An integrated ten-pump, eight-channel parallel LC/MS system for automated high-throughput analysis of proteins

Multidimensional approaches in LC and MS for phospholipid bioanalysis

The advancement of both LC and MS has contributed significantly to phospholipid analysis. Two major trends of developments have emerged in the past decade: application of dedicated online (or offline) LC–MS techniques including 2D and sophisticated chromatographic separations, and the development of so-called shotgun lipidomics represented by multidimensional MS-based techniques. However, neither of these techniques have been shown to be a universal solution for the increasing demand on the comprehensive information of lipid metabolomics in lipidomics studies. This is partially due to the intrinsic complexity of naturally occurring phospholipids in practice. It is evident that either chromatography or MS has to go multidimensional in order to fulfil this goal. This review focuses on recent developments of multidimensional MS, LC–MS and chromatographic approaches for lipidomics analysis. The perspectives and retrospectives of chromatography and MS in these aspects will be reviewed and discussed.

Parallel supercritical fluid chromatography/mass spectrometry system for high-throughput enantioselective optimization and separation

An automated parallel four-column supercritical fluid chromatography (SFC)/MS system to perform high-throughput enantioselective chromatographic method development and optimization is described in this paper. The initial screening was performed in parallel on four chiral SFC columns over several buffer conditions. Optimization of the separation of enantiomers was achieved on a single chiral column. The screening and optimization were accomplished in a fully automated, user-independent manner. Incorporation of column control valves in front of each chiral column allowed the system to switch from parallel four-column screening mode to single-column optimization mode. To facilitate the process, a custom software program, we termed, intelligent parallel optimization for chiral SFC separation (IPOCSS), was developed in-house. The custom software monitored each of the runs in real-time, processed each data set, and by incorporating user-defined criteria (e.g., resolution of the two enantiomer chromatographic peaks), selected the next set of experiments and automatically optimized the enantioseparation. This new approach, combining parallel SFC/MS screening and intelligent software-controlled method optimization, has resulted in a streamlined, high-throughput tool for enantioselective method development, which has been applied successfully to enantioseparations in support of drug discovery.

Multidimensional capillary array liquid chromatography and matrix-assisted laser desorption/ionization tandem mass spectrometry for high-throughput proteomic analysis

A two-dimensional capillary array liquid chromatography system coupled with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) was developed for high-throughput comprehensive proteomic analysis, in which one strong cation-exchange (SCX) capillary chromatographic column was used as the first separation dimension and 10 parallel reversed-phase liquid chromatographic (RPLC) capillary columns were used as the second separation dimension. A novel multi-channel interface was designed and fabricated for on-line coupling of the SCX to RPLC column array system. Besides the high resolution based on the combination of SCX and RPLC separation, the developed new system provided the most rapid two-dimensional liquid chromatography (2D-LC) separation. Ten three-way micro-splitter valves used as stop-and-flow switches in transferring SCX fractions onto RPLC columns. In addition, the three-way valves also acted as mixing chambers of RPLC effluent with matrix. The system enables on-line mixing of the LC array effluents with matrix solution during the elution and directly depositing the analyte/matrix mixtures on MALDI plates from the tenplexed channels in parallel through an array of capillary tips. With the novel system, thousands of peptides were well separated and deposited on MALDI plates only in 150min for a complex proteome sample. Compared with common 2D-LC system, the parallel 2D-LC system showed about 10-times faster analytical procedure. In combination with a high throughput tandem time of flight mass spectrometry, the system was proven to be very effective for proteome analysis by analyzing a complicated sample, soluble proteins extracted from a liver cancer tissue, in which over 1202 proteins were identified.

Preparation and characterization of methacrylate-based semi-micro monoliths for high-throughput bioanalysis

Hexyl methacrylate (HMA)-based monolithic semi-micro columns were prepared by in situ polymerization within the confines of 1.02-mm-i.d. silicosteel tubing for reversed-phase and/or precipitation-redissolution liquid chromatography. Practically useful monolithic columns with adequate separation efficiency, high permeability, and good mechanical strength were successfully obtained using a polymerization mixture comprising 24% hexyl methacrylate (HMA), 6% ethylene dimethacrylate (EDMA), 44.5% 1-propanol, and 25.5% 1,4-butanediol. The column performance was evaluated through the separations of a series of alkylbenzenes. At a normal flow rate of 50 microL min(-1), the produced HMA-based monolithic columns typically exhibited 3,000 theoretical plates for a 20-cm-long column, and the pressure drop was generally less than 1 MPa per 20 cm. The monolithic columns were resistant to at least 15 MPa, and could be properly operated at 15-20 times higher flow rate than normal, reducing the separation time to 1/15-1/20. The HMA-based monolithic columns were applied to rapid and efficient separations of proteins such as ribonuclease A, cytochrome c, transferrin, and ovalbumin in the precipitation-redissolution mode. Using a CH(3)CN gradient elution at a flow rate of 1,000 microL min(-1), four proteins were baseline separated within 20 s.

A liquid chromatography/mass spectrometry-based method for the selection of ATP competitive kinase inhibitors

The currently approved kinase inhibitors for therapeutic uses and a number of kinase inhibitors that are undergoing clinical trials are directed toward the adenosine triphosphate (ATP) binding site of protein kinases. The 5'-fluorosulfonylbenzoyl 5'-adenosine (FSBA) is an ATP-affinity reagent that covalently modifies a conserved lysine present in the nucleotide-binding site of most kinases. The authors have developed a liquid chromatography/mass spectrometry-based method to monitor binding of ATP competitive protein kinase inhibitors using FSBA as a nonselective activity-based probe for protein kinases. Their method provides a general, rapid, and reproducible means to screen and validate selective ATP competitive inhibitors of protein kinases.

