Flow-injection electrospray ionization mass spectrometry of crude cell extracts for high-throughput bacterial identification

Flow-injection electrospray ionization mass spectrometry (FI-ESI-MS) of unfractionated cell-free extracts obtained from bacterial cells suspended in a solvent mixture was investigated as a rapid analytical method for reproducible, high-throughput bacterial identification. Five bacterial strains (two Escherichia coli, two Bacillus spp. and one Brevibacillus laterosporus) were studied in this investigation. Axenically grown bacterial cells were suspended in an acidic organic solvent and the cell-free extract was sequentially injected into a solvent flow stream that was sprayed into the ionization chamber of the ESI-MS. The spectra produced contained reproducible information, which was useful for discriminating between the bacteria. Tandem mass spectrometry was used to characterize further the peaks, and at least three classes of macromolecules, namely phospholipids, glycolipids, and proteins, were found to contribute most to the spectral information. Bacterial extracts stored under different conditions gave very similar mass spectra for each of the five bacterial strains, indicating that the extracts were stable even at room temperature for up to 24 h, with no loss of information content, which has obvious implications for automated high-throughput analysis. An analysis of the components of the extracting solvent mixture and their effects on the spectral information showed that acetonitrile contributes most significantly to the extraction process and hence to the information content of the spectra.     

Multiplexed high-throughput electrokinetically-controlled immunoassay for the detection of specific bacterial antibodies in human serum

In previous studies we have developed a simple electrokinetically-controlled lab-on-a-chip for heterogeneous immunoassay. In that method, all the sequential operations in an immunoassay, such as reagent loading and washing, were performed automatically by electrokinetically controlling the flow in an H-shaped microchannel. Here, we demonstrated further development of a high-throughput immunoassay microfluidic chip, and the application of the new immunoassay microfluidic chip in assaying human serum. The microfluidic immunoassay analyzed ten samples in parallel in 22 min. Bacterial antibodies in samples were captured by antigens pre-patterned on the bottom wall of a microchannel and then bound with TRITC-labeled detection antibodies to generate fluorescent signals. With optimized surface concentration of antigen, the assay detected Escherichia coli O157:H7 antibody and Helicobacter pylori antibody from buffer solutions in concentration ranges of 0.02-10 μg mL⁻¹ and 0.1-50 μg mL⁻¹, respectively. Human sera that were E. coli-positive or H. pylori-positive were accurately distinguished from respective negative controls. Moreover, the two antibodies, anti-E. coli and anti- H. pylori antibodies, could be simultaneously detected from human serum. This electrokinetically-controlled immunoassay shows an excellent potential for efficiently detecting multiple pathogenic infections in clinical environments.     

Interpretation of mass spectrometry data for high-throughput proteomics

Recent developments in proteomics have revealed a bottleneck in bioinformatics: high-quality interpretation of acquired MS data. The ability to generate thousands of MS spectra per day, and the demand for this, makes manual methods inadequate for analysis and underlines the need to transfer the advanced capabilities of an expert human user into sophisticated MS interpretation algorithms. The identification rate in current high-throughput proteomics studies is not only a matter of instrumentation. We present software for high-throughput PMF identification, which enables robust and confident protein identification at higher rates. This has been achieved by automated calibration, peak rejection, and use of a meta search approach which employs various PMF search engines. The automatic calibration consists of a dynamic, spectral information-dependent algorithm, which combines various known calibration methods and iteratively establishes an optimised calibration. The peak rejection algorithm filters signals that are unrelated to the analysed protein by use of automatically generated and dataset-dependent exclusion lists. In the "meta search" several known PMF search engines are triggered and their results are merged by use of a meta score. The significance of the meta score was assessed by simulation of PMF identification with 10,000 artificial spectra resembling a data situation close to the measured dataset. By means of this simulation the meta score is linked to expectation values as a statistical measure. The presented software is part of the proteome database ProteinScape which links the information derived from MS data to other relevant proteomics data. We demonstrate the performance of the presented system with MS data from 1891 PMF spectra. As a result of automatic calibration and peak rejection the identification rate increased from 6% to 44%.Abbreviations 2-DE Two-dimensional gel electrophoresis - MALDI Matrix-assisted laser desorption ionisation - PMF Peptide mass fingerprinting - MS Mass spectrometry - TOF Time of flight     

Induced nanoelectrospray ionization for matrix-tolerant and high-throughput mass spectrometry

No-contact rule: The title method is ultra-sensitive, high-throughput (4 samples per second), easily multiplexed, and is compatible with serum, urine, and concentrated salt solutions. Other features of this method, which avoids physical contact between the electrode and the solvent, include sample economy and the ability to produce both positive and negative-ion spectra in one cycle.     

