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PubMedDate not supplied

Intact-protein based sample preparation strategies for proteome analysis in combination with mass spectrometry.

The complexity of tissue and cell proteomes and the vast dynamic range of protein abundance present a formidable challenge for analysis that no one analytical technique can overcome. As a result, there is a need to integrate technologies to achieve the high-resolution and high-sensitivity analysis of complex biological samples. The combined technologies of separation science and biological mass spectrometry (Bio-MS) are the current workhorse in proteomics, and are continuing to evolve to meet the needs for high sensitivity and high throughput. They are relied upon for protein quantification, identification, and analysis of post-translational modifications (PTMs). The standard technique of two dimensional poly-acrylamide gel electrophoresis (2D PAGE) offers relatively limited resolution and sensitivity for the simultaneous analysis of all cellular proteins, with only the most highly abundant proteins detectable in whole cell or tissue-derived samples. Hence, many alternative strategies are being explored. Numerous sample preparation procedures are currently available to reduce sample complexity and to increase the detectability of low-abundance proteins. Maintaining proteins intact during sample preparation has important advantages compared with strategies that digest proteins at an early step. These strategies include the ability to quantitate and recover proteins, and the assessment of PTMs. A review of current intact protein-based strategies for protein sample preparation prior to mass spectrometry (MS) is presented in the context of biomedically driven applications.

Animals↗
PubMed2001

Two-layer sample preparation method for MALDI mass spectrometric analysis of protein and peptide samples containing sodium dodecyl sulfate.

Sodium dodecyl sulfate (SDS) is widely used in protein sample workup. However, many mass spectrometric methods cannot tolerate the presence of this strong surfactant in a protein sample. We present a practical and robust technique based on a two-layer matrix/sample deposition method for the analysis of protein and peptide samples containing SDS by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The two-layer method involves the deposition of a mixture of sample and matrix on top of a thin layer of matrix crystals. It was found that for SDS-containing samples, the intensity of the MALDI signals can be affected by the conditions of sample preparation: on-probe washing, choice of matrix, deposition method, solvent system, and protein-to-SDS ratio. However, we found that, under appropriate conditions, the two-layer method gave reliable MALDI signals for samples with levels of SDS up to approximately 1%. The applications of this method are demonstrated for MALDI analysis of hydrophobic membrane proteins as well as bacterial extracts. We envision that this two-layer method capable of handling impure samples including those containing SDS will play an important role in protein molecular weight analysis as well as in proteome identification by MALDI-MS and MS/MS.

Bacterial Proteins↗
PubMed2001

Inert sampling and sample preparation--the influence of oxygen on heavy metal mobility in river sediments.

Two approaches have been used to investigate changes in the nature of metal binding in river sediments caused by atmospheric oxygen. Firstly, non-inert and inert sample preparation were applied, in combination with sequential extraction, to determine for which metals inert sample preparation is necessary for correct determination of metal mobility under environmental conditions. Secondly, the metal contents of sediments sampled before and after a river weir were fractionated by sequential extraction to study the effect of the oxygen impact at the weir on heavy metal mobility in the sediments. Different grain-size fractions from one sample were also extracted, to enable selection of the upper grain-size limit most suitable for answering this analytical question. The results showed the need for the inert sample preparation technique for Cd, Zn, Pb, Mn, and Fe, but not for Co, Ni, Cu, and Cr. No significant change of heavy metal mobility at the weir could be proved, although the mobilization behavior of some elements was different. The optimum upper grain-size limit was 63 microm.

Gas Chromatography-Mass Spectrometry↗
PubMed2004

Exploring the importance of the relative solubility of matrix and analyte in MALDI sample preparation using HPLC.

New insight into the role of solubility in the sample preparation process for MALDI MS is reported. Reversed-phase gradient HPLC conditions were developed that enable the analysis of a broad range of analyte polarities with a single method. This HPLC method was used to establish a relative polarity scale for a series of 15 MALDI matrix materials, a set of example peptides, and a series of model polymer materials with a broad range of polarity. Examples of each polymer type within the range of 6000-10,000 were analyzed with six matrixes that cover a broad range of polarity using MALDI TOFMS. With regard to polymer signal-to-noise ratio, the matrix and polymer combinations that had a close match of HPLC retention time produced the best MALDI spectra. Conversely, the matrix and polymer combinations that have a large difference in HPLC retention time produced poor MALDI spectra. The results suggest that there is a relationship between polarity (solubility) and effective MALDI sample preparation. The relative HPLC retention time of an unknown polymer can serve as a starting point for predicting the matrix (or range of matrixes) that would be most effective.

