High-throughput polymerase chain reaction analysis of clinical samples by capillary electrophoresis with UV detection

Routine genetic analysis of large numbers of individuals by polymerase chain reaction (PCR) using capillary electrophoresis is often restricted by the low throughput of standard protocols and the tedious sample preparation process. Here, we demonstrate that capillary electrophoresis with UV detection can be used in PCR-based DNA analysis starting from clinical samples without purification or complicated sample manipulation. After PCR reaction using cheek cells, blood, or HIV-1 gag DNA, the reaction mixtures were injected into a capillary array either on-line or off-line by base stacking. The use of multiplexed absorption detection and the elimination of any purification steps both before and after PCR reaction can potentially provide significant benefits compared to current methods for DNA analysis with regard to time, cost, and labor.     

Multivariate optimization of surfactant‐assisted directly suspended droplet microextraction combined with GC for the preconcentration and determination of tramadol in biological samples

In this work, a novel procedure based on surfactant‐assisted directly suspended droplet microextraction for the determination of tramadol prior to GC with flame ionization detection is proposed. In this technique, a free microdroplet of solvent is transferred to the surface of an immiscible aqueous sample containing Triton X‐100 and tramadol while being agitated by a stirring bar placed on the bottom of the sample vial. After the predetermined time, the microdroplet of solvent is withdrawn by a syringe and analyzed. The effective parameters such as the type of organic solvent, extraction time, microdroplet volume, salt content of the donor phase, stirring speed, the source phase pH, concentration of Triton X‐100, and extraction temperature were optimized. For this purpose, a multivariate strategy was applied based on an experimental design in order to screen and optimize the significant factors. This method requires minimal sample preparation, analysis time, solvent consumption, and represents significant advantages over customary analytical methods. The linearity ranged from 10 to 2000 μg/L with RSDs (n = 5) of 7.3–10. Preconcentration factors and the LODs were 391–466 and 2.5–6.5 μg/L, respectively. Finally, this method was applied to the analysis of biological samples and satisfactory results were obtained.     

Preparation, identification and analysis of stereoisomeric anti-benzo[a]pyrene diol epoxide-deoxyguanosine adducts using phenyl liquid chromatography with diode array, fluorescence and tandem mass spectrometry detection

Benzo[a]pyrene, a common environmental pollutant, can be metabolized into reactive anti-benzo[a]pyrene diol epoxide (anti-BPDE), which predominantly binds to deoxyguanine in DNA and forms four stereoisomeric adducts. To characterize the stereochemistry of these adduct isomers, preparation of single adducted deoxyguanosine (dG) is required for efficient enantiomeric analysis. Here, we demonstrate an improved method for preparation, identification, and analysis of four BPDE-adducted dGs, including (+)-trans-, (-)-trans-, (+)-cis-, and (-)-cis-anti-BPDE-N(2)-dG. These stereoisomerically adducted nucleosides were first synthesized by a direct reaction of (+/-)-anti-BPDE with dG, followed by optimized solid-phase extraction (SPE) and HPLC purification. The reaction of (+/-)-anti-BPDE and dG displayed a yield as high as 45%. The developed preparation method does not require any enzymatic digestion. Based on highly efficient separation achieved by optimization of stationary phase and mobile phase, LC-UV-MS/MS and LC-diode array detection (DAD)-fluorescence detection (FL) methods were established for characterization and analysis of the four stereoisomeric anti-BPDE-dGs. The established LC-DAD-FL method may provide characterization and analysis of four stereoisomeric anti-BPDE-dGs and two interfering anti-BPDE tetrols by taking advantage of their distinct fluorescence quenching.     

Functionalized gold nanoparticles for ultrasensitive DNA detection

A major challenge in the area of DNA detection is the development of rapid methods that do not require polymerase chain reaction (PCR) amplification of the genetic sample. The PCR amplification step increases the cost of the assay, the complexity of the detection, and the quantity of DNA required for the assay. In this context, methods that are able to perform DNA analyses with ultrasensitivity have recently been investigated with the aim of developing new PCR-free detection protocols. Functionalized gold nanoparticles have played a central role in the development of such methods. Here, possibilities offered by functionalized gold nanoparticle in the ultrasensitive detection of DNA are discussed. The different functionalization protocols available for gold nanoparticles and the principal DNA detection methods that are able to detect DNA at the femtomolar to attomolar level are presented.     

