation, the etched emitters were found to enable approximately four times as many LC-MS analyses of proteomic samples before failing compared with conventional pulled emitters. The fabrication procedure was also employed to taper the ends of polymer monolith-containing silica capillaries for use as ESI emitters. In contrast to previous work, the monolithic material protrudes beyond the fused-silica capillaries, improving the monolith-assisted electrospray process.

Hydrofluoric Acid↗

PubMed2006

Field asymmetric waveform ion mobility spectrometry studies of proteins: Dipole alignment in ion mobility spectrometry?

Approaches to separation and characterization of ions based on their mobilities in gases date back to the 1960s. Conventional ion mobility spectrometry (IMS) measures the absolute mobility, and field asymmetric waveform IMS (FAIMS) exploits the difference between mobilities at high and low electric fields. However, in all previous IMS and FAIMS experiments ions experienced an essentially free rotation; thus the separation was based on the orientationally averaged cross-sections Omega(avg) between ions and buffer gas molecules. Virtually all large ions are permanent electric dipoles that will be oriented by a sufficiently strong electric field. Under typical FAIMS conditions this will occur for dipole moments >400 D, found for many macroions including most proteins above approximately 30 kDa. Mobilities of aligned dipoles depend on directional cross-sections Omega(dir) (rather than Omega(avg)), which should have a major effect on FAIMS separation parameters. Here we report the FAIMS behavior of electrospray-ionization-generated ions for 10 proteins up to approximately 70 kDa. Those above 29 kDa exhibit a strong increase of mobility at high field, which is consistent with predicted ion dipole alignment. This effect expands the useful FAIMS separation power by an order of magnitude, allowing separation of up to approximately 10(2) distinct protein conformers and potentially revealing information about Omega(dir) and ion dipole moment that is of utility for structural characterization. Possible approaches to extending dipole alignment to smaller ions are discussed.

Electrochemistry↗

PubMed2006

Improving mass spectrometer sensitivity using a high-pressure electrodynamic ion funnel interface.

We report on a new electrodynamic ion funnel that operates at a pressure of 30 torr with no loss of ion transmission. The enhanced performance compared with previous ion funnel designs optimized for pressures of <5 torr was achieved by reducing the ion funnel capacitance and increasing the RF drive frequency (1.7 MHz) and amplitude (100-170 V peak-to-peak). No degradation of ion transmission was observed for pressures from 2 to 30 torr. The ability to operate at higher pressure enabled a new tandem ion funnel mass spectrometer interface design that can accommodate a greater gas load (e.g., from an ESI source). When combined with a multicapillary inlet, the interface provided more efficient introduction of ions, resulting in a significant enhancement in mass spectrometer sensitivity and detection limits.

Equipment Design↗

PubMed2006

High-resolution field asymmetric waveform ion mobility spectrometry using new planar geometry analyzers.

Field asymmetric waveform ion mobility spectrometry (FAIMS) has emerged as a powerful tool of broad utility for separation and characterization of gas-phase ions, especially in conjunction with mass spectrometry (MS). In FAIMS, ions are filtered by the dependence of mobility on electric field while being carried by gas flow through the analytical gap between two electrodes of either planar (p-) or cylindrical (c-) geometry. Most FAIMS/MS systems employ c-FAIMS because of its ease of coupling to MS, yet the merits of the two geometries have not been compared in detail. Here, a priori simulations reveal that reducing the FAIMS curvature always improves resolution at equal sensitivity. In particular, the resolving power of p-FAIMS exceeds that of c-FAIMS, typically by a factor of 2-4 depending on the ion species and carrier gas. We have constructed a new planar FAIMS incorporating a curtain plate interface for effective operation with an ESI ion source and joined to an MS using an ion funnel interface with a novel slit aperture. The resolution increases up to 4-fold over existing c-FAIMS, even though the analysis is approximately 2 times faster. This allows separation of species not feasible in previous FAIMS studies, e.g., protonated leucine and isoleucine or new bradykinin isomers. The improvement for protein conformers (of ubiquitin) is less significant, possibly because of multiple unresolved geometries.

Computer Simulation↗

PubMed2006

Characterizing the structures and folding of free proteins using 2-D gas-phase separations: observation of multiple unfolded conformers.

