In-Depth Host Cell Protein Analysis and Viral Protein Impurity Monitoring in Adeno-Associated Virus-Based Gene Therapy Products Using Optimized Wide Window Data-Dependent Acquisition Method.

Compared to other protein therapeutics, there is currently limited knowledge about the residual host cell proteins (HCPs) in adeno-associated virus (AAV)-based gene therapy products. This is primarily due to the lack of a robust and sensitive mass spectrometry-based method for HCP analysis in AAV samples. Existing liquid chromatography-mass spectrometry methods used for analyzing HCPs in therapeutic monoclonal antibodies (mAbs) often cannot be directly applied to AAVs, due to some unique characteristics of AAV samples encountered during their development such as limited sample availability/protein concentration and the presence of surfactants. In this study, we have developed a novel workflow for robust and in-depth HCP analysis of AAV samples by combining wide-window data-dependent acquisition for improved low-abundance HCP detection with single-pot, solid-phase-enhanced sample preparation (SP3) for low-input sample preparation. Using this newly developed method, we were able to detect more than 650 HCPs in a commercial AAV1 sample with a high quantitative reproducibility. This represents a greater than 5-fold increase in HCP protein identification compared to an in-solution digestion method followed by traditional data-dependent acquisition. Similar benefits can also be achieved for other AAV serotypes that were produced internally and purified through different processes. The detection limit of this method is as low as 0.06 ng/mL, enabling more comprehensive HCP coverage in AAV samples. Moreover, for the first time, we have identified several process-related viral proteins, such as Rep 78 and E4. These proteins need to be closely monitored during AAV process development as they may present a greater risk for immunogenicity compared to HCPs that are derived from human HEK293 cells.

Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling.

Recent advances in sample preparation and analysis have enabled direct profiling of protein expression in single mammalian cells and other trace samples. Several techniques to prepare and analyze low-input samples employ custom fluidics for nanoliter sample processing and manual sample injection onto a specialized separation column. While being effective, these highly specialized systems require significant expertise to fabricate and operate, which has greatly limited implementation in most proteomic laboratories. Here, we report a fully automated platform termed autoPOTS (automated preparation in one pot for trace samples) that uses only commercially available instrumentation for sample processing and analysis. An unmodified, low-cost commercial robotic pipetting platform was utilized for one-pot sample preparation. We used low-volume 384-well plates and periodically added water or buffer to the microwells to compensate for limited evaporation during sample incubation. Prepared samples were analyzed directly from the well plate with a commercial autosampler that was modified with a 10-port valve for compatibility with 30 µm i.d. nanoLC columns. We used autoPOTS to analyze 1-500 HeLa cells and observed only a moderate reduction in peptide coverage for 150 cells and a 24% reduction in coverage for single cells compared to our previously developed nanoPOTS platform. To evaluate clinical feasibility, we identified an average of 1095 protein groups from ∼130 sorted B or T lymphocytes. We anticipate that the straightforward implementation of autoPOTS will make it an attractive option for low-input and single-cell proteomics in many laboratories.

Improved Single-Cell Proteome Coverage Using Narrow-Bore Packed NanoLC Columns and Ultrasensitive Mass Spectrometry.

Single-cell proteomics can provide unique insights into biological processes by resolving heterogeneity that is obscured by bulk measurements. Gains in the overall sensitivity and proteome coverage through improvements in sample processing and analysis increase the information content obtained from each cell, particularly for less abundant proteins. Here we report on improved single-cell proteome coverage through the combination of the previously developed nanoPOTS platform with further miniaturization of liquid chromatography (LC) separations and implementation of an ultrasensitive latest generation mass spectrometer. Following nanoPOTS sample preparation, protein digests from single cells were separated using a 20 µm i.d. in-house-packed nanoLC column. Separated peptides were ionized using an etched fused-silica emitter capable of stable operation at the ∼20 nL/min flow rate provided by the LC separation. Ultrasensitive LC-MS analysis was achieved using the Orbitrap Eclipse Tribrid mass spectrometer. An average of 362 protein groups were identified by tandem mass spectrometry (MS/MS) from single HeLa cells, and 874 protein groups were identified using the Match Between Runs feature of MaxQuant. This represents an >70% increase in label-free proteome coverage for single cells relative to previous efforts using larger bore (30 µm i.d.) LC columns coupled to a previous-generation Orbitrap Fusion Lumos mass spectrometer.

Reduced Graphene Oxide-Hybridized Polymeric High-Internal Phase Emulsions for Highly Efficient Removal of Polycyclic Aromatic Hydrocarbons from Water Matrix.

