Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “sample preparation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,243 records · Page 69Linked to original sources
PubMed1992

Matrix-assisted laser desorption/ionization mass spectrometry of nucleic acids with wavelengths in the ultraviolet and infrared.

A number of different matrices have been tested and compared for ultraviolet and infrared (UV and IR) matrix-assisted laser desorption/ionization (MALDI) of oligodeoxyribonucleotides and mixtures thereof, as well as ribonucleic acids (tRNA from yeast and rRNA from E. coli). A new technique for removing alkali cations from nucleic acid samples during sample preparation on the sample support is demonstrated. The amount of oligonucleotide sample consumed during a typical measurement in IR-MALDI-MS was determined.

Angiotensin II↗
PubMed2002

A rapid and sensitive liquid chromatography/negative ion tandem mass spectrometry method for the determination of an indolocarbazole in human plasma using 96-well diatomaceous earth plates for solid-liquid extraction [correction of using internal standard (IS) 96-well diatomaceous earth plates for solid-liquid extraction].

A sensitive liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for the quantitation of a novel topoisomerase I inhibitor (indolocarbazole derivative I) in human plasma was developed to support clinical studies. Drug and internal standard were isolated from plasma by solid-liquid extraction using 96-well diatomaceous earth plates. Various extraction solvents were evaluated for extraction of I and 9% isopropyl alcohol (IPA) in methyl-tert-butyl ether (MtBE) was chosen as the optimal extraction solvent. The sensitivity of this LC/MS/MS method is 10x higher in negative ion mode using alkaline conditions than in positive ion mode using a wide range of pH's. A mobile phase with 2 mM ammonium hydroxide enhanced the sensitivity in negative ion mode over other volatile bases. The calibration curve for compound I is linear over the range 0.05-200 ng/mL in plasma and the lower limit of quantification (LLOQ) of the assay is 0.05 ng/mL, when 0.25 mL of plasma is processed. The method was fully validated and successfully applied to plasma samples from clinical studies. Performing chromatography at high pH, for enhanced negative ion sensitivity, eliminates the need for post-column addition of base. Furthermore, the 96-well diatomaceous earth plate extraction offers the following advantages over liquid-liquid extraction (LLE) or solid-phase extraction (SPE): clean sample extracts with reduced sample preparation time; increased sample throughput; no conditioning or washing steps; and a neutral eluate applicable to acid/base labile compounds.

Carbazoles↗
PubMed2002

Ink-bottle effect in mercury intrusion porosimetry of cement-based materials.

Mercury intrusion porosimetry (MIP) is a widely used method for studying porous materials, in particular, cement-based materials. The usual interpretation of such measurements is based on certain assumptions. One of these is that each pore is connected to the sample surface directly or through larger pores. Pores not meeting this assumption are called ink-bottle pores. The effect that sample size has on the MIP characteristics of concrete samples, like the ink-bottle effect and hysteresis, was studied by measuring additional extrusion and intrusion cycles. In order to characterize the extrusion and ink-bottle behavior, the amount of entrapped mercury chi(p) was estimated. Superimposition of extrusion and second intrusion curves is achieved if the contact angle theta is adjusted from theta(i), the intrusion contact angle, to theta(e), the extrusion contact angle. The threshold radius is often assumed to be a dominant pore radius, yet in this study the entrapped mercury content shows no evidence for the presence of a dominant pore radius. Even if characteristic properties of cement-based materials can be estimated with MIP, comparison of results is rendered difficult by the significant effects of sample preparation techniques and sample size and the ink-bottle effect due to randomly present air bubbles.

Journal Article↗
PubMed1998

The effects of cryoprotection on the structure and activity of p21 ras: implications for electron spin-echo envelope modulation spectroscopy.

