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PubMed2006

Simple urinary sample preparation for proteomic analysis.

Since the completion of the human genome sequence, attention has now focused on establishing reference maps of body fluids such as plasma and urine for detecting diagnostic markers of disease. Although some progress has been made, challenges still remain in the development of an optimal sample preparation method for proteomic analysis of urine. We have developed a simple and efficient urine preparation method for two-dimensional (2-D) gel electrophoresis which involves precipitation of proteins with simultaneous desalting. Acetonitrile precipitation produced 2-D gel separations with the highest resolution and the greatest number of protein spots compared to precipitation by other organic solvents. The method was applied to observe changes in the urinary proteome over a 6 week period and to establish a reference map of a healthy subject. A total of 339 proteins from 159 genes was identified from healthy male urine by peptide mass fingerprinting. The profiles of the urinary proteome at three times in 1 day and on four different days were compared and were found to vary in number and spatial location of the proteins on the map. The method was also shown to be applicable to the higher concentrations of protein found in the urine of an ovarian cancer subject. We have developed a facile and robust method for preparing urine for 2-D gels that will encourage further use of urine.

Adult↗
PubMed1999

The effects of sample preparation methods on the variability of the electrospray ionization response for model drug compounds.

A post-column infusion system was developed in order to analyze suppression of electrospray ionization (ESI) tandem mass spectrometry response in the presence of endogenous plasma interferences. By enabling direct detection of these interfering components, this experimental system was used to analyze the ability of several common extraction procedures to remove endogenous plasma components that cause changes in the ESI response of model drug substances. Methyl-t-butyl ether (MTBE) liquid-liquid, Oasis and Empore solid-phase, and acetonitrile (ACN) protein precipitation sample preparation methods were tested using the post-column infusion system. In all cases, ACN protein precipitation samples showed the greatest amount of ESI response suppression while liquid-liquid extracts demonstrated the least. In addition, the three test compounds, phenacetin, caffeine, and a representative Merck compound, demonstrated that ESI response suppression is compound dependent. Suppression was greatest with caffeine, the most polar analyte, and the smallest for the Merck compound, the least polar analyte. Copyright 1999 John Wiley & Sons, Ltd.

Journal Article↗
PubMed1982

Sample preparation in determination of lead in garden vegetables by flame atomic absorption spectrophotometry.

Dry and wet ashing methods have been used in the analysis of garden vegetables for Pb. The reliability of wet ashing has been verified by the method of standard additions. Comparison of dry and wet ashing showed good agreement for a variety of garden vegetables. Sample size was more strictly limited for the wet-ashed samples, which led to lower sensitivity. Vegetable samples are commonly analyzed for a number of trace elements, which introduces additional constraints on sample preparation, notably because of Cd loss on dry ashing. Pretreatment with HNO3/H2SO4 ash aid eliminated Cd loss. Reliability of dry ashing with pretreatment was shown with NBS SRM Orchard Leaves, Pine Needles, Spinach, and Tomato Leaves. The analysis was insensitive to ashing temperature in the range 480-625 degrees C. A practical detection limit for the method is about 2 ppm Pb, dry weight basis (DWB). Care must be exercised to avoid contamination of the sample with lead at this level by improper handling. Segregation and acid washing of glassware and protection of the sample from contact with any object not demonstrably clean was necessary. No evidence was found of Pb contamination at this level from tap water washing of fresh vegetables, forced-air oven drying, or grinding with mortar and pestle. No special clean room facilities or laboratory air purification measures were used. Sensitivity was increased 3-fold by extraction with dithizone in CHCl3 followed by back-extraction into dilute HCl. Detection limits were not improved, however, because of variation in the extraction results. The instrumental method for assessing effective correction for back-ground absorbance showed adequate compensation, although comparison of direct and extractive determinations showed a small but significant difference between the methods of about 1 ppm Pb (DWB).

Hot Temperature↗
PubMed2002

Interference-free sample preparation for the determination of plasma oxalate analyzed by HPLC-ER: preliminary results from calcium oxalate stone-formers and non-stone-formers.