Chromatography, High Pressure Liquid↗
PubMed2001

The concept of high angle wedge polishing and thickness monitoring in TEM sample preparation.

The concept of high angle wedge polishing for TEM non-metal sample preparation is introduced for the first time. Also, introduced is the concept of converting lateral distance measurement into vertical thickness measurement in monitoring TEM sample thickness. Based on the Tripod polisher, Quadripod was constructed using these two concepts. Fast and reliable TEM sample preparation (mechanical polishing down to electron transparency) can be achieved using the Quadripod. In addition, Quadripod offers the ability of locating a specific area of interest.

Journal Article↗
PubMed2006

Sample preparation and RPHPLC determination of diuretics in human body fluids.

This article describes reverse phase high-performance liquid chromatography (RPHPLC) methods for determination of diuretics in different human body fluids (whole blood, plasma, serum or urine). Sample preparation procedures, including solid-phase extraction, liquid-liquid extraction, dilution, precipitation as well as automated RPHPLC procedures, are discussed in order to present the advantages and disadvantages of each type of sample preparation. Also, values of analytical recovery of each procedure used for sample preparation are summarized. The most important RPHPLC parameters (detection mode, stationary phase, mobile phase, sensitivity, etc.) are also summarized and discussed.

Carbonic Anhydrase Inhibitors↗
PubMed2001

Fast sample preparation for analysis of tablets and capsules: the ball-mill extraction method.

A new ball-mill extraction method for solid dosage forms was developed. It was used for tablets, and compared with a conventional (powdering and sonication) method applied in pharmaceutical analysis of solid dosage forms. The ball-mill sample preparation procedure is both quantitative and fast. No powdering, weighing and sonication steps are needed in the sample preparation. The complete procedure takes 2 min (milling and extraction) and 5 min (centrifugation), respectively, much less than the conventional method in which sample preparation takes approximately 45-90 min. The samples are centrifuged in the mill vial, which saves time and avoids evaporation of solvent. Stainless steel extraction vials with different diameters were fabricated to enable the use of various extraction volumes. The extraction recovery was tested using various types of tablets (small, large and extended release tablets) with active compounds at low and higher concentrations, recoveries were comparable with the conventional method. The relative small investment and simplicity of the method makes it excellently suited for use in various pharmaceutical (development and quality assurance) laboratories.

Capsules↗
PubMed2000

New sample preparation method for the capillary electrophoretic determination of adenylate energy charge in human erythrocytes.

The first step in the separation of adenine nucleotides from different types of tissues or cells is deproteinization. Several sample preparation methods successfully used for a number of tissues or cells failed to work with erythrocytes. Use of strong acids or bases for deproteinization resulted in a low yield due to the hydrolysis of adenine nucleotides. Moreover, the neutralization of these acids or bases increased the ionic strength, resulting in broad and overlapping peaks. In neutral salt precipitation methods, saturated salts caused clogging of the capillaries. A new deproteinization procedure method was developed. The samples were deproteinized by heating of erythrocytes in boiling distilled water at 95 degrees C for 5 min. The denatured proteins were removed by centrifugation and membrane filtration. The adenine nucleotides were then separated using a polyacrylamide coated capillary. Depending on the type, diameter, length of the capillary and the voltage applied, an average of 16.50 min was sufficient for the separation of adenine nucleotides. All adenine nucleotides were clearly resolved and gave very sharp peaks. The amount of each adenine nucleotide was calculated from the areas under the peaks and AEC values were calculated using the integrator software. The AEC value of 0.91+/-0.04 (n=10) obtained for healthy persons was in good agreement with the literature value of 0.85-0.95. These reported method for sample preparation and capillary electrophoresis is simple, fast and inexpensive compared to the previously reported sample preparation, HPLC and enzymatic methods for the determination of AEC.

Adenine Nucleotides↗
PubMed2002

Ammonium dodecyl sulfate as an alternative to sodium dodecyl sulfate for protein sample preparation with improved performance in MALDI mass spectrometry.