Electron spin-echo envelope modulation (ESEEM) spectroscopy is widely used to investigate the active sites of biological molecules in frozen solutions. Various cryoprotection techniques, particularly the addition of co-solvents, are commonly employed in the preparation of such samples. In conjunction with ESEEM studies of Mn(II) guanosine nucleotide complexes of p21 ras, we have investigated the effects of cryoprotection on the spectroscopy, the structure, and the activity of this protein. Echo decay times, which typically govern ESEEM spectral resolution, were found to vary linearly with the concentration of glycerol or methyl alpha-D-glucopyranoside (MG), with both additives equally effective on a per-mole basis. The effect of glycerol and MG on the ESEEM amplitudes of various protein nucleiwas studied in ras p21.Mn(II). 5'guanylylimido-diphosphate(p21.Mn(II)-GMPPNP) complexes: these additives did not alter the distances of these nuclei from the Mn(II) ion. In particular, in p21 incorporating [2H-3]Thr, the Mn(II)-[2H-3]Thr35 distance was found to be unaffected by the concentration of cryoprotectant or the rate of freezing. The proximity of the cryoprotectants to the Mn(II) ion was probed by 2H ESEEM in solutions made with d5-glycerol and d7-methyl alpha-D-glucopyranoside (d7-MG). In p21.Mn(II)GMPPNP, the large deuterium modulations from the d5-glycerol exhibit saturation behavior with increasing d5-glycerol concentration, implying that glycerol, a widely used cryoprotectant, replaces the aquo ligands of the Mn(II) ion. The interaction between the Mn(II) ion of p21 and MG, however, is less intimate: the deuterium ESEEM amplitudes are much smaller for samples prepared with d7-MG than with d5-glycerol. Several polyhydroxylic compounds were found to have essentially no effect on the ability of the guanosine 5'-triphosphate (GTP) hydrolysis activating protein, GAP334, to catalyze hydrolysis of p21. guanosine 5'-triphosphate. This observation implies that the introduction of cryoprotectant does not significantly perturb the structure of p21 and gives insight into the mechanism of the GTPase reaction.

Cryoprotective Agents↗
PubMed1986

[A rapid computer-assisted method for the determination of urea in dairy products: skim milk powder from various sources].

The enzymatic determination of urea in spray-dried skim milk powders was transferred to a computer aided photometric analysing system. Sample preparation is optimal using ultrafiltration, but the direct use of a milk sample is also possible with this system. The precision including sample preparation as coefficient of variation was about 0.69%, the standard deviation of the assay was 0.115-0.135 at an average content of 5.4-5.5 mg urea per 100 ml skim milk. The method was tested on 147 spray-dried skim milk powders, which were of varying origin and collected at different times of the year (Jan.-Oct.). In this way a representative survey for the urea content of a great number of skim milk powders was possible. It was also shown, that the urea content is highly affected by season. It is very constant from February to May (0.25-0.26%), and rises from June to October up to nearly 0.32%.

Animals↗
PubMed2004

Development of a method to detect and quantify Aspergillus fumigatus conidia by quantitative PCR for environmental air samples.

Exposure to Aspergillus fumigatus is linked with respiratory diseases such as asthma, invasive aspergillosis, hypersensitivity pneumonitis, and allergic bronchopulmonary aspergillosis. Molecular methods using quantitative PCR (qPCR) offer advantages over culture and optical methods for estimating human exposures to microbiological agents such as fungi. We describe an assay that uses lyticase to digest A. fumigatus conidia followed by TaqMan qPCR to quantify released DNA. This method will allow analysis of airborne A. fumigatus samples collected over extended time periods and provide a more representative assessment of chronic exposure. The method was optimized for environmental samples and incorporates: single tube sample preparation to reduce sample loss, maintain simplicity, and avoid contamination; hot start amplification to reduce non-specific primer/probe annealing; and uracil-N-glycosylase to prevent carryover contamination. An A. fumigatus internal standard was developed and used to detect PCR inhibitors potentially found in air samples. The assay detected fewer than 10 A. fumigatus conidia per qPCR reaction and quantified conidia over a 4-log10 range with high linearity (R2 >0.99) and low variability among replicate standards (CV=2.0%) in less than 4 h. The sensitivity and linearity of qPCR for conidia deposited on filters was equivalent to conidia calibration standards. A. fumigatus DNA from 8 isolates was consistently quantified using this method, while non-specific DNA from 14 common environmental fungi, including 6 other Aspergillus species, was not detected. This method provides a means of analyzing long term air samples collected on filters which may enable investigators to correlate airborne environmental A. fumigatus conidia concentrations with adverse health effects.