BACKGROUND: Oxalate generation at pH-values above 5.0 and an oxalate-protein binding in acidified plasma would appear to complicate the determination of oxalate in plasma. METHODS: To avoid complex sample preparation we used a high-performance liquid chromatographic system with an inline enzyme reactor (HPLC-ER) containing immobilised oxalate oxidase. The detection limit was 0.68 micromol/l. Blood was drawn in lithium-heparin vessels and immediately centrifuged at 4 degrees C. The yielded plasma was ultrafiltered using a Centrisart-I-tube. To inhibit oxalate generation by ascorbic acid, the ultrafiltrate was acidified with 1 mol/l hydrochloric acid during ultrafiltration at 4 degrees C. The liquid thus yielded was used for HPLC-ER analysis. Blood samples were obtained from 133 healthy adults (63 men, 70 women, aged 20-94 years) with no history of renal disorder and from 79 patients (53 men, 26 women, aged 19-77 years) with a history of calcium oxalate stone formation. RESULTS: Mean plasma oxalate was 2.65 +/- 2.31 micromol/l for healthy subjects and 4.21 +/- 0.56 micromol/l for stone formers. CONCLUSIONS: Analysis yielded no significant differences between males and females. A correlation between age and plasma oxalate was found for the healthy adults (p < 0.001).

Adult↗
PubMed2000

Optimal sample preparation conditions for the determination of uranium in biological samples by kinetic phosphorescence analysis (KPA).

Kinetic phosphorescence analysis (KPA) is a proven technique for rapid, precise, and accurate determination of uranium in aqueous solutions. Uranium analysis of biological samples require dry-ashing in a muffle furnace between 400 and 600 degrees C followed by wet-ashing with concentrated nitric acid and hydrogen peroxide to digest the organic component in the sample that interferes with uranium determination by KPA. The optimal dry-ashing temperature was determined to be 450 degrees C. At dry-ashing temperatures greater than 450 degrees C, uranium loss was attributed to vaporization. High temperatures also caused increased background values that were attributed to uranium leaching from the glass vials. Dry-ashing temperatures less than 450 degrees C result in the samples needing additional wet-ashing steps. The recovery of uranium in urine samples was 99.2+/-4.02% between spiked concentrations of 1.98-1980 ng (0.198-198 microg l(-1)) uranium, whereas the recovery in whole blood was 89.9+/-7.33% between the same spiked concentrations. The limit of quantification in which uranium in urine and blood could be accurately measured above the background was determined to be 0.05 and 0.6 microg l(-1), respectively.

Humans↗
PubMed1994

Sample preparation technique for iodine determination in urine and water samples.

A simple method for iodine determination in urine and water samples is presented. After digestion of the sample with chromic acid, the iodate produced was converted to iodide by the addition of a strong solution of sodium sulphite. The iodide was then precipitated as palladium iodide using a solution of palladium chloride. The precipitate was filtered through membrane filter paper, air-dried and analyzed using the Energy Dispersive X-Ray Fluorescence (EDXRF) method.

Humans↗
PubMed1999

Nanoliter-scale sample preparation methods directly coupled to polymethylmethacrylate-based microchips and gel-filled capillaries for the analysis of oligonucleotides.

We are currently developing miniaturized, chip-based electrophoresis devices fabricated in plastics for the high-speed separation of oligonucleotides. One of the principal advantages associated with these devices is their small sample requirements, typically in the nanoliter to sub-nanoliter range. Unfortunately, most standard sample preparation protocols, especially for oligonucleotides, are done off-chip on a microliter-scale. Our work has focused on the development of capillary nanoreactors coupled to micro-separation platforms, such as micro-electrophoresis chips, for the preparation of sequencing ladders and also polymerase chain reactions (PCRs). These nanoreactors consist of fused-silica capillary tubes (10-20 cm x 20-50 microns I.D.) with fluid pumping accomplished using the electroosmotic flow generated by the tubes. These reactors were situated in fast thermal cyclers to perform cycle sequencing or PCR amplification of the DNAs. The reactors could be interfaced to either a micro-electrophoresis chips via capillary connectors micromachined in polymethylmethacrylate (PMMA) using deep X-ray etching (width 50 microns; depth 50 microns) or conventional capillary gel tubes using zero-dead volume glass unions. For our chips, they also contained an injector, separation channel (length 6 cm; width 30 microns; depth 50 microns) and a dual fiber optic, near-infrared fluorescence detector. The sequencing nanoreactor used surface immobilized templates attached to the wall via a biotin-streptavidin-biotin linkage. Sequencing tracks could be directly injected into gel-filled capillary tubes with minimal degradation in the efficiency of the separation process. The nanoreactor could also be configured to perform PCR reactions by filling the capillary tube with the PCR reagents and template. After thermal cycling, the PCR cocktail could be pooled from multiple reactors and loaded onto a slab gel or injected into a capillary tube or microchip device for fractionation.

Electrophoresis, Capillary↗
PubMed1996

Determination of nitrite in human blood by combination of a specific sample preparation with high-performance anion-exchange chromatography and electrochemical detection.