Multisample preparation methods for the solvent-free MALDI-MS analysis of synthetic polymers

A limitation of any current approach using solvent-free MALDI mass spectrometry is that only one sample at a time can be prepared and transferred to the MALDI-plate. For this reason, multiple-sample preparation approaches for solvent-free MALDI MS analysis of synthetic polymers were developed that are simple and practical. One approach multiplexed sample preparation by simultaneously preparing multiple samples. With this approach, as many as 384 samples could be prepared by addition of analyte, matrix, salt, and 1-mm metal beads to each well of a 384-well disposable bacti plate, capping the plate with the lid and homogenizing all samples simultaneously using a common laboratory vortex device. Besides the time savings achieved by a single vortex step for multiple samples, an additional advantage of this method relative to previously reported solvent-free preparation methods is that the mixing volume per sample is reduced, which allows a reduction in the amount of analyte required. This method, however, still requires the transfer of each homogenized sample to the MALDI plate for subsequent analysis. Here we report a novel approach that combines multiple simultaneous solvent-free sample preparation with automatic sample transfer to the MALDI target plate. This approach reduces the possibility of cross-contamination, the amount of sample and matrix consumed for an analysis, and the time required for preparation of multiple samples. These methods were shown to provide high-quality mass spectra for various synthetic polymer standards with M(n) values to 10 kDa. The methods are efficient in that small sample amounts are required, the sample/salt/matrix ratio is not critical, and the time necessary to achieve sufficient homogenization of multiple samples is less than 5 min.     

Analysis of individual platelet-derived microparticles,comparing flow cytometry and capillary electrophoresis with laser-induced fluorescence detection

Platelet-derived microparticles (PMPs) formed by vesiculation during platelet activation seem to play a role in blood coagulation and in pathological disease states. Flow cytometry is currently the gold standard to characterize platelets and PMPs. Using this technique we distinguished between platelets and PMPs based on size and the presence of phosphatidyl serine (PS); PMPs were arbitrarily defined to be smaller than one micrometer and capable of forming a stable complex with fluorescently-labeled Annexin V, a protein that forms a calcium-dependent complex with PS. Further confirmation of PMP and platelet identity was done by use of fluorescently-labeled antibodies against CD41a, a glycoprotein found on the surface of both platelets and PMPs. In this report we also introduce the use of capillary electrophoresis with post-column laser-induced fluorescence detection (CE-LIF) for the analysis of fluorescently labeled platelets and PMPs. While both flow cytometry and CE-LIF can measure individual fluorescent events, only CE-LIF allowed us to calculate individual electrophoretic mobilities of activated platelets and PMPs that were then represented as distributions. A comparison between distributions suggests that PMPs have less negative mobilities. The fact that activated platelet preparations include PMPs partially obscure the interpretation of the data. While PMP and platelet number ml(-1) determined by flow cytometry is lower than the same parameter determined by CE-LIF, signal-to-noise ratio was 20 fold better for flow cytometry than for CE-LIF. This is the first time that a direct comparison between these two techniques is reported.     

Detection of genetically modified crops and their derivatives: critical steps in sample preparation and extraction

The detection of genetically modified crops in foodstuff relies on detection of transgenic DNA or protein material in the sample matrix. Purified DNA or proteins are used as analytical material for polymerase chain reaction technologies and immunodiagnostics. Successful sample preparation is critical to the validity of subsequent analysis. For routine analysis, a good sample preparation technique should be simple, safe, and inexpensive while reproducibly generating DNA/protein of sufficient quality and yield. The suitability of isolated DNA or protein as an analyte for a detection or characterization technique depends on amount or concentration, purity, and integrity, each of which may be influenced by sample matrix and the extraction technique, and, in turn, may impact the validity of analytical techniques. The key sample preparation steps of homogenization, pretreatment, extraction, and purification are discussed as well as typical analytical methods. Consideration is given to application of these steps for particular sample matrixes to maximize yield, reduce inhibition effects, and minimize contamination. The choice of the most appropriate and valid methods for sample preparation from particular foods is discussed with respect to DNA analysis. Attention is also given to ease of use, cost, and generic applicability of the procedures.     