A novel mass spectrometry cluster for high-throughput quantitative proteomics

We have developed and implemented a novel mass spectrometry (MS) platform combining the advantages of high mass accuracy and resolving power of Fourier transform ion cyclotron resonance (FTICR) with the economy and speed of multiple ion traps for tandem mass spectrometry. The instruments are integrated using novel algorithms and software and work in concert as one system. Using chromatographic time compression, a single expensive FTICR mass spectrometer can match the throughput of multiple relatively inexpensive ion trap instruments. Liquid chromatography (LC)-mass spectrometry data from the two types of spectrometers are aligned and combined to hybrid datasets, from which peptides are identified using accurate mass from the FTICR data and tandem mass spectra from the ion trap data. In addition, the high resolving power and dynamic range of a 12 tesla FTICR also allows precise label-free quantitation. Using two ion traps in parallel with one LC allows simultaneous MS/MS experiments and optimal application of collision induced dissociation and electrontransfer dissociation throughout the chromatographic separation for increased proteome coverage, characterization of post-translational modifications and/or simultaneous measurement in positive and negative ionization mode. An FTICR-ion trap cluster can achieve similar performance and sample throughput as multiple hybrid ion trap-FTICR instruments, but at a lower cost. We here describe the first such FTICR-ion trap cluster, its performance and the idea of chromatographic compression.     

Multiple sprayer system for high-throughput electrospray ionization mass spectrometry

A multiple sprayer electrospray ion source for high-throughput analysis is described. The ion source is comprised of multiple electrospray capillaries, each with an ion lens located near the tip. The electric potentials applied to the ion lenses are used to control the sprayers. The use of ion lenses eliminates the need for mechanical blocking devices to selectively enable or disable the sprayers, and results in a less expensive and more reliable set-up. Sprayers can be enabled or disabled within approximately 50-250 ms when the lens potentials are controlled manually. For simultaneous operation of multiple electrospray capillaries, it is advantageous to orient the capillaries so that the spray from each passes directly in front of the entrance aperture of the mass spectrometer.     

Bromazepam determination in human plasma by high-performance liquid chromatography coupled to tandem mass spectrometry: a highly sensitive and specific tool for bioequivalence studies

A rapid, sensitive and specific method to quantify bromazepam in human plasma using diazepam as the internal standard (IS) is described. The analyte and the IS were extracted from plasma by liquid-liquid extraction using diethyl ether-hexane (80 : 20, v/v). The extracts were analyzed by high-performance liquid chromatography (HPLC) coupled to electrospray tandem mass spectrometry (MS/MS). Chromatography was performed isocratically on a Genesis C(18) analytical column (100 x 2.1 mm i.d., film thickness 4 microm). The method had a chromatographic run time of 5.0 min and a linear calibration curve over the range 5.0-150 ng ml(-1) (r(2) > 0.9952). The limit of quantification was 5 ng ml(-1). This HPLC/MS/MS procedure was used to assess the bioequivalence of two bromazepam 6 mg tablet formulations (bromazepam from Medley SA Indústria Farmacêutica as the test formulation and Lexotan from Produtos Roche Químico e Farmacêutico SA as the reference formulation). A single 6 mg dose of each formulation was administered to 24 healthy volunteers (12 males and 12 females). The study was conducted using an open, randomized, two-period crossover design with a 3 week washout interval. Since the 90% CI for C(max), AUC(last), AUC(0-240 h) (linear) and AUC((0- infinity )) ratios were all inside the 80-125% interval proposed by the US Food and Drug Administration, it was concluded that the bromazepam formulation from Medley is bioequivalent to the Lexotan formulation for both the rate and the extent of absorption.     

