Detection of single nucleotide polymorphisms using electrospray ionization mass spectrometry: validation of a one-well assay and quantitative pooling studies

Single nucleotide polymorphisms (SNPs) are currently being mapped and databased at a remarkable pace, providing a viable means for understanding disease susceptibility, differential drug response and human evolution. Consequently, there is an increasing demand for SNP genotyping technologies that are simple, rapid, cost effective and readily amenable to automation for high-throughput analyses. In this study, we improved the Survivor Assay, a SNP detection method based on electrospray ionization mass spectrometry (ESI-MS), with several developments. One improvement is the development of a one-well assay, requiring no off-line purification of the polymerase chain reaction product, achieved by simple addition of reagent solution into a single well. Another is the on-line separation of magnesium and dideoxynucleotides using an in-house made monolithic metal chelating column, eliminating any off-line sample preparation prior to mass spectrometric analysis. Here the Survivor Assay is extended from a proof-of-principle concept to a validated method by genotyping six SNPs from five different regions of human genomic DNA in 55 individual samples with 100% accuracy. This improved Survivor Assay eliminates the tedious and time-consuming steps of sample preparation, minimizes sample handing and offers a high-throughput analysis of SNPs by ESI-MS. The current combined preparation and analysis time is 2 min per sample. The simplicity of this method has potential for full automation and parallel chromatography and, thus, reduced analysis time. In addition, we have adapted the Survivor Assay for quantitative SNP analysis in pooled DNA samples. The capabilities and sensitivity of this approach were evaluated. We demonstrate that an allele occurring at a frequency of 2% can consistently be quantitated.     

Selective flow injection analysis of ultra-trace amounts of Cr(VI), preconcentration of it by solvent extraction, and determination by electrothermal atomic absorption spectrometry (ETAAS)

A rapid, robust, sensitive and selective time-based flow injection (FI) on-line solvent extraction system interfaced with electrothermal atomic absorption spectrometry (ETAAS) is described for analyzing ultra-trace amounts of Cr(VI). The sample is initially mixed on-line with isobutyl methyl ketone (IBMK). The Cr(VI) is complexed by reaction with ammonium pyrrolidine dithiocarbamate (APDC), and the non-charged Cr(VI)–PDC chelate formed is extracted into IBMK in a knotted reactor made from PTFE tubing. The organic extractant is separated from the aqueous phase by a gravity phase separator with a small conical cavity and delivered into a collector tube, from which 55 μl organic concentrate is subsequently introduced via an air flow into the graphite tube of the ETAAS instrument. The operations of the FI-system and the ETAAS detector are synchronously coupled. A significant advantage of the approach is that matrix constituents, such as high salt contents, effectively are eliminated. The extraction procedure was optimized by a simplex approach. A central composite design was subsequently employed to verify the estimated operational optimum. An 18-fold enhancement in sensitivity of Cr(VI) was achieved after preconcentration for 99 s at a sample flow rate of 5.5 ml min⁻¹, as compared to direct introduction of 55 μl of sample, yielding a detection limit (3σ) of 3.3 ng l⁻¹. The sampling frequency was 24.2 samples h⁻¹. The proposed method was successfully evaluated by analyzing a NIST Cr(VI)-reference material, synthetic seawater and waste waters, and waste water samples from an incineration plant and a desulphurization plant, respectively.     

On-line preconcentration using dual mini-columns for the speciation of chromium(III) and chromium(VI) and its application to water samples as studied by inductively coupled plasma-atomic emission spectrometry

On-line preconcentration system for the selective, sensitive and simultaneous determination of chromium species was investigated. Dual mini-columns containing chelating resin were utilized for the speciation and preconcentration of Cr(III) and Cr(VI) in water samples. In this system, Cr(III) was collected on first column packed with iminodiacetate resin. Cr(VI) in the effluent from the first column was reduced to Cr(III), which was collected on the second column packed with iminodiacetate resin. Hydroxyammonium chloride was examined as a potential reducing agent for Cr(VI) to Cr(III).The effects of pH, sample flow rate, column length, and interfering ions on the recoveries of Cr(III) were carefully studied. Five millilitres of a sample solution was introduced into the system. The collected species were then sequentially washed by 1 M ammonium acetate, eluted by 2 M nitric acid and measured by ICP-AES. The detection limit for Cr(III) and Cr(VI) was 0.08 and 0.15 μg l⁻¹, respectively. The total analysis time was about 9.4 min.The developed method was successfully applied to the speciation of chromium in river, tap water and wastewater samples with satisfied results.     