All photometric or HPLC methods described to date have been unable to detect nitrite, a reliable marker of NO synthase activity, in human blood because of its rapid metabolism within the erythrocytes. We now elaborate on method to prevent nitrite degradation during sample preparation which in combination with high-performance anion-exchange chromatography and electrochemical detection allows a sensitive measurement of nitrite. A linear current response in the concentration range of 10-1000 nmol/l nitrite was observed yielding a correlation coefficient of 0.99. In addition, the combination of the electrochemical with a UV detector allowed us to simultaneously quantify nitrate within one analytical run, which is the end product of NO/nitrite metabolism. Basal levels for nitrate and nitrite in human blood were determined with 25 +/- 4 mumol/l and 578 +/- 116 nmol/l (n = 8), respectively and thus were in the same concentration range as expected from NO measurement in saline perfused isolated organs or cultured endothelial cells. Therefore, the presented method may be used to assess activity of endothelial constitutive NO synthase in humans under physiological and pathophysiological conditions.

Biomarkers↗
PubMed1988

Effects of different sample preparations on enumeration of large granular lymphocytes (LGLs), and demonstration of a sex difference of LGLs.

Peripheral natural killer (NK) cells were identified by their morphologic appearance as large granular lymphocytes (LGLs) in a cytocentrifuged or spun blood film but not in thin wedge blood film. The authors studied the effect of different methods of sample preparation and staining on the enumeration of peripheral human LGLs as a routine test. In the blood film made from anticoagulated venous blood, LGLs were scattered in a field and sometimes deformed by compression of erythrocytes. In a blood film made from mononuclear cells, LGLs were shrunken, rendering it difficult to always identify cytoplasmic granules. In contrast, LGLs were easily and accurately identified in a blood film made from leukocyte-rich plasma, displaying none of the above artifacts. As well, the percentage of LGLs obtained was similar to that obtained from a blood film made from anticoagulated venous blood. In addition, May-Grünwald-Giemsa (MGG) stained azurophilic granules more clearly than did Giemsa above. As a result of these observations, a blood film that was made from leukocyte-rich plasma and that was stained by MGG was considered to be most suitable for the routine enumeration of LGL. Using this method, the authors found a significant correlation between the percentages of LGLs and Leu-7+ cells in the same subjects (r = 0.71; n = 22; P less than 0.001) and also a significant sex difference in the percentages of peripheral LGLs, which were significantly lower in women (17.0 +/- 3.6%; n = 35; P less than 0.05) than in men (19.5 +/- 5.3%; n = 20). Furthermore, the percentage of LGLs with abundant cytoplasmic granules, which might have greater NK activity, was also significantly lower in women (15.9 +/- 3.1%; n = 35; P less than 0.01) than in men (17.9 +/- 4.0%; n = 20).

Adult↗
PubMed2001

Determination of Cremophor EL in plasma after sample preparation with solid phase extraction and plasma protein precipitation.

The non-ionic emulsifier Cremophor EL can be quantified using a special potentiometric titration technique with barium chloride activation and precipitation with sodium tetraphenylborate. The end point of the titration is indicated by an ionsensitive coated wire electrode which responds to an excess of tetraphenylborate ions. Sample preparation is necessary to quantify the excipient in plasma of patients receiving ciclosporin formulations with Cremophor EL (Sandimmun), since plasma proteins cause disturbances of the titration. Solid phase extraction was tested with various sorbent materials. Although some of the sorbents yielded good extraction rates of Cremophor EL from aqueous solutions, the extraction rates from plasma were significantly lower. Therefore, plasma protein precipitation with acetonitrile has been examined as an alternative to SPE and has been proved the superior method. Using the precipitation technique, a recovery rate of above 90% was achieved. Furthermore, the limit of detection from plasma was found to be 30 microg, in analogy to the determination from aqueous solutions. The combination of the plasma protein precipitation with the potentiometric titration allows quantitation and thus pharmakokinetic investigations of Cremophor EL in patients treated with Sandimmun after kidney-transplantation.

Animals↗
PubMed1996

Solvent-free sample preparation by headspace solid-phase microextraction applied to the tracing of n-butyl nitrite abuse.