Rapid separation and sensitive detection method for beta-blockers by pressure-assisted capillary electrochromatography-electrospray ionization mass spectrometry

A new method for rapid separation and sensitive detection of beta-blockers by pressure-assisted capillary electrochromatography (pCEC) with electrospray ionization mass spectrometry (ESI-MS) using silica-based monolithic column was studied in this paper. The proposed method has been confirmed to be very powerful since the fast mass transfer property and good permeability of silica monolithic column was used in this pCEC-ESI-MS system. In this work, a silica monolithic column was prepared with sol-gel method for simultaneous fast separation of beta-blockers. Furthermore, in order to obtain the highly selective and sensitive result of pCEC-ESI-MS, both the CEC separation and MS detection parameters were optimized in detail. Under the optimized conditions, namely 80% acetonitrile and 20% 20 mmol/L ammonium acetate (pH 6.0) as the mobile phase, 20 kV and 8 bar as the separation voltage and the assisted pressure, isopropanol/water (1:1, v/v) containing 7.5 mmol/L acetic acid as the sheath liquid, and 3 microL/min as the flow rate of sheath liquid, seven beta-blockers were well separated within 11 min with detection limits in the range of 0.15-0.80 ng/mL (defined as S/N=3). The recoveries of spiked urine samples of these beta-blockers were between 86.3 and 103% with the RSDs lower than 8.0%. The real samples from some male volunteers were successfully analyzed and confirmed with the proposed method. Comparing with GC-MS or LC-MS, the new method has some superiority (such as fast analysis capacity and simple pretreatment) in clinical practice and doping control.     

Reactive extractive electrospray ionization tandem mass spectrometry for sensitive detection of tetrabromobisphenol A derivatives

Sensitive detection of tetrabromobisphenol A (TBBPA) and its derivatives, a group of emerging toxic contaminants, is highly necessitated in environmental investigation. Herein a novel analytical strategy based on reactive extractive electrospray ionization (EESI) tandem mass spectrometry for detection of tetrabromobisphenol A bis(2-hydroxyethyl ether) (TBBPA-BHEE), tetrabromobisphenol A bis(glycidyl ether) (TBBPA-BGE), tetrabromobisphenol A bis(allylether) (TBBPA-BAE), and tetrabromobisphenol S bis(allylether) (TBBPS-BAE) in industrial waste water samples was developed. Active silver cations (Ag⁺), generated by electrospraying a silver nitrate methanol solution (10 mg L⁻¹), collides the neutral TBBPA derivatives molecules in the EESI source to form [M + Ag]⁺ complexes of the analytes under the ambient conditions. Upon collision-induced dissociation (CID), characteristic fragments of the [M + Ag]⁺ complexes were identified for confident and sensitive detection of the four TBBPA derivatives. Under the optimized experimental conditions, the instrumental limits of detection (LODs) of TBBPA-BHEE, TBBPA-BGE, TBBPA-BAE and TBBPS-BAE were 0.37, 0.050, 0.76, and 4.6 μg L⁻¹, respectively. The linear ranges extended to 1000 μg L⁻¹ (R² ≥ 0.9919), and the relative standard deviations (RSDs), inter-day variation and intra-day variation were less than 7.8% (n = 9), 10.0% (n = 5), and 14.8% (n = 1 per day for 5 days) for all derivatives. TBBPA derivative manufacturing industrial waste water, river water and tap water samples were fast analyzed with the proposed method. The contents of TBBPA derivatives were various in the collected samples, with the highest 19.9 ± 0.3 μg L⁻¹ of TBBPA-BAE in the waste water samples.     

MS-Express: data-extracting and -processing software for high-throughput experimentation with mass spectrometry

High-throughput experiments (HTE) result in large amounts of raw data that have to be evaluated for sample classification. Especially mass spectrometry, a widely used detection method in catalytic HTE applications, produces enormous amounts of data. In the past few years, in catalysts research, several test rigs based on mass spectrometric detection have been independently reported by different groups. In a typical HTE, the catalysts are tested sequentially; the recording of the scans, however, occurs continuously. For this reason, the scans of interest have to be extracted from the raw data, and scans belonging to the same sample have to be averaged in a tedious procedure before further processing. In this publication, we present our custom-designed software MS-Express (mass spectrometry data-extracting and -processing software), an efficient tool for HTE MS data evaluation. MS-Express not only sorts the data, it also establishes statistical significance with the help of reference and blank data and provides concise information about abundance and intensity distributions of expected peaks. A special feature is that the program also reports unexpected MS signals, which potentially lead to unexpected discoveries.     