Rapid liquid chromatographic determination of oxytetracycline in milk.

A simple method for the determination of residual oxytetracycline (OTC) in milk by high-performance liquid chromatography (HPLC) was developed. The sample preparation could be made without complex extraction and clean-up procedures. A LiChrospher 100 RP-8 end-capped column and a mobile phase of acetonitrile-acetic acid-water (28:4:68, v/v/v) with a photo-diode array detector was used. The average recoveries from spiked OTC (0.1, 0.5 and 1.0 microgram/ml) were in excess of 89.8% with coefficients of variation between 0.6 and 4.1%. The limit of detection was 0.05 microgram/ml. The total time required for the analysis of one sample was below 10 min.     

干果类食品的样品前处理与分析检测方法研究进展

坚果、果脯等干果类食品含有丰富的营养成分,深受国内外广大消费者的喜爱.但这些食品在果实生产、加工、储运时会使用农药或产生霉变等,造成干果中农药、重金属、霉菌毒素或添加剂等有害成分残留,甚至超过国家限量要求,带来严重的食品安全问题.因此,加强干果类食品的质量监督具有重要的经济和社会意义.但干果类食品基质复杂,有害物质种类...     

Reproducibility of serum protein profiling by systematic assessment using solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry

Protein profiling of human serum by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is potentially a new diagnostic tool for early detection of human diseases, including cancer. Sample preparation is a key issue in MALDI MS and the analysis of complex samples such as serum requires optimized, reproducible methods for handling and deposition of protein samples. Data acquisition in MALDI MS is also a critical issue, since heterogeneity of sample deposits leads to attenuation of ion signals in MALDI MS. In order to improve the robustness and reproducibility of MALDI MS for serum protein profiling we investigated a range of sample preparation techniques and developed a statistical method based on repeated analyses for evaluation of protein-profiling performance of MALDI MS. Two different solid-phase extraction (SPE) methods were investigated, namely custom-made microcolumns and commercially available magnetic beads. Using these two methods, nineteen different sample preparation methods for serum profiling by MALDI MS were systematically tested with regard to matrix selection, stationary phase, selectivity, and reproducibility. Microcolumns were tested with regard to chromatographic properties; reversed phase (C8, C18, SDB-XC), ion-exchange (anion, weak cation, mixed-phase (SDB-RPS)) and magnetic beads were tested with regard to chromatographic properties; reversed phase (C8) or affinity chromatography (Cu-IMAC). The reproducibility of each sample preparation method was determined by enumeration and analysis of protein signals that were detected in at least six out of nine spectra obtained by three triplicate analyses of one serum sample.A candidate for best overall performance as evaluated by the number of peaks generated and the reproducibility of mass spectra was found among the tested methods. Up to 418 reproducible peaks were detected in one cancer serum sample. These protein peaks can be part of a possible diagnostic profile, suggesting that this sample preparation method and data acquisition approach is suitable for large-scale analysis of serum samples for protein profiling.     

Nonenzymatic protocol for Pseudomonas aeruginosa DNA preparation and rapid subtyping by mini pulsed-field gel electrophoresis.

The fastest protocol for Pseudomonas aeruginosa subtyping by contour clamped homogeneous electric field (CHEF) electrophoresis takes around 20 h. It includes enzymatic sample preparation, DNA restriction and fragment separation. Here, P. aeruginosa cells embedded in agarose miniplugs were lysed and deproteinized by incubating the miniplugs for 30 min in a single nonenzymatic solution. DNA molecules were digested for 2 h with 5 U of XbaI, and fragments were separated in 4.96 h by miniCHEF electrophoresis at 10 V/cm. Total time for P. aeruginosa subtyping was 8 h. Control experiments included DNA preparation by enzymatic or nonenzymatic protocols, different times of DNA restriction and comparisons of DNA separations done by miniCHEF or CHEF electrophoresis. Both methods and chambers gave similar results, but the rapid nonenzymatic method and the miniCHEF gave them in less time. Cells grown in broth or on plates were useful for nonenzymatic DNA preparation. Thirteen P. aeruginosa isolates were successfully fingerprinted using the protocol described here.     