The most common alkyl nitrites encountered in forensic toxicology are iso-butyl, n-butyl and iso-pentyl(amyl) nitrites. All have become popular as an aphrodisiac, especially among the homosexual population. Alkyl nitrites are a volatile and unstable group of compounds, which hydrolyse in aqueous matrices to the alcohol and nitrite ion. Here we describe a fast, clean and sensitive procedure for the detection of hydrolysed n-butyl nitrite in whole human blood using a new, solvent-free sampling technique, the headspace solid-phase micro-extraction (HSPME), combined with GC/FID analysis. Sample preparation was investigated using two different stationary phases (100 microns polydimethylsiloxane and 85 microns polyacrylate), coating a fused silica fibre. The effect of different sampling times at fixed temperatures was also studied. Our results demonstrate that the HSPME/GC/FID procedure allows tracing of n-butyl nitrite abuse and detects hydrolysed n-butyl nitrite, i.e., released n-butanol, in whole blood at the 1 ng/mL level.

Autopsy↗
PubMed1989

Solid-phase sample preparation method for prostaglandins: integration of procedures for isolation and derivatization for gas chromatographic determination.

A procedure using a solid-phase support has been developed for the isolation and derivatization of prostaglandins from biological matrices. The styrene-divinylbenzene cross-linked copolymeric macroreticular resin, XAD-2, was used as an adsorbent for prostaglandin E2 from biological samples, as a support for the oximation of the carbonyl group and as a catalyst for pentafluorobenzylation. The reactor bed was then linked to a Florisil column for a final chromatographic clean-up. Matrix effects were found to affect the yield, but recovery of the desired electrophoric products was comparable with methods reported in the literature. The ease of sample preparation suggests that this technique may be a viable approach to automating the processes for preparing prostaglandins from biological matrices for gas chromatographic analysis.

Animals↗
PubMed1984

[Determination of the concentration of a new antiarrhythmic, flecainide, in plasma using high pressure liquid chromatography (HPLC): sample preparation with extraction columns].

A method is described for the rapid determination of flecainid (Tambocor) in human plasma. Flecainid is removed from alkalized plasma by binding to a C-18 extraction column. After washing the column with methanol/water (1 + 1, by vol.) and acetonitrile/water (45 + 55, by vol.), the drug is extracted with methanol and determined by HPLC. Sample preparation takes about 15 minutes. With this method, flecainid can be determined directly in the concentration range 100-2000 micrograms/l, with an accuracy of 5-10% depending on the concentration. The results agree well with those obtained by the longer established but lengthy liquid extraction method.

Anti-Arrhythmia Agents↗
PubMed2001

A new sample preparation method for biological soft X-ray microscopy: nitrogen-based contrast and radiation tolerance properties of glycol methacrylate-embedded and sectioned tissue.

We describe the preparation of a biological tissue for imaging in a transmission soft X-ray microscope. Sections of exocrine pancreas embedded in glycol methacrylate polymer, an embedding medium widely used in visible light and electron microscopy, were examined. Contrast was based primarily on the nitrogen content of the tissue, and dual-wavelength imaging at the nitrogen K-shell absorption edge was used to map the distribution and provide quantitative densitometry of both the protein and embedding matrix components of the sample. The measurements were calibrated by obtaining the absorption spectrum of protein near the nitrogen edge. The contrast was consistent and reproducible, making possible the first large-scale X-ray microscopic study on sections of plastic-embedded soft tissue. At radiation doses of up to 10(8) Gray, much more than required for routine imaging, no distortion and little mass loss were observed. This sample preparation method should permit routine imaging of tissues in X-ray microscopes, previously a difficult task, as well as multimodal imaging (using visible light, X-ray, electron, and scanned probe microscopies) on the same sample.

Animals↗
PubMed2003

Rapid diagnosis of extrapulmonary tuberculosis by PCR: impact of sample preparation and DNA extraction.

In cases of suspected extrapulmonary tuberculosis, rapid and accurate laboratory diagnosis is of prime importance, since traditional techniques of detecting acid-fast bacilli have limitations. The major difficulty with mycobacteria is achieving optimal cell lysis. Buffers used in commercial kits do not allow this complete lysis in a number of clinical specimens. A comparison of two sample preparation methods, pretreatment with proteinase K (PK-Roche) and complete DNA purification (cetyltrimethylammonium bromide [CTAB]-Roche), was conducted on 144 extrapulmonary specimens collected from 120 patients to evaluate the impact on the Cobas-Amplicor method. Thirty patients were diagnosed with tuberculosis, with 15 patients culture positive for Mycobacterium tuberculosis. Amplification and detection of the amplicons were impaired by a high number of inhibitory specimens (39 to 52%). CTAB-Roche allowed the detection of more culture-positive specimens by PCR than PK-Roche. Comparison with the final diagnoses of tuberculosis confirmed that CTAB-Roche produced the best sensitivity (53.8%) compared to culture (43.3%), PK-Roche (16%), and smear (13%). However, the specificity of the PCR assay with CTAB-Roche-extracted material was always lower (78.8%) than those with culture (100%) and PK-Roche (96.5%). False-positive specimens were lung biopsy material, lymph node biopsy material and aspirate, or bone marrow aspirate, mainly from immunocompromised patients. Despite the efficiency of complete DNA extraction for the rapid diagnosis by PCR of extrapulmonary tuberculosis, the false-positive results challenge our understanding of PCR results.

