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Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry.

A method to extract peptides and low molecular weight proteins from serum under denaturing conditions using acetonitrile containing 0.1% trifluoroacetic acid has been developed. The extraction procedure precipitates large, abundant proteins to simplify subsequent mass spectral analysis. This sample preparation method provides an efficient way to extract serum peptides, enabling them to be compared and identified using different mass spectrometry approaches. Surface-enhanced laser desorption/ionization-time of flight mass spectrometry analysis of mouse blood serum samples prepared by this method allowed detection of two markers which were significantly reduced in mice with B cell lymphoma tumor. One of these markers has been identified as apolipoprotein A-II.

Acetonitriles↗

Influence of sample preparation on cellular glutathione recovery from adherent cells in culture.

During the last decade, the unbound glutathione content of cultured adherent cells has become a very important biological marker for many pharmacological and toxicological in vitro studies with regard to the protective role of the tripeptide in its reduced form (GSH). However, the literature does not provide extensive information on the influence of sample preparation on cellular GSH and thiol analyses. Using the fibroblast-like V79 cell line as model, we undertook a comparative study of the efficiency of different procedures reported in the literature with respect to GSH recovery. Depending on the preanalytical step, up to 10-fold discrepancies could be observed in the recovery of intracellular GSH. Different parameters that must be controlled in order to maximize GSH recovery are discussed. The optimal strategy consisted in rapid perchloric acid deproteinization performed directly in the dish, which was extremely valuable for preparing GSH samples from adherent cells, and especially from cells expressing elevated gamma-glutamyl transferase activity.

Animals↗

Improvement of resolution, mass accuracy, and reproducibility in reflected mode DE-MALDI-TOF analysis of DNA using fast evaporation--overlayer sample preparations.

DNA analysis by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is hindered by two processes: alkali metal adduction and fragmentation of the intact ionized molecule. The adverse effects of both processes can be reduced by adding ammonium ion salts or compounds such as fructose to the sample preparations. Matrix additives improve sensitivity and resolution of DNA analysis by MALDI. In addition, spot-to-spot reproducibility, resolution, and mass accuracy for DNA oligonucleotides (< or = 12 mer) can be improved by the use of overlayer sample preparations with matrixes that have low aqueous solubilities, such as alpha-cyano-4-hydroxycinnamic acid, ferulic acid, and 2,4,6-trihydroxyacetophenone. For example, resolution for 5-12-mer oligonucleotides is greater than 7000 using overlayer matrix preparations and mass accuracy values are well below 20 ppm. In addition to these methods, a new method for analyzing DNA in positive ion mode is reported using acidified 3-hydroxypicolinic acid. This method does not lose sensitivity for higher mass oligonucleotides as quickly as overlayer methods, and spectra retain > 6000 resolution and mass accuracies of approximately 20 ppm between different overlayer depositions.

DNA↗

Fast liquid chromatography-mass spectrometry glutathione measurement in whole blood: micromolar GSSG is a sample preparation artifact.

We describe a new, fast (6 min) and reliable method to measure reduced or oxidized glutathione (GSH) or (GSSG) in whole blood. The method is based on a LC/MS measurement in positive electrospray ionization mode after a chromatographic separation on a specific column which does not need any counter-ion in the mobile phase, improving the sensitivity of detection. A 50 microl sample of whole blood is sufficient for analysis. We demonstrate that the lack of an alkylating agent during the sample preparation brings out an underestimation of GSH and an artefactual production of GSSG, corresponding to 2-3% of GSH. The simultaneous use of N-ethyl-maleimide and a strong deproteinising acid prevents these two drawbacks. This efficient and new method of preparation and analysis lets us show that, unexpectedly, GSH is stable in whole blood for some hours and that deproteinised samples can be stored without GSH loss for at least three weeks at -20 or -80 degrees C. The reference interval, measured on 22 volunteers, on blood samples collected either with heparin or with EDTA, is 1310 +/- 118 microM for GSH and 0.62 microM for GSSG. The within-run precision of this method, with gamma glutamyl-glutamic acid as an internal standard, evaluated in three successive series (n = 30), lies between 2.1 and 4.8% for a GSH level at 580 or 1150 microM. The one step sample preparation we propose seems well suited for GSH routine measurements in hospital laboratories and avoids any underestimation of GSH, a now well accepted biomarker of oxidative stress.