Reduced graphene oxide (RGO)-hybridized polymeric high-internal phase emulsions (RGO/polyHIPEs) with an open-cell structure and hydrophobicity have been successfully prepared using 2-ethylhexyl acrylate and ethylene glycol dimethacrylate as the monomer and the cross-linker, respectively. The adsorption mechanism and performance of this RGO/polyHIPEs to polycyclic aromatic hydrocarbons (PAHs) were investigated. Adsorption isotherms of PAHs on RGO/polyHIPEs show that the saturated adsorption capacity is 47.5 mg/g and the equilibrium time is 8 h. Cycling tests show that the adsorption capacity of RGO/polyHIPEs remains stable in 10 adsorption-desorption cycles without observable structure change in RGO/polyHIPEs. Moreover, the PAH residues in water samples after being purified by RGO/polyHIPEs are lower than the limit values in drinking water set by the European Food Safety Authority. These results demonstrate that the RGO/polyHIPEs have great potentiality in PAH removal and water purification.

Electrokinetic sample preconcentration and hydrodynamic sample injection for microchip electrophoresis using a pneumatic microvalve.

A microfluidic platform was developed to perform online electrokinetic sample preconcentration and rapid hydrodynamic sample injection for zone electrophoresis using a single microvalve. The polydimethylsiloxane microchip comprises a separation channel, a side channel for sample introduction, and a control channel which is used as a pneumatic microvalve aligned at the intersection of the two flow channels. The closed microvalve, created by multilayer soft lithography, serves as a nanochannel preconcentrator under an applied electric potential, enabling current to pass through while preventing bulk flow. Once analytes are concentrated, the valve is briefly opened and the stacked sample is pressure injected into the separation channel for electrophoretic separation. Fluorescently labeled peptides were enriched by a factor of ∼450 in 230 s. This method enables both rapid analyte concentration and controlled injection volume for high sensitivity, high-resolution CE.

ITP of lanthanides in microfluidic PMMA chip.

An ITP separation of eight lanthanides on a serpentine PMMA microchip with a tee junction and a 230-mm-long serpentine channel is described. The cover of the PMMA chip is 175 µm thick so that a C(4) D in microchip mode can be used to detect the lanthanides as they migrate through the microchannel. Acetate and α-hydroxyisobutyric acid are used as complexing agents to increase the electrophoretic mobility difference between the lanthanides. Eight lanthanides are concentrated within ∼ 6 min by ITP in the microchip using 10 mM ammonium acetate at pH 4.5 as the leading electrolyte and 10 mM acetic acid at ∼ pH 3.0 as the terminating electrolyte. In addition, a 2D numerical simulation of the lanthanides undergoing ITP in the microchip is compared with experimental results using COMSOL Multiphysics v4.3a.

Counterflow isotachophoresis in a monolithic column.

This study describes stationary counterflow isotachophoresis (ITP) in a poly(acrylamide-co-N,N'-methylenebisacrylamide) monolithic column as a means for improving ITP processing capacity and reducing dispersion. The flow profile in the monolith was predicted using COMSOL's Brinkman Equation application mode, which revealed that the flow profile was mainly determined by monolith permeability. As monolith permeability decreases, the flow profile changes from a parabolic shape to a plug shape. An experimental monolithic column was prepared in a fused-silica capillary using an ultraviolet-initiated polymerization method. A monolithic column made from 8% (wt.) monomer was chosen for the stationary counterflow ITP experiments. Counterflow ITP in the monolithic column showed undistorted analyte zones with significantly reduced dispersion compared to the severe dispersion observed in an open capillary. Particularly, for r-phycoerythrin focused by counterflow ITP, its zone width in the monolithic column was only one-third that observed in an open capillary. These experiments demonstrate that stationary counterflow ITP in monoliths can be a robust and practical electrofocusing method.

Adapting a Low-Cost and Open-Source Commercial Pipetting Robot for Nanoliter Liquid Handling.

Low-volume liquid handling capabilities in bioanalytical workflows can dramatically improve sample processing efficiency and reduce reagent costs, yet many commercial nanoliter liquid handlers cost tens of thousands of dollars or more. We have successfully adapted a low-cost and open-source commercial pipetting robot, the Opentrons OT-1, to accurately aspirate and dispense nanoliter volumes. Based on fluorescence measurements, the modified OT-1 was able to reproducibly transfer 50 nL of water with less than 3% measurement error and 5% coefficient of variation (CV). For 15 nL transfers, the volume measurements indicated less than 4% error and 4% CV. We applied this platform to the preparation of low-nanogram proteomic samples for liquid chromatography-mass spectrometry analysis, demonstrating that the modified OT-1 is an effective platform for nanoliter liquid handling. At a total materials cost of less than $6000, including the commercial liquid handler and all modifications, this system is also far less expensive than other platforms with similar capabilities, placing automated nanoliter handling within reach of a far broader scientific community.

Protein separation using free-flow electrophoresis microchip etched in a single step.