Understanding the 3-D structure and dynamics of proteins and other biological macromolecules in various environments is among the central challenges of chemistry. Electrospray ionization can often transfer ions from solution to gas phase with only limited structural distortion, allowing their profiling using mass spectrometry and other gas-phase approaches. Ion mobility spectrometry (IMS) can separate and characterize macroion conformations with high sensitivity and speed. However, IMS separation power is generally insufficient for full resolution of major structural variants of protein ions and elucidation of their interconversion dynamics. Here we report characterization of macromolecular conformations using field asymmetric waveform IMS (FAIMS) coupled to conventional IMS in conjunction with mass spectrometry. The collisional heating of ions in the electrodynamic funnel trap between FAIMS and IMS stages enables investigating the structural evolution of particular isomeric precursors as a function of the intensity and duration of activation that can be varied over large ranges. These new capabilities are demonstrated for ubiquitin and cytochrome c, two common model proteins for structure and folding studies. For nearly all charge states, two-dimensional FAIMS/IMS separations distinguish many more conformations than either FAIMS or IMS alone, including some with very low abundance. For cytochrome c in high charge states, we find several abundant "unfolded" isomer series not distinguishable by IMS, possibly corresponding to different "string of beads" geometries. The unfolding of specific ubiquitin conformers selected by FAIMS has been studied by employing their heating in the FAIMS/IMS interface.

Cytochromes c↗

PubMed2006

Ultra-sensitive and quantitative characterization of proteomes.

Electrospray ionization mass spectrometry combined with high efficiency capillary liquid chromatography provides high sensitivity and broad dynamic range measurements for the characterization of biological macromolecules in complex matrices, and is an increasingly powerful analytical tool for systems biology research.

Animals↗

PubMed2006

Theoretical and experimental evaluation of the low m/z transmission of an electrodynamic ion funnel.

The transmission of ions at low m/z can often be either necessary for an application or problematic (e.g., when large numbers of low m/z ions consume a large fraction of an ion trap's capacity). The low m/z ion transmission limit of an electrodynamic ion funnel has been characterized using both experimental and theoretical approaches. A theoretical model is developed based on a series of infinite wire conductors that represent the ring electrodes of the ion funnel. Mathematical relationships for both low and high m/z cutoffs of the idealized two-dimensional system are derived. The low m/z cutoff is also evaluated through a series of experiments that show it is influenced by both the RF frequency and the DC electric field gradient. However, unlike multipole ion guides, there is no marked dependence of the low m/z cutoff on the RF amplitude, in agreement with theoretical results. With this new understanding, ion funnels can be designed and configured to better match the m/z range requirements for various applications.

Electrochemistry↗

PubMed2006

More sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic LC columns with electrospray ionization-mass spectrometry.

The sensitivity of proteomics measurements using liquid chromatography (LC) separations interfaced with electrospray ionization-mass spectrometry (ESI-MS) improves approximately inversely with liquid flow rate (for the columns having the same separation efficiency, linear velocity, and porosity), making attractive the use of smaller inner diameter LC columns. We report the development and initial application of 10 microm i.d. silica-based monolithic LC columns providing more sensitive proteomics measurements. A 50-microm-i.d. micro solid-phase extraction precolumn was used for ease of sample injection and cleanup prior to the reversed-phase LC separation, enabling the sample volume loading speed to be increased by approximately 50-fold. Greater than 10-fold improvement in sensitivity was obtained compared to analyses using more conventional capillary LC, enabling e.g. the identification of >5000 different peptides by MS/MS from 100-ng of a Shewanella oneidensis tryptic digest using an ion trap MS. The low nL/min LC flow rates provide more uniform responses for different peptides, and provided improved quantitative measurements compared to conventional separation systems without the use of internal standards or isotopic labeling. The improved sensitivity allowed LC-MS measurements of immunopurified protein phosphatase 5 that were in good agreement with quantitative Western blot analyses.

Amino Acid Sequence↗

PubMed2006

Phosphoproteome profiling of human skin fibroblast cells in response to low- and high-dose irradiation.

A hallmark of the response to high-dose radiation is the up-regulation and phosphorylation of proteins involved in cell cycle checkpoint control, DNA damage signaling, DNA repair, and apoptosis. Exposure of cells to low doses of radiation has well documented biological effects, but the underlying regulatory mechanisms are still poorly understood. The objective of this study is to provide an initial profile of the normal human skin fibroblast (HSF) phosphoproteome and explore potential differences between low- and high-dose irradiation responses at the protein phosphorylation level. Several techniques including Trizol extraction of proteins, methylation of tryptic peptides, enrichment of phosphopeptides with immobilized metal affinity chromatography (IMAC), nanoflow reversed-phase HPLC (nano-LC)/electrospray ionization, and tandem mass spectrometry were combined for analysis of the HSF cell phosphoproteome. Among 494 unique phosphopeptides, 232 were singly phosphorylated, while 262 peptides had multiple phosphorylation sites indicating the overall effectiveness of the IMAC technique to enrich both singly and multiply phosphorylated peptides. We observed approximately 1.9-fold and approximately 3.6-fold increases in the number of identified phosphopeptides in low-dose and high-dose samples respectively, suggesting both radiation levels stimulate cell signaling pathways. A 6-fold increase in the phosphorylation of cyclin dependent kinase (cdk) motifs was observed after low- dose irradiation, while high-dose irradiation stimulated phosphorylation of 3-phosphoinositide-dependent protein kinase-1 (PDK1) and AKT/RSK motifs 8.5- and 5.5-fold, respectively. High- dose radiation resulted in the increased phosphorylation of proteins involved in cell signaling pathways as well as apoptosis while low-dose and control phosphoproteins were broadly distributed among biological processes.