Adult↗

Simplified sample preparation method for protein identification by matrix-assisted laser desorption/ionization mass spectrometry: in-gel digestion on the probe surface.

Identification and detailed characterization of complex mixtures of proteins separated by polyacrylamide gel electrophoresis (PAGE) require optimized and robust methods for interfacing electrophoretic techniques to mass spectrometry. Peptide mapping by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) is used as the first protein screening method in many laboratories because of its inherent simplicity, mass accuracy, sensitivity and relatively high sample throughput. We present a simplified sample preparation method for MALDI-MS that enables in-gel digestion of protein samples directly on the MALDI-MS metal probe. Removal of detergent and reagents as well as protein reduction and S-alkylation were performed prior to cutting of protein samples from the polyacrylamide gel slab. The general utility of this approach was demonstrated by on-probe digestion and MALDI-MS peptide mapping of femtomole amounts of standard proteins isolated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A representative set of 47 human proteins obtained from a silver stained two-dimensional electrophoretic gel was analyzed by the new method and resulted in a success rate for protein identification similar to that obtained by the traditional protocols for in-gel digestion and MALDI peptide mass mapping of human proteins, i.e. approximately 60%. The overall performance of the novel on-probe digestion method is comparable with that of the standard in-gel sample preparation protocol while being less labour intensive and more cost-effective due to minimal consumption of reagents, enzymes and consumables. Preliminary data obtained on a MALDI quadrupole-TOF tandem mass spectrometer demonstrated the utility of the on-probe digestion protocol for peptide mass mapping and peptide sequencing on this instrument. Automation of the on-probe protein digestion procedure and its combination with automated MALDI tandem mass spectrometry should be advantageous in proteomics research aimed at the systematic identification and analysis of large sets of proteins from electrophoretic gels.

Amino Acid Sequence↗

Automated sample preparation and LC-MS for high-throughput ADME quantification.

Bioanalytical groups in the pharmaceutical industry provide quantitative data to support all stages of drug discovery. The increased use of 96-well plates and robotic liquid handling systems, the availability of robust triple quadruple mass spectrometers, and developments in chromatographic and samples preparation techniques, have all increased the rate at which this data can be generated. This review describes currently used methods and emerging technologies for automation of high-throughput quantitative bioanalysis. The focus is on recent applications of sample preparation and chromatography techniques compatible with detection by triple quadruple mass spectrometers.

Absorption↗

Focused ion beam for microscopy and in situ sample preparation: application on a crustacean digestive system.

We prove that the focused ion beam (FIB) machine can be used as a microscope and as an in situ cutting device for tissue and cells. For the first time we obtain high-resolution ion images, complemented by electron imaging of different animal tissues both from uncoated and coated samples. In our study, we select the digestive system of Porcellio scaber (isopoda, crustacea) as a test system for FIB microscopy and in situ sample preparation. After the milling operation, some of the ultrastructural elements of hepatopancreatic cells can clearly be recognized. Also, FIB operation reveals significant differences in structural integrity between the apical and basal parts of hepatopancreatic cells, which have not been observed before by classical microscopy techniques. FIB microscopy and in situ sample preparation have advantages over classical microscopy techniques because of: 1. in situ site-specific 2-D sectioning and imaging of subsurface microstructures; 2. no need to embed the sample prior to sectioning; and 3. a wide range of magnifications while imaging the same sample.

Animals↗

A new on-line sample preparation system for the liquid chromatography/time-of-flight mass spectrometry simultaneous analysis of pesticides in river water.