Sodium dodecyl sulfate (SDS) is a strong surfactant that is widely used in protein sample preparation. While protein and peptide samples containing up to approximately 1% SDS can be analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) using a two-layer matrix/sample deposition method, the presence of SDS in a protein sample generally degrades mass resolution and mass measurement accuracy. This degradation in performance is found to be related to the formation of sodium-protein adducts in the MALDI process. If the instrument resolving power is insufficient to separate these adduct peaks from the protonated molecular ion peak, peak broadening is observed in the protein molecular ion region, and as a result, the peak centroid shifts to a higher mass. In this work, we present a method using ammonium dodecyl sulfate as a viable alternative to SDS for protein sample preparation with much improved MALDI MS performance. Three non-sodium-based dodecyl sulfate surfactants, ammonium dodecyl sulfate (ADS), hydrogen dodecyl sulfate, and tris(hydroxymethyl)aminomethane dodecyl sulfate were investigated. Of the three surfactants tested, it is found that ADS gives the best performance in MALDI. For proteins with moderate molecular masses (i.e., up to approximately 25 kDa), the presence of ADS in a protein sample does not result in significant degradation in mass resolution and accuracy, and the protonated molecular ion peak is the dominant peak in the MALDI spectrum. The ammonium adduct ions dominate the MALDI spectra when the protein mass exceeds approximately 25 kDa; however, ADS still gives better results than SDS. The behavior of ADS in gel electrophoresis was also investigated. It is shown that cell extracts dissolved in ADS can be separated by normal SDS-polyacrylamide gel electrophoresis by simply mixing them with the SDS sample buffer. The application of ADS as the surfactant for protein solubilization with improved performance in MALDI analysis is demonstrated in the study of a detergent insoluble fraction from a Raji/CD9 B-cell lymphocyte lysate.

B-Lymphocytes↗
PubMed2004

Rapid quantification of Yersinia enterocolitica in pork samples by a novel sample preparation method, flotation, prior to real-time PCR.

The development of real-time PCR thermal cycles in the late 1990s has opened up the possibility of accurate quantification of microorganisms in clinical, environmental, and food samples. However, a lack of suitable sample preparation methods that allow rapid quantification of the nucleic acids, remove PCR inhibitors, and prevent false-positive results due to DNA originating from dead cells has limited the use of quantitative PCR. We have used for the first time a new variant of density gradient centrifugation, called flotation, as a user-friendly sample preparation method prior to PCR. This paper describes the use of this sample preparation method, without DNA purification, for direct detection and quantification of Yersinia enterocolitica in PCR-inhibitory meat juice from pork. Flotation combined with qPCR could overcome PCR interference in juice from pork, as was shown by amplification efficiencies of 1.006 +/- 0.021 and 1.007 +/- 0.025, which are comparable to the amplification efficiency obtained for purified DNA samples (1.005 +/- 0.059). Applying flotation to meat juice samples containing natural background flora and spiked with different levels of Y. enterocolitica showed that direct quantification of Y. enterocolitica was possible down to a level of at least 4.2 x 10(3) CFU per ml of meat juice, even in the presence of 10(6) CFU of background flora per ml. Finally, the results showed that samples containing large amounts of Y. enterocolitica DNA did not result in a positive PCR signal. This indicates that the risk of false-positive results due to detection of DNA originating from dead cells can be greatly reduced by using flotation prior to PCR.

Animals↗
PubMed1994

Enhanced sensitivity in PCR detection of Listeria monocytogenes in soft cheese through use of an aqueous two-phase system as a sample preparation method.

A sample treatment method based on an aqueous two-phase system containing polyethylene glycol and dextran was developed for enhancing sensitivity in the detection of Listeria monocytogenes in soft cheese with PCR. The results suggest that the improved detection sensitivity following partitioning of the cheese homogenate in an aqueous two-phase system may be due to partitioning of the PCR inhibitors to the polyethylene glycol phase.

Base Sequence↗
PubMed1999

Influence of sample preparation technique on two-dimensional gel electrophoresis of proteins from Porphyromonas gingivalis.

Sample preparation methods were compared for two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of cellular proteins from the proteolytic bacterium Porphyromonas gingivalis. Standard solubilization buffer yielded poorly resolved protein spots, but pre-treatment of cells with trichloroacetic acid or inclusion of the protease inhibitor TLCK during solubilization improved definition and separation. The latter approach allowed reliable detection of a 55 kDa immunodominant surface antigen by Western immunoblotting. Further improvements in resolution occurred when SDS was included in the sample preparation. Thus, controlling proteolysis and optimizing protein solubilization were essential for reproducible separations and maximal protein recovery during 2D-PAGE of P. gingivalis.

Bacterial Proteins↗
PubMed2004

Fast detection of Noroviruses using a real-time PCR assay and automated sample preparation.