Analysis of Paraben Preservatives in Cosmetic Samples: Comparison of Three Different Dynamic Hollow Fiber Liquid-Phase Microextraction Methods

This study focused on a comparison of three different dynamic hollow fiber-based liquid-phase microextraction (DHF-LPME) methods for extraction and preconcentration of parabens from wastewater, toothpaste, cream, and shampoo samples. The first method is two-phase DHF-LPME, in which n-octanol was used as the extraction solvent. The second is three-phase DHF-LPME, in which n-octanol and basic aqueous solution were used as the extraction solvent and acceptor phase, respectively. High-performance liquid chromatography with UV detection (HPLC–UV) was applied for determination of the parabens in both methods. The third method is a recently introduced method; three-phase DHF-LPME based on two immiscible organic solvents (n-dodecane as organic solvent and acetonitrile as an acceptor phase). The quantitative analyses were performed by the use of gas chromatography-mass spectrometry (GC–MS) after injection port derivatization. The effect of different extraction conditions (i.e., extraction solvent, pH, ionic strength, stirring rate, and dynamic and extraction times) on the extraction efficiency of the parabens was investigated and optimized. All the three procedures provide similar working parameters characterized by high repeatability (3.9–6.3 %) and good linearity (correlation coefficient ranging from 0.989 to 0.998). Results of real sample analyses obtained by these three methods were highly correlated. Although all methods provide compatible alternatives for paraben analysis, the three-phase DHF-LPME based on two immiscible organic solvents may be a more appropriate technique due to its higher extraction efficiency and thus lower limits of detection (LODs). LODs for all the parabens ranged from 0.2 to 5.0 μg L^?1 using the two first methods combined with HPLC–UV. An improvement in sensitivity of several orders of magnitude was achieved using three-phase DHF-LPME based on two immiscible organic solvents followed by single-ion monitoring GC–MS analyses (0.01–0.2 μg L^?1) due to compatibility of this technique with GC instrument.     

Liquid-chromatographic determination of sulfadimidine in milk and eggs

A method for the determination/identification of residual sulfadimidine (SDD) in milk and eggs by high-performance liquid chromatography (HPLC) with a photo-diode array detector was developed. The sample preparation was performed by shaking with a mixture of 20% (w/v) trichloroacetic acid-methanol (4:1, v/v) followed by ultra-filtration using Molcut II^®. A LiChrospher^® 100 RP-8 (e) column and a mobile phase of 4% (v/v) acetic acid solution-acetonitrile (6:4, v/v) were used. The average recoveries from spiked SDD samples were 80.8–88.0% with coefficients of variation of 2.8–5.5%. The limits of detection in milk and eggs were 0.01 μg/mL and 0.01 μg/g, respectively. The total time required for the analysis of one sample was less than 20 min.     

A surface topography assisted droplet manipulation platform for biomarker detection and pathogen identification

This paper reports a droplet microfluidic, sample-to-answer platform for the detection of disease biomarkers and infectious pathogens using crude biosamples. The platform exploited the dual functionality of silica superparamagnetic particles (SSP) for solid phase extraction of DNA and magnetic actuation. This enabled the integration of sample preparation and genetic analysis within discrete droplets, including the steps of cell lysis, DNA binding, washing, elution, amplification and detection. The microfluidic device was self contained, with all reagents stored in droplets, thereby eliminating the need for fluidic coupling to external reagent reservoirs. The device incorporated unique surface topographic features to assist droplet manipulation. Pairs of micro-elevations were created to form slits that facilitated efficient splitting of SSP from droplets. In addition, a compact sample handling stage, which integrated the magnet manipulator, the droplet microfluidic device and a Peltier thermal cycler, was built for convenient droplet manipulation and real-time detection. The feasibility of the platform was demonstrated by analysing ovarian cancer biomarker Rsf-1 and detecting Escherichia coli with real time polymerase chain reaction and real time helicase dependent amplification.     

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.     