Synthesis of amberlite XAD-2-PC resin for preconcentration and determination of trace elements in food samples by flame atomic absorption spectrometry

A new chelating sorbent has been developed using Amberlite XAD-2 resin anchored with pyrocatechol through –N=C– group. This sorbent, characterised by elemental analysis and infrared (IR) spectra, was used as packing for the minicolumn in an on-line system preconcentration system for cadmium, cobalt, copper and nickel determination. Metal ions were sorbed in the minicolumn, from which it could be eluted directly to the nebulizer–burner system of the flame atomic absorption spectrometer (FAAS). Elution of all metals from minicolumn can be made with 0.50 mol L^− 1 HCl or HNO₃. The enrichment factors obtained were 16 (Cd), 24 (Co), 15 (Cu) and 19 (Ni), for 60 s preconcentration time, and 39 (Cd), 69 (Co), 36 (Cu) and 41 (Ni), if used 180 s preconcentration time. Under the optimum conditions, the proposed procedure allowed the determination of cadmium, cobalt, copper and nickel with detection limits of 0.31, 0.32, 0.39 and 1.64 μg L^− 1, respectively, when used preconcentration periods of 180 s. The accuracy of the developed procedure was sufficient and evaluated by the analysis of the certified reference materials NIST 1515 apple leaves and NIST 1570a spinach leaves. The method was applied to the analysis of food samples (spinach, black tea and rice flour).     

Development of a competitive liposome-based lateral flow assay for the rapid detection of the allergenic peanut protein Ara h1

A competitive lateral flow assay for detecting the major peanut allergen, Ara h1, has been developed. The detector reagents are Ara h1-tagged liposomes, and the capture reagents are anti-Ara h1 polyclonal antibodies. Two types of rabbit polyclonal antibodies were raised either against the entire Ara h1 molecules (anti-Ara h1 Ab) or against an immunodominant epitope on Ara h1 (anti-peptide Ab). All of them reacted specifically with Ara h1 in Western Blot against crude peanut proteins. Moreover, the anti-Ara h1 Ab was chosen for this assay development because of its highest immunoactivity to Ara h1-tagged liposomes in the lateral flow assay. The calculated limit of detection (LOD) of this assay is 0.45 g mL^–1 of Ara h1 with a dynamic range between 0.1 and 10 g mL^–1 of Ara h1 in buffer. Additionally, the visually determined detection range is from 1 to 10 g mL^–1 of Ara h1 in buffer. Results using this assay can be obtained within 30 min without the need of sophisticated equipment or techniques; therefore, this lateral flow assay has the potential to be a cost-effective, fast, simple, and sensitive method for on-site screening of peanut allergens.     

Fast and highly selective determination of cyanide with 2,2-dihydroxy-1,3-indanedione

A very simple, accurate, fast, selective and sensitive assay of cyanide based on its reaction with 2,2-dihydroxy-l,3-indanedione at basic pH is proposed. As little as 0.01 μg ml⁻¹ of cyanide can be determined. The molar absorptivity may reach 5.1–8.0×10⁴ l mol⁻¹ cm⁻¹ depending on the reaction conditions. Thus, 1 ml of sample solution is mixed with 500 μl of 5 mg ml⁻¹ solution of 2,2-dihydroxy-1,3-indanedione monohydrate in 2% sodium carbonate. The absorbance of the purple color is measured at 510 nm in 1-cm glass cuvettes, 10–15 min after mixing the reagents. The procedure could also be used to identify free CN⁻ in natural waters and hydrocyanic acid in the environment.     

Determination of phenolic compounds in water samples by on-line solid-phase extraction—supercritical-fluid chromatography with diode-array detection

Summary The eleven Environmental Protection Agency (EPA) priority phenolic compounds have been determined by solid-phase extraction (SPE) coupled on-line to supercritical-fluid chromatography (SFC) with diodearray detection. The variables affecting chromatographic separation were optimized and the analytes were separated at 40 °C in two diol columns connected in series; a gradient of methanol, as modifier, and CO₂ was used as mobile phase. Under these conditions, all the compounds studied were separated to baseline in less than 13 min. PLRP-S and LiChrolut EN were tested as sorbents in a 10×3 mm i.d. laboratory-packed precolumn for solid-phase extraction. An ion-pair reagent, tetrabutylammonium bromide (TBA), was used in the extraction process to increase break-through volumes. The performance of the method was checked with tap and river waters and the pre-concentration of 20 mL of sample in a PLRP-S pre-column enabled phenolic compounds to be determined at low μg L⁻¹ levels with limits of detection ranging between 0.4 and 2 μg L⁻¹. The repeatability and reproducibility between days (n=3) for real samples spiked at 10 μg L⁻¹ were lower than 10%.     