BACKGROUND: Noroviruses (NoV) have become one of the most commonly reported causative agents of large outbreaks of non-bacterial acute gastroenteritis worldwide as well as sporadic gastroenteritis in the community. Currently, reverse transcriptase polymerase chain reaction (RT-PCR) assays have been implemented in NoV diagnosis, but improvements that simplify and standardize sample preparation, amplification, and detection will be further needed. The combination of automated sample preparation and real-time PCR offers such refinements. METHODS: We have designed a new real-time RT-PCR assay on the LightCycler (LC) with SYBR Green detection and melting curve analysis (Tm) to detect NoV RNA in patient stool samples. The performance of the real-time PCR assay was compared with that obtained in parallel with a commercially available enzyme immunoassay (ELISA) for antigen detection by testing a panel of 52 stool samples. Additionally, in a collaborative study with the Baden-Wuerttemberg State Health office, Stuttgart (Germany) the real-time PCR results were blindly assessed using a previously well-established nested PCR (nPCR) as the reference method, since PCR-based techniques are now considered as the "gold standard" for NoV detection in stool specimens. RESULTS: Analysis of 52 clinical stool samples by real-time PCR yielded results that were consistent with reference nPCR results, while marked differences between the two PCR-based methods and antigen ELISA were observed. Our results indicate that PCR-based procedures are more sensitive and specific than antigen ELISA for detecting NoV in stool specimens. CONCLUSIONS: The combination of automated sample preparation and real-time PCR provided reliable diagnostic results in less time than conventional RT-PCR assays. These benefits make it a valuable tool for routine laboratory practice especially in terms of rapid and appropriate outbreak-control measures in health-care facilities and other settings.

Adolescent↗
PubMed1993

Automated sample preparation by on-line dialysis and trace enrichment. Analysis of morphine, 6-monoacetylmorphine, codeine, ethylmorphine and pholcodine in plasma and whole blood by capillary gas chromatography and capillary gas chromatography-mass spectrometry.

A fully automated sample preparation method for the determination of five opiates in human plasma and whole blood is described. The technique combines dialysis and trace enrichment prior to gas chromatography and gas chromatography-mass spectrometry. Dialysis and trace enrichment on a polymer column was shown to be a highly reliable method for sample preparation. The method can be used, after minor modification, to determine other basic drugs in plasma and whole blood. The method demonstrates the potential of the automated sequential trace enrichment of dialysate (ASTED) system for automated sample preparation.

Automation↗
PubMedDate not supplied

Impact of sample preparation on mineralogical analysis of zero-valent iron reactive barrier materials.

Permeable reactive barriers (PRBs) of zero-valent iron (Fe(0)) are increasingly being used to remediate contaminated ground water. Corrosion of Fe(0) filings and the formation of precipitates can occur when the PRB material comes in contact with ground water and may reduce the lifespan and effectiveness of the barrier. At present, there are no routine procedures for preparing and analyzing the mineral precipitates from Fe(0) PRB material. These procedures are needed because mineralogical composition of corrosion products used to interpret the barrier processes can change with iron oxidation and sample preparation. The objectives of this study were (i) to investigate a method of preparing Fe(0) reactive barrier material for mineralogical analysis by X-ray diffraction (XRD), and (ii) to identify Fe mineral phases and rates of transformations induced by different mineralogical preparation techniques. Materials from an in situ Fe(0) PRB were collected by undisturbed coring and processed for XRD analysis after different times since sampling for three size fractions and by various drying treatments. We found that whole-sample preparation for analysis was necessary because mineral precipitates occurred within the PRB material in different size fractions of the samples. Green rusts quickly disappeared from acetone-dried samples and were not present in air-dried and oven-dried samples. Maghemite/magnetite content increased over time and in oven-dried samples, especially after heating to 105 degrees C. We conclude that care must be taken during sample preparation of Fe(0) PRB material, especially for detection of green rusts, to ensure accurate identification of minerals present within the barrier system.

Chemical Precipitation↗
PubMed2004

High-throughput sample preparation procedures for the quantitation of a new bone integrin alpha(nu)beta(3) antagonist in human plasma and urine using liquid chromatography-tandem mass spectrometry.