Air↗
PubMedDate not supplied

An alternative procedure for ESR identification of irradiated chicken drumsticks.

The ESR spectroscopy is, at present, the most established technique for quantitative analysis of irradiated chicken bone using the additive dose method. In this paper we tried a different approach to the problem analyzing the ESR behavior of a batch of chicken bone samples coming randomly from the market. Using a suitable and standardized sample preparation technique and sample positioning in the microwave cavity, we obtained a coefficient of variation of about 30% for the batch response. The calibration curve, obtained using the batch behavior up to 10 kGy, was used for a quantitative test on unknown samples.

Animals↗
PubMed2006

Merging microfluidics with microarray-based bioassays.

Microarray technologies provide powerful tools for biomedical researchers and medicine, since arrays can be configured to monitor the presence of molecular signatures in a highly parallel fashion and can be configured to search either for nucleic acids (DNA microarrays) or proteins (antibody-based microarrays) as well as different types of cells. Microfluidics on the other hand, provides the ability to analyze small volumes (micro-, nano- or even pico-liters) of sample and minimize costly reagent consumption as well as automate sample preparation and reduce sample processing time. The marriage of microarray technologies with the emerging field of microfluidics provides a number of advantages such as, reduction in reagent cost, reductions in hybridization assay times, high-throughput sample processing, and integration and automation capabilities of the front-end sample processing steps. However, this potential marriage is also fraught with some challenges as well, such as developing low-cost manufacturing methods of the fluidic chips, providing good interfaces to the macro-world, minimizing non-specific analyte/wall interactions due to the high surface-to-volume ratio associated with microfluidics, the development of materials that accommodate the optical readout phases of the assay and complete integration of peripheral components (optical and electrical) to the microfluidic to produce autonomous systems appropriate for point-of-care testing. In this review, we provide an overview and recent advances on the coupling of DNA, protein and cell microarrays to microfluidics and discuss potential improvements required for the implementation of these technologies into biomedical and clinical applications.

Biological Assay↗
PubMed2004

Enrichment of proteinaceous materials on a strong cation-exchange diol silica restricted access material: protein-protein displacement and interaction effects.

A study of size exclusion and enrichment of proteins employing strong cation-exchange diol silica restricted access material (SCX-RAM) under saturation conditions is presented. Experiments were carried out with bacitracin, protamine, ribonuclease, lysozyme and bovine serum albumin as individual proteinaceous analytes as well as comprehensive binary mixtures and with human urine samples. Protein size dependent capacity features of the SCX-RAM column was observed. Bacitracin demonstrated the highest capacity followed by protamine while adsorption capacities of both ribonuclease and lysozyme were found smaller by a factor of 10. Applying binary protein samples occurring displacement effects were apparent: proteins with strong cationic properties displaced those already adsorbed by the bonded cation-exchange ligands. Bacitracin was displaced in all binary mixture experiments in particular by protamine. Furthermore, the binary mixtures displayed increased adsorption for some proteins due to complex formation. Lysozyme and ribonuclease showed double capacity values when paired with bacitracin. Both phenomena, displacement and enhanced adsorption occurred in the saturated state and led to changes in the urine composition during sample preparation. Injecting urine samples the relative proportions of fractions changed from 4 up to more than 20 times, due to the differences of the protein adsorption capacities on the SCX-RAM column. Analysing urine samples the SCX-RAM column provided extensive long-term stability.