Current on-line solid-phase extraction methods combined with HPLC for shortening the clean-up operation are not suitable for simultaneously detecting compounds that have a wide variety of hydrophobicities. To solve these problems, we designed a new on-line sample preparation system. The system consists of an eluting pump, a mixing TEE connector, a 10-port 2-position valve and a solid-phase extraction precolumn. The eluate from the precolumn is diluted with a weak solvent from the HPLC at the TEE connection to load low hydrophobic compounds onto the analytical column. The proposed on-line sample preparation system was successfully applied to the simultaneous analysis of 21 pesticides in river water using LC/TOF-MS. In this method, the recoveries from river water samples were 67 to 126% (mean 83%), the reproducibility (CV%) was in the range from 1.1 to 11% (mean 5.6%), the calibration curve was linear in the range from 1 ppb to 500 ppb (r > 0.999) and the detection limits (S/N = 3) were in the range from 0.0034 ppb (daimuron) to 3.3 ppb (oxine-copper).

Automation↗

XTEM sample preparation technique for n-type compound semiconductors using photochemical etching.

A sample preparation technique based on photochemical etching (PCE) is described for cross-sectional transmission electron microscopy (XTEM) of n-type compound semiconductors. XTEM samples of an InGaAsP/InP single-layer structure, prepared by using a moderately focused laser beam and Br2-methanol solution, gave high quality, damage-free XTEM images. The PCE technique is applicable to other n-type compound semiconductors.

Microscopy, Electron↗

Multiwell in-gel protein digestion and microscale sample preparation for protein identification by mass spectrometry.

In-gel peptide digestion has become a widely used technique for characterizing proteins resolved by two-dimensional gel electrophoresis. Peptides generated from gel pieces are frequently contaminated with detergent and salts. Prior to matrix-assisted laser desorption/ionization-time of flight mass spectrometry analysis, these contaminants are removed using micro scale C18 sample preparation columns. In this paper, data are presented to demonstrate the application of a solvent resistant MultiScreen 96-well plate with a low peptide binding membrane and ZipTip micropipette based sample preparation. Recoveries of peptides (m/z of 1000 to 5000 Da) derived from standard protein protease digests, were estimated at various stages of the analytical process. An optimized protocol has been established and all the reagents and consumables have been packaged in a ready to use commercial kit. Data will be presented to show the application of this technology package to accelerate the throughput of protein characterization by protease fragmentation.

Blood Protein Electrophoresis↗

[Comparative characteristics of various methods of sample preparation for determining ethanol in muscle tissue].

Three methods for sample preparation for ethanol detection by gas chromatography are compared. The highest ethanol output was obtained after preparation by 5-min heating of the biological object and the internal reference object with addition of trichloroacetic acid as the acidifier. Relationship between the results of ethanol measurements and the degree of muscle crushing was evaluated.

Chromatography, Gas↗

Noncontact laser microdissection and pressure catapulting: sample preparation for genomic, transcriptomic, and proteomic analysis.

The understanding of the molecular mechanisms of cellular metabolism and proliferation necessitates accurate identification, isolation, and finally characterization of a specific cell or a population of cells and subsequently their subsets of biomolecules. For the simultaneous analysis of thousands of molecular parameters within a single experiment, as realized by DNA, RNA, and protein microarray technologies, a defined number of homogeneous cells derived from a distinct morphological origin is required. Sample preparation is therefore a very crucial step for high-resolution downstream applications. Laser microdissection and laser pressure catapulting (LMPC) enables such pure and homogeneous sample preparation, resulting in an eminent increase in the specificity of molecular analyses. For microdissection, the force of focused laser light is used to excise selected cells or large tissue areas from object slides or from living cell culture down to a resolution of individual single cells and subcellular components like organelles or chromosomes, respectively. After microdissection this sample is directly catapulted into an appropriate collection device. As the entire process works without any mechanical contact, it enables pure sample retrieval from morphologically defined origin without cross contamination. Wherever homogenous samples are required for subsequent analysis of, e.g., cell areas, single cells, or chromosomes, the PALM MicroBeam system is an indispensable tool. The integration of image analysis platforms fully automates screening, identification, and finally subsequent high-throughput sample handling. These samples can be directly linked into versatile downstream applications, such as single-cell mRNA-extraction, different PCR methods, microarray techniques, and many others. Acceleration in sample generation vastly increases the throughput in molecular laboratories and leads to an increasing knowledge about differentially regulated mRNAs and expressed proteins, providing new insights into cellular mechanisms and therefore enabling the development of systems for tumor biomarker identification, early detection of disease-causing alterations, therapeutic targeting and/or patient-tailored therapy.