Determination of trace elements in seawater samples by on-line column extraction/graphite furnace atomic absorption spectrometry

An innovative procedure for the on-line coupling of ion chromatography with graphite furnace atomic absorption spectrometry is described, which is particularly effective for the determination of trace metals in seawater samples. The Capillary Injection Device (CID) is used as an interface which allows the eluent to be transferred from the chromatographic column into the graphite tube at a flow rate of as high as 2 ml/min. The analytical procedure is based on the metal complex formation with 8-hydroxyquinoline in the sample solution, followed by the preconcentration of the complexes in a chromatographic column packed with XAD-2 resin. The complexes were then eluted from the column with methanol, and quantitatively injected into the furnace. The procedure was validated by determining cadmium and lead in certified reference seawater samples at a level of 30–40 pg/g, with a typical reproducibility of 10% and an accuracy of better than 5%. Finally, it was tested on a real sample of seawater. Due to the high reproducibility, a pg/g concentration level can be measured.     

Quantification of phytochelatins in plants by reversed-phase HPLC–ESI–MS–MS

An on-line HPLC–ESI–MS–MS method has been developed for determination of glutathione and phytochelatins (PC) in plant tissues. For sample pretreatment, dithiothreitol (DTT) must be added at the very beginning, as an anti-oxidant. Optimization of instrumental conditions i.e. composition of HPLC mobile phase, ionization efficiency of the electrospray interface, and MS–MS detection in the multiple ion-monitoring mode, are the central aspects of this work. A polystyrene-packed column was found to be superior to a standard silica-packed reversed-phase column. A concave quadratic gradient of ammonium formate buffer and acetonitrile was found to be optimum. The limits of quantitation were 0.2 mol kg^–1 plant tissue for glutathione and PC. The method has been applied to analysis of tissue samples from Vicia faba grown in Cd-containing nutrient solutions.Dedicated to the memory of Wilhelm Fresenius     

Determination of Human Alpha-Fetoprotein (AFP) by Solid Substrate Room Temperature Phosphorescence Enzyme-Linked Immune Response Using Luminescent Nanoparticles

Luminescent nanoparticles of silicon dioxide (SiO₂) containing fluorescein isothiocyanate (FITC) with a particle size of 20 nm were synthesized using the Sol–Gel method (abbreviated FITC–SiO₂). FITC–SiO₂ nanoparticles whose surfaces are modified (FITC–SiO₂–S–CH₂COOH) can emit strong and stable solid substrate room temperature phosphorescence (SS-RTP) on acetyl cellulose membranes. When the original color-producing agent (R) in the enzyme-linked immunosorbent assay (ELISA) kits for determination of alpha-fetoprotein (AFP) was substituted with (FITC–SiO₂–S–CH₂COOH), the system maintained good FITC–SiO₂ phosphorescence properties. Furthermore, the phosphorescence intensity enhanced markedly after the ELISA reaction. The relationship between the phosphorescence intensity and the content of AFP obeyed Beer’s law. Based on the facts stated above, a new method for the determination of human AFP by SS-RTP-ELISA (using the luminescent nanoparticle as marker) was established. The linear range of this method is 0.040–16.0 pg of human AFP per spot (sample volume: 0.40 μL spot⁻¹, corresponding concentration: 0.10–40.0 ng mL⁻¹). The regression equation of the working curve is ΔIp = −6.289+18.075 m_AFP (pg spot⁻¹) (r = 0.9960, n = 6). The detection limit (LD) of this method calculated by 3 S_b/k is 6.7 fg spot⁻¹ (corresponding concentration: 17 ng L⁻¹). Compared to the ELISA method using a traditional color-producing agent, the new method exhibited a 34.8 times higher sensitivity and a wider linear range. The method has been successfully applied to the determination of human AFP in serum.