High throughput LC-MS/MS assays to quantitate a new alpha(nu)beta(3) bone integrin antagonist (I) in human plasma and urine have been developed using instruments programmed to automate sample preparation procedures. Packard liquid handling system-MultiPROBE II EX was programmed for preparing calibration standards in control plasma and urine, acidifying all standards, quality control (QC), and clinical samples with necessary dilutions, and adding the internal standard to the acidified samples. TOMTEC Quadra 96 was programmed to perform the solid phase extraction (SPE) process on a 3M 96-well mixed phase cation standard density (MPC-SD) plate to isolate the analytes from the sample matrix. The extract collected from both types of matrices was directly injected into reversed-phase LC-MS/MS system with a Turbo Ion Spray (TIS) interface in the positive ionization mode. The plasma and urine assays have the calibration range of 0.5-1500 and 2-6000 ng/mL, respectively. Validation of the automated and the manual plasma assays showed that application of MultiPROBE II to sample preparation gave comparable accuracy and precision. Overall, the automated approaches with minimum manual intervention enhanced the throughput of sample preparation.

Bone and Bones↗
PubMed2003

Simultaneous sample preparation and species-specific isotope dilution mass spectrometry analysis of monomethylmercury and tributyltin in a certified oyster tissue.

A rapid, accurate, sensitive, and simple method for simultaneous speciation analysis of mercury and tin in biological samples has been developed. Integrated simultaneous sample preparation for tin and mercury species includes open focused microwave extraction and derivatization via ethylation. Capillary gas chromatography-inductively plasma mass spectrometry (CGC-ICPMS) conditions and parameters affecting the analytical performance were carefully optimized both for species-specific isotope dilution analysis of MMHg and TBT and for conventional analysis of MBT and DBT201Hg-enriched monomethylmercury and 117Sn-enriched tributyltin were used for species-specific isotope dilution mass spectrometry (SIDMS) analysis. As important, accurate isotope dilution analysis requires equilibration between the spike and the analyte to achieve successful analytical procedures. Since the spike stabilization and solubilization are the most critical and time-consuming steps in isotope dilution analysis, different spiking procedures were tested. Simultaneous microwave-assisted spike stabilization and solubilization can be achieved within less than 5 min. This study originally introduces a method for the simultaneous speciation and isotope dilution of mercury and tin in biological tissues. The sample throughput of the procedure was drastically reduced by fastening sample preparation and GC separation steps. The accuracy of the method was tested by both external calibration analysis and species-specific isotope dilution analysis using the first biological reference material certified for multielemental speciation (oyster tissue, CRM 710, IRMM). The results obtained demonstrate that isotope dilution analysis is a powerful method allowing the simultaneous speciation of TBT and MMHg with high precision and excellent accuracy. Analytical problems related to low recovery during sample preparation are thus minimized by SIDMS. In addition, a rapid procedure allows us to establish a performant routine method using CGC-ICPMS technique.

Animals↗
PubMed2000

Sample preparation for the analysis of flavors and off-flavors in foods.

Off-flavors in foods may originate from environmental pollutants, the growth of microorganisms, oxidation of lipids, or endogenous enzymatic decomposition in the foods. The chromatographic analysis of flavors and off-flavors in foods usually requires that the samples first be processed to remove as many interfering compounds as possible. For analysis of foods by gas chromatography (GC), sample preparation may include mincing, homogenation, centrifugation, distillation, simple solvent extraction, supercritical fluid extraction, pressurized-fluid extraction, microwave-assisted extraction, Soxhlet extraction, or methylation. For high-performance liquid chromatography of amines in fish, cheese, sausage and olive oil or aldehydes in fruit juice, sample preparation may include solvent extraction and derivatization. Headspace GC analysis of orange juice, fish, dehydrated potatoes, and milk requires almost no sample preparation. Purge-and-trap GC analysis of dairy products, seafoods, and garlic may require heating, microwave-mediated distillation, purging the sample with inert gases and trapping the analytes with Tenax or C18, thermal desorption, cryofocusing, or elution with ethyl acetate. Solid-phase microextraction GC analysis of spices, milk and fish can involve microwave-mediated distillation, and usually requires adsorption on poly(dimethyl)siloxane or electrodeposition on fibers followed by thermal desorption. For short-path thermal desorption GC analysis of spices, herbs, coffee, peanuts, candy, mushrooms, beverages, olive oil, honey, and milk, samples are placed in a glass-lined stainless steel thermal desorption tube, which is purged with helium and then heated gradually to desorb the volatiles for analysis. Few of the methods that are available for analysis of food flavors and off-flavors can be described simultaneously as cheap, easy and good.

Flavoring Agents↗