Animals↗

Submicro scale NMR sample preparation for volatile chemicals.

A simple, inexpensive, and highly efficient NMR sample preparation technique for volatile chemicals has been devised using a micropreparative GC system. The recovery efficiency of a volatile chemical using this technique was >80% with sample sizes of 0.05 to 0.5 microg. The purity of the acquired NMR samples was sufficient for high sensitive NMR analyses including two dimensional experiments.

Chromatography, Gas↗

Use of solid-phase extraction in various of its modalities for sample preparation in the determination of estrogens and progestogens in sediment and water.

The environmental analysis of estrogens and progestogens at physiologically active concentrations (low ng/l range) requires the use of very sensitive and selective methods, which, in most cases, make necessary an extraction/purification step. In this study, various procedures for the determination of several estrogens (estriol, estradiol, ethynyl estradiol, estrone, and diethylstilbestrol) and progestogens (progesterone, norethindrone, and levonorgestrel) in environmental matrices, including water and river sediment, are described. In all procedures, final analysis of the target compounds is performed by reversed-phase liquid chromatography-diode array detection-mass spectrometry, whereas sample preparation always includes a solid-phase extraction (SPE) step. For this SPE step. various types of sorbents, protocols, and devices have been used, and their respective advantages and disadvantages are discussed. For the off-line SPE of estrogens and progestogens from water samples, a syringe type cartridge LiChrolut RP-18 (500 mg) was selected out of two other sorbents--LiChrolut EN (200 mg) and Isolut ENV (500 mg)--for use with the automated sample preparation instrument ASPEC XL. For the on-line SPE and analysis of water samples the 10 mm x 2 mm I.D. HySphere-Resin-GP cartridge, was preferred to the C18 Baker, the PLRP-S, and the Oasis HLB. for use with the Prospekt system. A completely manual protocol based on the use of Sep-Pak C18 Plus cartridges was developed for purification of sediment extracts. All procedures were shown to be linear over a wide range of concentration, exhibited satisfactory repeatability and accuracy, and reached limits of detection usually in the low ng/l and ng/g range. Comparatively, the on-line method was shown to be advantageous in terms of automation and general method performance.

Chromatography, Liquid↗

Sample preparation for beta-exotoxin determination in Bacillus thuringiensis cultures by reversed-phase high-performance liquid chromatography.

Beta-exotoxin is a nucleotide analogue produced by the entomopathogenic bacterium Bacillus thuringiensis. We have defined two new HPLC procedures for quantification of this exotoxin in culture supernatants of B. thuringiensis grown in poor or rich medium. The sample is prepared either by precipitation in solvent or by solid-phase extraction. Solvent precipitation is achieved treating the sample with acetone and acetonitrile. Solid-phase extraction is performed with a C18 and an anion-exchange cartridge. Reversed-phase HPLC with gradient elution of the prepared samples gives a limit of quantitation of 2 microg/ml for samples prepared by solvent precipitation and of 0.3 microg/ml for samples prepared by solid-phase extraction.

Acetone↗

One step and highly sensitive headspace solid-phase microextraction sample preparation approach for the analysis of methamphetamine and amphetamine in human urine.