Cation Exchange Resins↗
PubMed2003

Size-exclusion flow extraction of bisphenol A in human urine for liquid chromatography-mass spectrometry.

We report an approach for assessing human exposure to bisphenol A (BPA), which involves measuring the glucuronide in urine sample that were subjected to a novel size-exclusion flow extraction method. The present approach includes the addition of 13C(12)-BPA, enzymatic deconjugation, and the proposed sample preparation method. The sample solution is separated and detected by liquid chromatography-mass spectrometry (LC-MS). The following are used for the LC-MS: a reversed-phase separation column, electrospray ionization (ESI), negative mode, and single ion monitoring (SIM) with m/z 227 for BPA and m/z 239 for 13C(12)-BPA. The detection limit was 0.1 ng ml(-1) and the calibration curves (0.45-90 ng ml(-1)) had correlation coefficients exceeding 0.999. To urine samples requiring deglucuronidation, beta-glucuronidase was added followed by incubation at 37 degrees C for 3 h. After the enzymatic treatment, the samples were subjected to the extraction in the reversed-phase (ODS) and size-exclusion (GPC) modes. It was possible to extract, clean up and concentrate BPA in a single run of 20 min by means of the novel extraction method. The method enables the determination of standards and may be applied to the detection of trace amounts of BPA in human urine samples.

Adult↗
PubMed2004

Determination of heterocyclic aromatic amines in beef extract, cooked meat and rat urine by liquid chromatography with coulometric electrode array detection.

This paper describes a method for the determination of heterocyclic aromatic amines (HAs; DMIP, IQ, MeIQ, MeIQx, 4,8-DiMeIQx, 7,8-DiMeIQx, AalphaC, PhIP) by high-performance liquid chromatography (HPLC) with coulometric electrode array detection. The compounds are separated on reversed phase columns (LiChroCart Superspher 60 RP-select B, 250 mm x 2 mm, 4 microm and LiChrospher 60 RP-select B, 250 mm x 4 mm, 5 microm) using mobile phases consisting of acetonitrile/buffer/distilled water and detected at eight working electrodes at potentials between +190 and +680 mV against modified palladium electrodes. In the context of an EU-interlaboratory exercise, the method was applied to analyse a standardised test solution and--after isolation of the analytes by several clean-up steps--for the analysis of standardised beef extract and grilled meat. Further, the method could be applied for the analysis of HAs in suspensions of bacteria and rat urine without any sample preparation step beyond sample dilution. The data obtained show that HPLC with coulometric electrode array detection gives accurate results.

Amines↗
PubMed2006

On-line sample extraction and enrichment of non-steroidal anti-inflammatory drugs by pre-column in capillary liquid chromatography mass spectrometry.

A rapid and sensitive analytical method has been developed for the simultaneous determination of 16 non-steroidal anti-inflammatory drugs (NSAIDs) in human plasma by capillary liquid chromatography (LC) and quadrupole mass spectrometry with electrospray ionization operated in the negative ion mode. The sample clean-up and enrichment on a pre-column were accomplished on-line to improve the sensitivity. This method greatly reduced sample preparation time and sample volume compared with off-line sample extraction methods and conventional LC methods, respectively. The recoveries of NSAIDs from human plasma were 56.7-96.9%. The total analytical time for a single analytical run was approximately 15 min. The detection limits of NSAIDs were 0.001-0.075 microg ml(-1) using a selected ion monitoring mode.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed2005

Simultaneous determination of Z-3-[(2,4-dimethylpyrrol-5-yl)methylidenyl]-2-indolinone (SU5416) and its interconvertible geometric isomer (SU5886) in rat plasma by LC/MS/MS.