Simultaneous high-throughput determination of interaction kinetics for drugs and cyclodextrins by high performance affinity chromatography with mass spectrometry detection

The individual determination of the apparent dissociation rate constant (k_d,app) using high performance affinity chromatography (HPAC) is a tedious process requiring numerous separate tests and massive data fitting, unable to provide the apparent association rate constant (k_a) and equilibrium binding constant (K_a). In this study, a HPAC with mass spectrometry detection (HPAC-MS/MS) was employed to determine the drug-cyclodextrin (CD) interaction kinetics with low sample loading quantity (<10 ng per injection for single compound) and high-throughput yield as twenty drugs determined in one injection. The k_d,app measured by HPAC-MS/MS approach were 0.89 ± 0.07, 4.34 ± 0.01, 1.48 ± 0.01 and 7.77 ± 0.04 s⁻¹ for ketoprofen, trimethoprim, indapamide and acetaminophen, with k_d,app for acetaminophen consistent with that from the HPAC method with UV detector in our previous studies. For twenty drugs with diverse structures and chemical properties, good correlationship was found between k_d,app measured by single compound analysis method and high-throughput HPAC-MS/MS approach, with the correlation coefficient of 0.987 and the significance F less than 0.001. Comprehensive quantification of k_a,app, k_d,app and K_a values was further performed based on the measurement of k_d,app by peak profiling method and K_a by the peak fitting method. And the investigation of the drug-CD interaction kinetics under different conditions indicated that the column temperature and mobile phase composition significantly affected the determination of k_a,app, k_d,app and K_a while also dependent on the acidity and basicity of drugs. In summary, the high-throughput HPAC-MS/MS approach has been demonstrated high efficiency in determination of the drug-CD primary interaction kinetic parameter, especially, k_d,app, being proven as a novel tool in screening the right CD for the solubilization of the right drug.     

Hardware-accelerated protein identification for mass spectrometry

An ongoing issue in mass spectrometry is the time it takes to search DNA sequences with MS/MS peptide fragments (see, e.g., Choudary et al., Proteomics 2001; 1: 651-667.) Search times are far longer than spectra acquisition time, and parallelization of search software on clusters requires doubling the size of a conventional computing cluster to cut the search time in half. Field programmable gate arrays (FPGAs) are used to create hardware-accelerated algorithms that reduce operating costs and improve search speed compared to large clusters. We present a novel hardware design that takes full spectra and computes 6-frame translation word searches on DNA databases at a rate of approximately 3 billion base pairs per second, with queries of up to 10 amino acids in length and arbitrary wildcard positions. Hardware post-processing identifies in silico tryptic peptides and scores them using a variety of techniques including mass frequency expected values. With faster FPGAs protein identifications from the human genome can be achieved in less than a second, and this makes it an ideal solution for a number of proteome-scale applications.     

Novel applications of highly sensitive liquid chromatography/mass spectrometry/mass spectrometry for the direct detection of ultra-trace levels of contaminants in water

Recent advances in the sensitivity of liquid chromatography/mass spectrometry (LC/MS) instrument technology provide the basis for the direct detection, i.e. without sample pre-concentration, of organic contaminants in water in the ng/L range. Novel applications for the analysis of atrazine and some of its desalkylated and hydroxylated degradation products, the pharmaceutical compounds diclofenac and carbamazepine, sulfonylurea herbicides, and iodinated X-ray contrast media have been developed. For each analyte a specific tandem mass spectrometric (MS/MS) transition has been selected and the corresponding mass spectrometric parameters optimised. All analytes could be analysed within three specific analytical runs including different high-performance liquid chromatography (HPLC) conditions. Detection limits were determined to be better than 10 ng/L for the direct analysis of the compounds in water except for X-ray contrast media, for which detection limits were found to be up to one order of magnitude higher. The methods have been successfully utilised for the analysis of natural waters. Matrix effects frequently occurring in LC/MS have shown to be low to moderate in the case of X-ray contrast media. This work demonstrates that for the analysis of a large number of water contaminants, the sample pre-concentration step could possibly be omitted.     