A fiber-stable, repeatable and highly sensitive headspace solid-phase microextraction (HS-SPME) method was developed for the analysis of methamphetamine (MA) and amphetamine (AM) in urine using gas chromatography-mass spectrometry (GC-MS) in the selected ion monitoring mode. For sample preparation, the test specimen was placed in a 7 ml vial along with the additives (KOH and NaCl) and the internal standards (d8-MA and d8-AM), a glass insert containing heptafluorobutyric anhydride (HFBA) and heptafluorobutyric chloride (HFBCl) as derivatizing reagents was inserted into the vial, the vial was then sealed tightly. A SPME device with a 100 microm polydimethylsiloxane fiber was inserted into the vial and the fiber was exposed to the headspace in the insert, then the vial was heated and stirred at 100 degrees C and 600 rpm for 20 min for evaporation/adsorption/derivatization. The vaporized analytes (AM and MA) in the vial diffused into the glass insert though the holes on the insert, they absorbed onto the fiber, and then interacted with the vapor of the derivatizing reagent. Some of the analytes in the headspace of the glass insert may react with the vapor of the derivatizing reagent first, and then adsorb onto the fiber. The needle was finally removed and inserted into the injection port to desorb the analytes with the fiber exposed to the liner of the GC-MS system for analysis. By combining HFBCl and HFBA as derivatizing reagents and placing them in an insert, the HS-SPME method achieves high sensitivity for the analysis of AM and MA. Correlation coefficients derived from typical calibration curves in the 1.0-1700 ng ml(-1) range are 0.998 for MA and 0.994 for AM. The limits of detection and the limits of quantitation using a sample size of 1 ml are 0.3 and 1.0 ng ml(-1), respectively, for both MA and AM in urine specimens. Because the water hydrolysis of derivatizing reagent is much faster than the acylation reaction of the primary and secondary amines with the derivatizing reagent, the amphetamines cannot be acylated effectively over heated aqueous solution, and therefore this study provides a new acylation design in moisture surroundings. The proposed process also simplifies the procedure for urine sample preparation, and makes the automation of SPME possible.

Amphetamine↗

Suppression of sodium dodecyl sulfate-polyacrylamide gel electrophoresis sample preparation artifacts for analysis of IgG4 half-antibody.

Human IgG4 subtype antibodies have often been reported to have a significant portion (5-50%) of a heavy chain-light chain dimer ("half-antibody") on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), in which the heavy chain is not covalently linked through the hinge disulfides to another heavy chain. We demonstrate here that there can be artifactual sources of half-antibody. One occurred during SDS-PAGE sample preparation where rapid disulfide scrambling was initiated by preexisting free sulfhydryls in the monoclonal antibody (mAb) and by free sulfhydryl produced by destruction of disulfide bonds during heating. Inclusion of N-ethylmaleimide in the sample buffer prevented the disulfide scrambling. Presumably, cyclization of the flexible IgG4 hinge during this disulfide scrambling leads to the preferential separation of heavy chains. A second condition producing half-antibody was reoxidation after exposure to reductant, where 46% of the antibody was trapped in the intrachain disulfide form. The amount of half-antibody was reduced to 4% by reoxidation in the presence of a mixture of oxidized and reduced glutathione. When the improved sample preparation conditions were used, IgG4 mAb freshly isolated from cells contained 4.5-15% half-antibody, indicating that equilibration of the interchain and intrachain hinge disulfide pairing was not always attained in cells.

Antibodies, Monoclonal↗

Detection of cytomegalovirus in blood donors by PCR using the digene SHARP signal system assay: effects of sample preparation and detection methodology.

Cytomegalovirus (CMV) is an important cause of transfusion-associated morbidity and mortality; however, only 0.4 to 12% of the blood products obtained from seropositive blood donors transmit infection. The effects of three commercially available whole-blood sample preparation kits on the detection of CMV PCR products by a semiquantitative adaptation of the Digene SHARP Signal System Assay (DSSSA) in samples from volunteer blood donors was assessed. Of 101 samples from seropositive blood donors, CMV was detected in 0 (0%) of the samples extracted with a QIAamp blood kit (QIAGEN), 1 (1%) of the samples extracted with an Amplicor whole-blood specimen preparation kit (Roche), and 8 (8%) of the samples extracted with an Isoquick nucleic acid extraction kit (modified by the addition of carrier tRNA) (Microprobe). CMV DNA was not detected in samples from seronegative blood donors (n = 13). Nested PCR of selected samples confirmed the detection of CMV in the sane eight samples extracted with the modified Isoquick nucleic acid extraction kit and detected an additional nine CMV-positive samples (n = 50). Samples from volunteer blood donors contain low copy numbers of CMV DNA. PCR amplification of such specimens can result in analytical sampling errors, giving results similar to the variations in titers recognized during determinations of the 50% tissue culture infective dose. The detection of CMV in blood samples from volunteer blood donors by PCR is a function of sample preparation, amplification conditions, and detection methodology. Accurate assessments of the clinical utility of CMV DNA detection by nucleic acid amplification for blood product screening and patients will require highly standardized and quantitative methodology.

Blood Donors↗