Z-3-[(2,4-Dimethylpyrrol-5-yl)methylidenyl]-2-indolinone (SU5416) is a cytostatic substance in development as an anti-angiogenic agent. SU5416 exists as the thermodynamically stable cis or Z-isomer as a solid. Studies have shown that in light exposed solutions of SU5416, the unstable trans or E-isomer, namely SU5886, is formed. The E-isomer converts back to the Z-isomer when protected from light. The E-isomer is unstable for synthesis and isolation; therefore, the analytical standard of the E-isomer is not available. In this study, a simple, fast and reliable LC/MS/MS method has been developed to determinate both isomers simultaneously in rat plasma samples to support the study of disposition kinetics of SU5416. This method is sensitive (limit of quantitation (LOQ=0.5 ng/mL)), reproducible and has a wide linear range (0.5-2500 ng/mL). There was no conversion between E- and Z-isomer during sample preparation procedure and sample determination with LC/MS/MS. Experimental results proved that SU5416 and SU5886 have identical detection response. Therefore, SU5416 (Z-isomer) was used successfully as analytical standard for SU5886 (E-isomer). This method has been applied to rat plasma samples obtained from a pharmacokinetic study. This study underscores the use of LC/MS/MS technique for bioanalytical methods where analytical standards are not available and analytes are interconvertible.

Angiogenesis Inhibitors↗
PubMed2024

Universal Identification of Pathogenic Viruses by Liquid Chromatography Coupled with Tandem Mass Spectrometry Proteotyping.

Accurate and rapid identification of viruses is crucial for an effective medical diagnosis when dealing with infections. Conventional methods, including DNA amplification techniques or lateral-flow assays, are constrained to a specific set of targets to search for. In this study, we introduce a novel tandem mass spectrometry proteotyping-based method that offers a universal approach for the identification of pathogenic viruses and other components, eliminating the need for a priori knowledge of the sample composition. Our protocol relies on a time and cost-efficient peptide sample preparation, followed by an analysis with liquid chromatography coupled to high-resolution tandem mass spectrometry. As a proof of concept, we first assessed our method on publicly available shotgun proteomics datasets obtained from virus preparations and fecal samples of infected individuals. Successful virus identification was achieved with 53 public datasets, spanning 23 distinct viral species. Furthermore, we illustrated the method's capability to discriminate closely related viruses within the same sample, using alphaviruses as an example. The clinical applicability of our method was demonstrated by the accurate detection of the vaccinia virus in spiked saliva, a matrix of paramount clinical significance due to its non-invasive and easily obtainable nature. This innovative approach represents a significant advancement in pathogen detection and paves the way for enhanced diagnostic capabilities.

Tandem Mass Spectrometry↗
PubMed1993

Light scattering analysis of fibril growth from the amino-terminal fragment beta(1-28) of beta-amyloid peptide.

beta-Amyloid protein (beta-A/4) is the major protein component of Alzheimer disease-related senile plaques and has been postulated to be a significant contributing factor in the onset and/or progression of the disease. In the senile plaque, beta-A/4 appears as bundles of amyloid fibrils. The biological activity of beta-A/4 may be related to its state of aggregation. In this work, self-assembly, fibril formation, and interfibrillary aggregation of beta(1-28), a synthetic peptide homologous with the amino-terminal fragment of beta-A/4, were investigated. The predominant form of beta(1-28) detected by size-exclusion chromatography and polyacrylamide gel electrophoresis was apparently a tetramer which does not bind Congo red. Aggregates containing cross-beta sheet structures which bind Congo red and thioflavin T were observed at concentrations of approximately 0.3 mg/ml or greater. Concentrations of 0.5-1 mg/ml were necessary for aggregation into fibrils to be detectable by classical or quasielastic light scattering. Both fibril elongation and fibril-fibril aggregation occur over the time scale investigated. The kinetics of aggregation were much faster at physiological salt concentrations than at lower ionic strength. Ionic strength also appeared to influence the morphology of the fibril aggregates. The data indicate that sample preparation method and sample history influence fibril size and number density.