Quantitative high-throughput determination of endogenous retinoids in human plasma using triple-stage liquid chromatography/tandem mass spectrometry

A high-throughput ultrasensitive analytical method based on liquid chromatography with positive ion atmospheric pressure chemical ionization (APCI) coupled to tandem mass spectrometric detection (LC/MS/MS) was developed for the determination of all-trans-4-oxo-retinoic acid (at4oxoRA), 13-cis-4-oxo-retinoic acid (13c4oxoRA), 13-cis-retinoic acid (13cRA), all-trans-retinoic acid (atRA) and all-trans-retinol (atROH) in human plasma. A stable isotope of atRA was used as internal standard (IS). The analytes and IS were isolated from 100 microL plasma by acetonitrile mono-phase extraction (MPE) performed in black 96-well microtiterplates. A 100 microL injection was focused on-column and chromatographed on an Agilent ZORBAX SB-C18 rapid-resolution high-throughput (RRHT) column with 1.8-microm particles (4.6 mmx50 mm) maintained at 60 degrees C. The initial mobile phase composition was acetonitrile/water/formic acid (10:90:0.1, v/v/v) delivered at 1.8 mL/min. Elution was accomplished by a fast gradient to acetonitrile/methanol/formic acid (90:10:0.1, v/v/v). The method had a chromatographic total run time of 7 min. An Applied Biosystems 4000 Q TRAP linear tandem mass spectrometer equipped with a heated nebulizer (APCI) ionization source was operated in multiple reaction monitoring (MRM) mode with the precursor-to-product ion transitions m/z 315.4-->297 (4-oxo-retinoic acids), 301.2-->205 (retinoic acids), 305.0-->209 (IS) and 269.2-->93 (retinol) used for quantification. The assay was fully validated and found to have acceptable accuracy, precision, linearity, sensitivity and selectivity. The mean extraction recoveries from spiked plasma samples were 80-105% for the various retinoids at three different levels. The intra-day accuracy of the assay was within 8% of nominal and intra-day precision was better than 8% coefficient of variance (CV) for retinoic acids. Inter-day precision results for quality control samples run over a 12-day period alongside clinical samples showed mean precision better than 12.5% CV. The limit of quantification was in the range of 0.1-0.2 ng/mL and the mass limit of detection (mLOD) was in the range 1-4 pg on column for the retinoic acids. The assay has been successfully applied to the analysis of 1700 plasma samples.     

Toward a high-throughput approach to quantitative proteomic analysis: Expression-dependent protein identification by mass spectrometry

The isotope-coded affinity tag (ICAT) [1] technology enables the concurrent identification and comparative quantitative analysis of proteins present in biological samples such as cell and tissue extracts and biological fluids by mass spectrometry. The initial implementation of this technology was based on microcapillary chromatography coupled on-line with electrospray ionization tandem mass spectrometry. This implementation lacked the ability to select proteins for identification based on their relative abundance and therefore to focus on differentially expressed proteins. In order to improve the sample throughput of this technology, we have developed a two-step approach that is focused on those proteins for which the abundance changes between samples: First, a new software program for the automated quantification of ICAT reagent labeled peptides analyzed by microcapillary electrospray ionization time-of-flight mass spectrometry determines those peptides that differ in their abundance and second, these peptides are identified by tandem mass spectrometry using an electrospray quadrupole time-of flight mass spectrometer and sequence database searching. Results from the application of this approach to the analysis of differentially expressed proteins secreted from nontumorigenic human prostate epithelial cells and metastatic cancerous human prostate epithelial cells are shown.     

Electrospray mass spectrometry: a tool for elemental speciation

Recent progress in the development of electrospray mass spectrometry (ESMS) as a tool for elemental speciation is reviewed. Reports wherein ESMS is used to qualitatively determine the presence of metal ions (inorganic, organometallic and complexed) and non-metallic inorganic species have grown exponentially over the last decade. In addition to elemental speciation, impact in other areas such as gas-phase chemistry, inorganic–organometallic chemistry and biological mass spectrometry has been prolific. The review is structured to cover each of the areas listed above, and also includes a brief introduction, discussion of the electrospray process, discussion of instrumentation and other relevant application areas. An overview of the types of species/complexes studied is given in each section along with a brief discussion of the application objectives and analytical aspects. Analytical considerations for the development of ESMS as a tool for elemental speciation are also raised, including, application, quantitation, sensitivity, limitations and future directions. The impact of speciation strategies involving stand-alone ESMS, ESMS coupled with on-line separation techniques and the inclusion of ESMS in dual (multiple) technique strategies are presented. High backgrounds due to chemical noise and signal suppression (matrix effects) appear to be two important factors limiting sensitive detection of most analytes. The use of sample pre-treatment, pre-concentration or separation techniques is necessary to alleviate these problems. Although ESMS currently suffers from a number of limitations, continued instrumentation and methods development will improve its capability and diversify the impact of ESMS as a tool for elemental speciation.