3-Phosphoinositide-Dependent Protein Kinases↗

PubMed2005

Two-dimensional gas-phase separations coupled to mass spectrometry for analysis of complex mixtures.

Ion mobility spectrometry (IMS) has been explored for decades, and its versatility in separation and identification of gas-phase ions is well established. Recently, field asymmetric waveform IMS (FAIMS) has been gaining acceptance in similar applications. Coupled to mass spectrometry (MS), both IMS and FAIMS have shown the potential for broad utility in proteomics and other biological analyses. A major attraction of these separations is extremely high speed, exceeding that of condensed-phase alternatives by orders of magnitude. However, modest separation peak capacities have limited the utility of FAIMS and IMS for analyses of complex mixtures. We report 2-D gas-phase separations that join FAIMS to IMS, in conjunction with high-resolution and accuracy time-of-flight (TOF) MS. Implementation of FAIMS/IMS and IMS/MS interfaces using electrodynamic ion funnels greatly improves sensitivity. Evaluation of FAIMS/IMS/TOF performance for a protein mixture tryptic digest reveals high orthogonality between FAIMS and IMS dimensions and, hence, the benefit of FAIMS filtering prior to IMS/MS. The effective peak capacities in analyses of tryptic peptides are approximately 500 for FAIMS/IMS separations and approximately 10(6) for 3-D FAIMS/IMS/MS, providing a potential platform for ultrahigh-throughput analyses of complex mixtures.

Gases↗

PubMed2005

High-sensitivity ion mobility spectrometry/mass spectrometry using electrodynamic ion funnel interfaces.

The utility of ion mobility spectrometry (IMS) for separation of mixtures and structural characterization of ions has been demonstrated extensively, including in biological and nanoscience contexts. A major attraction of IMS is its speed, several orders of magnitude greater than that of condensed-phase separations. Nonetheless, IMS combined with mass spectrometry (MS) has remained a niche technique, substantially because of limited sensitivity resulting from ion losses at the IMS-MS junction. We have developed a new electrospray ionization (ESI)-IMS-QTOF MS instrument that incorporates electrodynamic ion funnels at both front ESI-IMS and rear IMS-QTOF interfaces. The front funnel is of the novel "hourglass" design that efficiently accumulates ions and pulses them into the IMS drift tube. Even for drift tubes of 2-m length, ion transmission through IMS and on to QTOF is essentially lossless across the range of ion masses relevant to most applications. The rf ion focusing at the IMS terminus does not degrade IMS resolving power, which exceeds 100 (for singly charged ions) and is close to the theoretical limit. The overall sensitivity of the present ESI-IMS-MS system is comparable to that of commercial ESI-MS, which should make IMS-MS suitable for analyses of complex mixtures with ultrahigh sensitivity and exceptional throughput.

Electrochemistry↗

PubMed2005

Variable low-mass filtering using an electrodynamic ion funnel.

An adjustable low-mass filter has been developed for an electrospray ionization (ESI) source to block ions associated with unwanted background species from entering the mass spectrometer. The low-mass filter is made by using an adjustable potential energy barrier from the conductance-limiting plate of an electrodynamic ion funnel, which prohibits species with higher ion mobilities from exiting the ESI source. We show that this arrangement provides a linear voltage adjustment for low-mass filtering from m/z 0 to 500. Mass filtering above m/z 500 is also performed; however, higher-mass species are attenuated. The mass filter was tested with a liquid chromatography/mass spectrometry (LC/MS) analysis of a bovine serum albumin (BSA) tryptic digest and resulted in the ability to block low-mass, background species, which accounted for 40-70% of the total ion current immediately behind the ESI source during peak elution and detection.

Animals↗

PubMed2005

Optimization of the design and operation of FAIMS analyzers.

Field asymmetric waveform ion mobility spectrometry (FAIMS) holds significant promise for post-ionization separations in conjunction with mass-spectrometric analyses. However, a limited understanding of fundamentals of FAIMS analyzers has made their design and operation largely an empirical exercise. Recently, we developed an a priori simulation of FAIMS that accounts for both ion diffusion (including anisotropic components) and Coulomb repulsion, and validated it by extensive comparisons with FAIMS/MS data. Here it is corroborated further by FAIMS-only measurements, and applied to explore how key instrumental parameters (analytical gap width and length, waveform frequency and profile, the identity and flow speed of buffer gas) affect FAIMS response. We find that the trade-off between resolution and sensitivity can be managed by varying gap width, RF frequency, and (in certain cases) buffer gas, with equivalent outcome. In particular, the resolving power can be approximately doubled compared to "typical" conditions. Throughput may be increased by either accelerating the gas flow (preferable) or shortening the device, but below certain minimum residence times performance deteriorates. Bisinusoidal and clipped-sinusoidal waveforms have comparable merit, but switching to rectangular waveforms would improve resolution and/or sensitivity. For any waveform profile, the ratio of two between voltages in high and low portions of the cycle produces the best performance.