Amino Acid Sequence↗
PubMed1987

Improvement of chemical analysis of antibiotics. X. Determination of eight tetracyclines using thin-layer and high-performance liquid chromatography.

Analytical methods for eight tetracyclines (TCs) were established using silica gel high-performance thin-layer chromatography (HPTLC), reversed-phase thin-layer chromatography (RP-TLC) and high-performance liquid chromatography (HPLC). Good separations of eight TCs were obtained using chloroform-methanol-5% disodium ethylenediaminetetraacetate solution (65:20:5) (lower layer) and methanol acetonitrile 0.5 M oxalic acid solution (1:1:4) (pH 3.0) on silica gel HPTLC and C8 TLC plates, respectively. A combination of HPTLC and RP-TLC made possible the identification of the eight TCs. Each calibration graph was linear between 0.1 and 1.0 microgram using UV densitometry except for rolitetracycline. For detection reagents, the diazonium salts including Fast Violet B gave variously coloured spots with the eight TCs and good sensitivities were obtained except with minocycline. In HPLC, the simultaneous analysis of the eight TCs on a C8 column was possible using methanol-acetonitrile-0.01 M oxalic acid solution (1:1.5:7) adjusted to pH 3.0 as the mobile phase. A linear relationship was obtained between 1.0 and 10 ng using the usual sample preparation except for rolitetracycline. The direct determination of rolitetracycline was possible using tetrahydrofuran, dimethyl sulphoxide and the mobile phase as solvents for preparation of the sample. For the determination of residual rolitetracycline, it was effective to measure the amount of rolitetracycline as tetracycline by HPLC, HPTLC and RP-TLC after conversion of rolitetracycline to tetracycline by incubating for 5 min in methanol at 50 degrees C.

Anti-Bacterial Agents↗
PubMed2005

Separation of liposome-entrapped mitoxantrone from nonliposomal mitoxantrone in plasma: pharmacokinetics in mice.

A method is described for quantification of the liposomal and nonliposomal forms of mitoxantrone (MTO) in mouse plasma after intravenous administration of liposome-entrapped MTO Easy-to-Use (LEM-ETU) formulation. This is based on the property of liposome-entrapped MTO (LEM) to pass through reversed-phase C(18) silica gel cartridges, while nonliposomal MTO or free MTO is retained with strong hydrophobicity and later is eluted with acidic methanol. Extraction of LEM and free MTO from plasma is performed in two steps. This technique is rapid and sensitive and can be used for a large series of sample preparation. The plasma samples are found stable after one freeze-thaw cycle. The recovery of MTO, as well as the precision, linearity, and accuracy of the method for both free and liposomal MTO, appears satisfactory for pharmacokinetic studies. The pharmacokinetic results in mice show a sustained release of MTO from LEM-ETU.

Animals↗
PubMed2006

Expression profiling of glycosyltransferases and related enzymes using gene microarrays.

Gene expression analysis has become a standard tool for studies of biological models of disease processes, growth, and development and has been used increasingly in the field of clinical research. The completion of the human genome sequence is now providing the glycomics research community with the tools to develop a synergism with related fields such as MS glycan profiling and proteomics. The use of microarray technology to measure changes in gene expression is a useful approach for the study of the expression profiles of glycosyltransferases, carbohydrate binding proteins, and related enzymes. The availability of standardized microarray platforms, high-quality reagents for sample preparation and hybridization, and image and statistical analysis tools has contributed to recent advances in the application of this technology to glycobiology. Most microarray experiments today are done within specialized core facilities equipped with instrumentation, software, and personnel with expertise in their application. The focus of this chapter is on aspects of microarray analysis common to all platforms and within the realm of the glycobiologist: consideration of experimental design issues and methods for the preparation of RNA samples from a variety of tissue sources suitable for microarray analysis.

Animals↗