Tailoring 3D shapes of polyhedral milliparticles by adjusting orthogonal projection in a microfluidic channel

Polyhedral milliparticles (PMPs) have promising applications in self-assembly, tissue engineering, mechanical engineering, and photonics. The shapes and sizes of the PMPs have great impact on their functions. To date, the reported methods for adjusting the shapes and sizes of PMPs are still limited. Especially, it remains a challenge to fabricate the PMPs with high asymmetry. Here, we present a facile and efficient approach that focuses on the alteration of the relative positions between the microchannel and the UV light to tailor the shaping process of the PMPs. By tuning the rotation angle and translation displacement, a variety of monodisperse PMPs with both centrosymmetric and noncentrosymmetrical structures are synthesized, including tetrahedra, pentahedra, hexahedra, and so forth. Moreover, the polymeric PMPs are loaded with silica nanoparticles and further sintered into silica. The obtained silica PMPs hold great potential for the applications such as machining tools, abrasives, and electronics.     

Comparison of hydrophilic interaction and reversed-phase liquid chromatography coupled with tandem mass spectrometric detection for the determination of three pharmaceuticals in human plasma

In the present study, hydrophilic interaction liquid chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) combined with tandem mass spectrometric detection (MS/MS) were evaluated and compared for the determination of donepezil, cetirizine and loratadine in human plasma, in terms of sensitivity and sample preparation procedure. A retention study for the above compounds of various polarities was performed, using both C(18) and silica columns, with several aqueous-organic mobile phase ratios, in order to investigate their retention mechanism profile under HILIC and RPLC. Both chromatographic conditions were compared for chromatographic analysis of plasma samples processed with a liquid-liquid extraction (LLE) method for donepezil determination, resulting in significantly higher sensitivity under HILIC. Furthermore, HILIC and RPLC were compared for direct injection, and novel methods including LLE, solid-phase extraction and protein precipitation protocols were developed. Direct injection technique significantly reduced sample preparation time, increasing at the same time method sensitivity. The current study contributes to broadening the range of analyzable compounds by HILIC-MS/MS to molecules of medium polarity.     

Methods for generating protein molecular ions in ToF-SIMS

One of the greatest challenges in mass spectrometry lies in the generation and detection of molecular ions that can be used to directly identify the protein from the molecular weight of the molecular ion. Typically, proteins are large (MW > 1000), nonvolatile, and/or thermally labile, but the vaporization process produced by many mass spectrometry techniques including time-of-flight secondary ion mass spectrometry (ToF-SIMS) is inherently limited to generating ions from smaller compounds or fragments of the parent molecule, making the identification of proteins complex. The application of specific molecules to aid in the generation of high molecular weight ions in ToF-SIMS has been recognized for some time. In this study we have developed a matrix-SAM substrate preparation technique based on the self-assembly of a matrix-like molecule, mercaptonicotinic acid (MNA), on gold. We then compare this substrate with two existing ToF-SIMS sample preparation techniques, cationized alkane thiol and matrix-enhanced SIMS (MESIMS). The results of this study illustrate that while there is a range of methods that can be used to improve the molecular ion yield of proteins in ToF-SIMS, their efficacy and reproducibility vary considerably and crucially are linked to the sample preparation and/or protein application methods used. Critically, the MNA modified substrate was able to simultaneously induce molecular ions for each protein present in a multicomponent solution, suggesting that this sample preparation technique may have future application in proteomics and DNA analysis.     

Liquid-chromatographic determination of sulfadimidine in milk and eggs

A method for the determination/identification of residual sulfadimidine (SDD) in milk and eggs by high-performance liquid chromatography (HPLC) with a photo-diode array detector was developed. The sample preparation was performed by shaking with a mixture of 20% (w/v) trichloroacetic acid-methanol (4:1, v/v) followed by ultra-filtration using Molcut II^?. A LiChrospher^? 100 RP-8 (e) column and a mobile phase of 4% (v/v) acetic acid solution-acetonitrile (6:4, v/v) were used. The average recoveries from spiked SDD samples were 80.8–88.0% with coefficients of variation of 2.8–5.5%. The limits of detection in milk and eggs were 0.01 μg/mL and 0.01 μg/g, respectively. The total time required for the analysis of one sample was less than 20 min. Received: 7 October 1998 / Revised: 29 December 1998 / Accepted: 30 December 1998