A one-step etching method was developed to fabricate glass free-flow electrophoresis microchips with a rectangle separation microchamber (42 mm-long, 23 mm-wide and 28 microm-deep), in which two glass bridges (0.5 mm-wide) were made simultaneously to prevent bubbles formed by electrolysis near the Pt electrode from entering the separation chamber. By microchip free-flow zone electrophoresis, with 200 V voltage applied, the baseline separation of three FITC labeled proteins, ribonuclease B, myoglobin and beta-lactoglobulin, was achieved, with resolution over 1.78. Furthermore, with 2.5 mM Na(2)SO(4) added into the electrode buffer to form higher electrical field strength across separation microchamber than electrode compartments, similar resolution of samples was achieved with the applied voltage decreased to 75 V, which could obviously decrease Joule heat during continuous separation. All these results demonstrate that the free-flow electrophoresis microchip fabricated by one-step etching method is suitable for the continuous separation of proteins, which might become an effective pre-fractionation method for proteome study.

Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell.

We report on the combination of nanodroplet sample preparation, ultra-low-flow nanoLC, high-field asymmetric ion mobility spectrometry (FAIMS), and the latest-generation Orbitrap Eclipse Tribrid mass spectrometer for greatly improved single-cell proteome profiling. FAIMS effectively filtered out singly charged ions for more effective MS analysis of multiply charged peptides, resulting in an average of 1056 protein groups identified from single HeLa cells without MS1-level feature matching. This is 2.3 times more identifications than without FAIMS and a far greater level of proteome coverage for single mammalian cells than has been previously reported for a label-free study. Differential analysis of single microdissected motor neurons and interneurons from human spinal tissue indicated a similar level of proteome coverage, and the two subpopulations of cells were readily differentiated based on single-cell label-free quantification.

Microchip isoelectric focusing with monolithic immobilized pH gradient materials for proteins separation.

Monolithic immobilized pH gradient (M-IPG) materials were prepared in microchannles by photoinitiated polymerization of acrylamide, glycidylmethacrylate and Bis, followed by the attachment of focused Ampholine onto the surface of porous monoliths via epoxide groups. With M-IPG materials as matrix, FITC-labeled ribonuclease B, myoglobin and alpha-casein were well separated by microchip isoelectric focusing (muCIEF) without carrier amphocytes (CAs) added in the buffer. Both chemical and pressure mobilization were applied to drive focused zones for LIF detection. Our experimental results showed that pressure mobilization was preferable with neglectable band broadening, and good peak shape and high detection sensitivity were obtained. All these results demonstrate that muCIEF with M-IPG materials is not only an efficient mode for protein enrichment and separation but also attractive to couple with other CE modes to achieve multi-dimensional separation or MS for further identification, without the interference of mobile CAs.

Improved protein separation by microchip isoelectric focusing with stepwise gradient of electric field strength.

A stepwise gradient of electric field strength was proposed for microchip IEF-based protein separation, by which after focusing at low voltages, IEF was performed by applying higher separation voltages step-by-step. A linear relationship between the focusing time and the inverse of the electric field strength was found. In addition, the conductivity of an established pH gradient showed a negative but nonlinear correlation with the applied voltage. Based on the above-mentioned results, a stepwise gradient of electric field strength, ranging from 160 to 1500 V/cm was applied in the separation of proteins extracted from Escherichia coli in a straight glass microchip channel permanently coated by polyacrylamide. Compared to the conventional separation performed under a constant field strength of 750 V/cm, the increased stepwise gradient of electric field strength resulted in improved resolution and decreased focusing time, while without the negative effects of Joule heat for protein separation. All these results demonstrated that such a method might be of great significance to achieve high resolution and high-throughput analysis of complex protein samples for microchip IEF.

Mass spectrometry-based monitoring of millisecond protein-ligand binding dynamics using an automated microfluidic platform.

Characterizing protein-ligand binding dynamics is crucial for understanding protein function and for developing new therapeutic agents. We present a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and an integrated electrospray ionization source for mass spectrometry-based monitoring of protein-ligand binding dynamics. This platform offers many advantages, including solution-based binding, label-free detection, automated operation, rapid mixing, and low sample consumption.

Miniaturized two-dimensional capillary electrophoresis on a microchip for analysis of the tryptic digest of proteins.

A two-dimensional capillary electrophoresis platform, combining isoelectric focusing (IEF) and capillary zone electrophoresis (CZE), was established on a microchip with the channel width and depth as 100 mum and 40 mum, respectively. With polyacrylamide as permanent coating, EOF in the microchannel, which could impair the separation, was decreased to 3.4x10(-9)m(2).V(-1).s(-1), about 1/10 of that obtained in the uncoated set-up. During the separation, peptides were first focused by IEF in the first dimensional channel, and then directly driven into the perpendicular channel by controlling the applied voltages, and separated by CZE. Effects of various experimental parameters, including the electric field strength, channel length, and injection frequency from the first to the second dimensional separation channel, were studied. Under optimized condition, the digests of BSA and proteins extracted from E. coli were separated, and a peak capacity of 540 was obtained, which was far greater than that obtained by each single dimensional separation. All these results showed the promise of multidimensional separation on a microchip for the high-throughput and high-resolution analysis of complex samples.