Computer Simulation↗

PubMed2005

Automatic gain control in mass spectrometry using a jet disrupter electrode in an electrodynamic ion funnel.

We report on the use of a jet disrupter electrode in an electrodynamic ion funnel as an electronic valve to regulate the intensity of the ion beam transmitted through the interface of a mass spectrometer in order to perform automatic gain control (AGC). The ion flux is determined by either directly detecting the ion current on the conductance limiting orifice of the ion funnel or using a short mass spectrometry acquisition. Based upon the ion flux intensity, the voltage of the jet disrupter is adjusted to alter the transmission efficiency of the ion funnel to provide a desired ion population to the mass analyzer. Ion beam regulation by an ion funnel is shown to provide control to within a few percent of a targeted ion intensity or abundance. The utility of ion funnel AGC was evaluated using a protein tryptic digest analyzed with liquid chromatography Fourier transform ion cyclotron resonance (LC-FTICR) mass spectrometry. The ion population in the ICR cell was accurately controlled to selected levels, which improved data quality and provided better mass measurement accuracy.

Electrodes↗

PubMed2005

FAIMS operation for realistic gas flow profile and asymmetric waveforms including electronic noise and ripple.

The use of field asymmetric waveform ion mobility spectrometry (FAIMS) has rapidly grown with the advent of commercial FAIMS systems coupled to mass spectrometry. However, many fundamental aspects of FAIMS remain obscure, hindering its technological improvement and expansion of analytical utility. Recently, we developed a comprehensive numerical simulation approach to FAIMS that can handle any device geometry and operating conditions. The formalism was originally set up in one dimension for a uniform gas flow and limited to ideal asymmetric voltage waveforms. Here we extend the model to account for a realistic gas flow velocity distribution in the analytical gap, axial ion diffusion, and waveform imperfections (e.g., noise and ripple). The nonuniformity of the gas flow velocity profile has only a minor effect, slightly improving resolution. Waveform perturbations are significant even at very low levels, in some cases approximately 0.01% of the nominal voltage. These perturbations always improve resolution and decrease sensitivity, a trade-off controllable by variation of noise or ripple amplitude. This trade-off is physically inferior to that obtained by adjusting the gap width and/or asymmetric waveform frequency. However, the disadvantage is negligible when the perturbation period is much shorter than the residence time in FAIMS, and ripple adjustment appears to offer a practical method for modifying FAIMS resolution.

Algorithms↗

PubMed2004

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.

Carbon Dioxide↗

PubMed2004

An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics.

We describe a fully automated high performance liquid chromatography 9.4 tesla Fourier transform ion resonance cyclotron (FTICR) mass spectrometer system designed for proteomics research. A synergistic suite of ion introduction and manipulation technologies were developed and integrated as a high-performance front-end to a commercial Bruker Daltonics FTICR instrument. The developments incorporated included a dual-ESI-emitter ion source; a dual-channel electrodynamic ion funnel; tandem quadrupoles for collisional cooling and focusing, ion selection, and ion accumulation, and served to significantly improve the sensitivity, dynamic range, and mass measurement accuracy of the mass spectrometer. In addition, a novel technique for accumulating ions in the ICR cell was developed that improved both resolution and mass measurement accuracy. A new calibration methodology is also described where calibrant ions are introduced and controlled via a separate channel of the dual-channel ion funnel, allowing calibrant species to be introduced to sample spectra on a real-time basis, if needed. We also report on overall instrument automation developments that facilitate high-throughput and unattended operation. These included an automated version of the previously reported very high resolution, high pressure reversed phase gradient capillary liquid chromatography (LC) system as the separations component. A commercial autosampler was integrated to facilitate 24 h/day operation. Unattended operation of the instrument revealed exceptional overall performance: Reproducibility (1-5% deviation in uncorrected elution times), repeatability (<20% deviation in detected abundances for more abundant peptides from the same aliquot analyzed a few weeks apart), and robustness (high-throughput operation for 5 months without significant downtime). When combined with modulated-ion-energy gated trapping, the dynamic calibration of FTICR mass spectra provided decreased mass measurement errors for peptide identifications in conjunction with high resolution capillary LC separations over a dynamic range of peptide peak intensities for each spectrum of 10(3), and >10(5) for peptide abundances in the overall separation.

Amino Acid Sequence↗