Abscess↗
PubMed2003

Sample preparation effects in matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry of partially depolymerised methyl cellulose.

Methyl cellulose (MC) was partially depolymerised and the oligomers thus obtained were studied by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS). The depolymerisation was either enzymatic or acidic. Fractions of enzymatically depolymerised MC were collected from size-exclusion chromatography and subjected to a sample preparation investigation. Several MALDI matrices and solvents were evaluated. The results showed that the solvent choice had a significant effect on the measured degree of substitution (DS). Aprotic solvents produced higher DS values, which was most likely due to poor solubility of species with low DS. The obtained signal intensity, however, did not correlate with the solubility but seemed to be more dependent on certain matrix/solvent combinations. All the matrices attempted produced mass spectra with sufficient signal intensity for accurate peak area calculation. The choice of matrix did not have any significant effect on the measured DS. Sample spots obtained from organic solvents had a more homogeneous distribution of the analyte and smaller crystals than those obtained from water. This increased both the reproducibility and peak resolution and in addition the analysis time was shorter. DS measurements were performed on two acidically depolymerised MCs with different nominal DS values. It was easy to distinguish between the two MCs, and the measured DS values agreed well with the values supplied by the manufacturers.

Biopolymers↗
PubMed1999

Natural Products in High Throughput Screening: Automated High-Quality Sample Preparation.

At present, compound libraries from combinatorial chemistry are the major source for high throughput screening (HTS) programs in drug discovery. On the other hand, nature has been proven to be an outstanding source for new and innovative drugs. Secondary metabolites from plants, animals, and microorganisms show a striking structural diversity that supplements chemically synthesized compounds or libraries in drug discovery programs. Unfortunately, extracts from natural sources are usually complex mixtures of compounds, often generated in time-consuming and, for the most part, manual processes. Because quality and quantity of the provided samples play a pivotal role in the success of HTS programs, this poses serious problems. In order to make samples of natural origin competitive with synthetic compound libraries, we devised a novel, automated sample preparation procedure based on solid-phase extraction (SPE). By making use of modified Zymark (Hopkinton, MA) RapidTrace® SPE workstations, we developed an easy-to-handle and effective fractionation method that generates high-quality samples from natural origin, fulfilling the requirements for an integration in high throughput drug discovery programs.

Journal Article↗
PubMed2007

Characteristics of the m2000 automated sample preparation and multiplex real-time PCR system for detection of Chlamydia trachomatis and Neisseria gonorrhoeae.

We evaluated a new real-time PCR-based prototype assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae developed by Abbott Molecular Inc. This assay is designed to be performed on an Abbott m2000 real-time instrument system, which consists of an m2000sp instrument for sample preparation and an m2000rt instrument for real-time PCR amplification and detection. The limit of detection of this prototype assay was determined to be 20 copies of target DNA for both C. trachomatis and N. gonorrhoeae, using serially diluted linearized plasmids. No cross-reactivity could be detected when 55 nongonococcal Neisseria isolates and 3 non-C. trachomatis Chlamydia isolates were tested at 1 million genome equivalents per reaction. Concordance with the Roche Amplicor, BDProbeTec ET, and Gen-Probe APTIMA Combo 2 tests was assessed using unlinked/deidentified surplus clinical specimens previously analyzed with these tests. For C. trachomatis, concordance for positive results ranged from 93.7% to 100%, while concordance for negative results ranged from 98.2% to 100%. For N. gonorrhoeae, concordance for positive and negative results ranged from 91.4% to 100% and 99.3% to 100%, respectively. A workflow analysis of the prototype assay was conducted to obtain information on throughput under laboratory conditions. At 48 samples/run, the time to first result for both C. trachomatis and N. gonorrhoeae was 4.5 h. A total of 135 patient specimens could be analyzed in 8.9 h, with 75 min of hands-on time. This study demonstrated the technical and clinical feasibility of the new Abbott real-time PCR C. trachomatis/N. gonorrhoeae assay.

Automation↗