Preparative parallel protein purification (P4)

In state of the art drug discovery, it is essential to gain structural information of pharmacologically relevant proteins. Increasing the output of novel protein structures requires improved preparative methods for high throughput (HT) protein purification. Currently, most HT platforms are limited to small-scale and available technology for increasing throughput at larger scales is scarce. We have adapted a 10-channel parallel flash chromatography system for protein purification applications. The system enables us to perform 10 different purifications in parallel with individual gradients and UV monitoring. Typical protein purification applications were set up. Methods for ion exchange chromatography were developed for different sample proteins and columns. Affinity chromatography was optimized for His-tagged proteins using metal chelating media and buffer exchange by gel filtration was also tested. The results from the present system were comparable, with respect to resolution and reproducibility, with those from control experiments on an AKTA purifier system. Finally, lysates from 10 E. coli cultures expressing different His-tagged proteins were subjected to a three-step parallel purification procedure, combining the above-mentioned procedures. Nine proteins were successfully purified whereas one failed probably due to lack of expression.

Role of mass spectrometry in the purification of peptides and proteins

Experiments were carried out to evaluate the fractionation of proteins and peptides according to mass. Model mixtures were separated by either reversed-phase or ion-exchange chromatography with mass spectrometry-compatible mobile phase additives. Fraction collection was triggered by the mass/charge ratio of each one of the components of the mixture. Chromatography was additionally monitored with a UV-Vis detector in order to compare the new technique with generally accepted in separations. The results indicated that adequate purification is achieved by this new technique. Fraction collection triggered by changes in the mass/charge ratio reduces sample handling and analysis time. This study demonstrates the utility of mass-directed fractionation of peptides and proteins when mass spectrometry-compatible mobile phase additives are used.

Parallel high-throughput accurate mass measurement using a nine-channel multiplexed electrospray liquid chromatography ultraviolet time-of-flight mass spectrometry system

A nine-channel multiplexed electrospray (MUX) liquid chromatography ultraviolet time-of-flight mass spectrometry (LC/UV/TOFMS) system has been used to simultaneously measure accurate masses of eluting components from eight parallel gradient LC columns. Accuracies better than 5 and 10 ppm were achieved for 50 and 80% of samples, respectively, from a single batch analysis of ten plates (960 samples) of a Fmoc-Asp(OtBu)-OH and reserpine mixture. Combinatorial library compounds were analyzed using this parallel high-throughput system in both positive and negative modes to rigorously verify expected products and identify side products. A mass accuracy of 10 ppm root mean square (RMS) is routinely obtained for combinatorial library samples from this high-throughput accurate mass LC/MS system followed by automated data processing. This mass accuracy is critical in revealing combinatorial synthesis problems that would be missed by unit mass measurement.

High-throughput liquid chromatography ultraviolet/mass spectrometric analysis of combinatorial libraries using an eight-channel multiplexed electrospray time-of-flight mass spectrometer

We report a high-throughput liquid chromatography/mass spectrometry (LC/MS) protocol for analyzing large combinatorial libraries using an eight-channel parallel LC/UV/MS (MUX-LCT) system. System configuration, linear response range in UV absorbance, LC column selection, and flow rate were optimized for 24 h/7 day unattended operations. Combinatorial libraries were analyzed on this system at a rate of 3200 compounds per day for a 3.5 min cycle time per injection. This parallel system is compared with a single-channel system in terms of performance and operation.

Investigation of an enhanced resolution triple quadrupole mass spectrometer for high-throughput liquid chromatography/tandem mass spectrometry assays

Triple quadrupole mass spectrometers, when operated in multiple reaction monitoring (MRM) mode, offer a unique combination of sensitivity, specificity, and dynamic range. Consequently, the triple quadrupole is the workhorse for high-throughput quantitation within the pharmaceutical industry. However, in the past, the unit mass resolution of quadrupole instruments has been a limitation when interference from matrix or metabolites cannot be eliminated. With recent advances in instrument design, triple quadrupole instruments now afford mass resolution of less than 0.1 Dalton (Da) full width at half maximum (FWHM). This paper describes the evaluation of an enhanced resolution triple quadrupole mass spectrometer for high-throughput bioanalysis with emphasis on comparison of selectivity, sensitivity, dynamic range, precision, accuracy, and stability under both unit mass (1 Da FWHM) and enhanced (<or=0.1 Da FWHM) resolution. The advantage of enhanced resolution was demonstrated in the case of mometasone with polypropylene glycol (PPG) interference. At unit mass resolution, the transmitted precursor ion from the first quadrupole contained not only protonated molecules from mometasone, but also PPG interference. At enhanced resolution only selected mometasone peaks were transmitted, and no interference from PPG was detected. Sensitivity of the instrument was demonstrated with 10 femtograms of descarboethoxyloratadine injected on-column, for which a signal-to-noise (S/N) ratio of 24 was obtained for MRM chromatograms at both unit and enhanced resolution. Absolute signals obtained at enhanced resolution were about one-third those obtained at unit mass resolution. However, S/N was maintained at enhanced resolution due to the proportional decrease in noise level. Finally, the stability of the instrument operating at enhanced resolution was demonstrated during an overnight 17 h period that was used to validate a liquid chromatography/tandem mass spectrometry (LC/MS/MS) assay for the quantitation of loratadine and descarboethoxyloratadine in human plasma. Assay performances (dynamic range, correlation coefficients for standard curves, precision and accuracy for QC samples) under unit and enhanced resolution were both within current pharmaceutical and regulatory guidelines demonstrating the stability of the mass spectrometer operating at enhanced resolution for typical bioanalytical high-throughput applications.