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PubMed2026

A streamlined workflow for high throughput metaproteomic analysis of the rumen microbiome.

Metaproteomics can provide direct functional insights into complex microbial communities, yet its application in rumen research remains limited due to labor-intensive and low-throughput sample preparation workflows before the MS analysis. This work aimed to develop and characterize a streamlined, high throughput metaproteomic workflow optimized for rumen samples. Key steps, including microbial cell extraction, cell lysis, protein digestion, and LC-MS/MS acquisition, were systematically assessed and optimized to reduce hands-on time while maintaining deep proteome coverage. The optimized workflow integrates a minimized cell extraction protocol using 0.5 g starting material and in-solution tryptic digestion. Application of the final workflow to 72 samples from in vitro fermentation revealed that biological variability between inocula dominated technical variability, which remained moderate (median CV of 21-24% across batches). Overall, the optimized workflow supports robust taxonomic and functional characterization of the rumen microbiome with improved scalability. These advances provide a foundation for applying metaproteomics to larger experimental designs, including nutritional trials and cohort studies, thereby enabling broader functional interrogation of rumen microbial ecosystems. SIGNIFICANCE: This study addresses current limitations in the application of metaproteomics to rumen microbiome research by developing a streamlined and scalable sample preparation workflow. By optimizing key steps and reducing sample input while maintaining reproducibility and proteome coverage, this work enables more efficient processing of larger sample sets. These advances support the broader use of metaproteomics in rumen studies and facilitate functional investigations relevant to animal nutrition and sustainable livestock production.

Animals↗
PubMedDate not supplied

[Homogenization of samples for the culture of mycobacteria. A comparative study of samples with and without centrifugation].

A homogenization method for sputum samples for the culture of acid-fast bacilli that omits the use of centrifugation, passage test tubes and balances is described. 10% sodium phosphate was used as decontaminating substance. This method facilitates the laboratory work since the samples so treated are incubated at 37 degrees C up to the next day when they are then cultured. 676 samples prepared according to this method were compared with samples prepared according to the standard method; a 6,21% positivity in the former compared to a 5,47% in the latter as well as a lower percentage of contamination were obtained. Contamination occurred in 9,91% of samples without centrifugation and in 14,35% of centrifuged samples.

Bacteriological Techniques↗
PubMed1979

Ultrasonic absorption in liver tissue.

Ultrasonic attenuation coefficients were measured in mammalian liver for frequencies ranging from 0.5 to 10 MHz and for a range of sample preparations. Certain preparative procedures were found to greatly increase the low-frequency attenuation coefficient due to the introduction of bubbles into the sample. The low-frequency attenuation was reduced by storage at low temperatures or by pressurization, each caused the bubbles to go into solution, resulting in an attenuation coefficient that was a simple power function of frequency. Absorption coefficients of in vitro and in vivo samples were found to be similar and to show much less dependence on sample preparation than the attenuation measurements. These studies suggest that properties of carefully prepared in vitro samples are indicative of the in vivo properties.

Animals↗
PubMed2000

High-throughput approaches to the quantitative analysis of ketoconazole, a potent inhibitor of cytochrome P450 3A4, in human plasma.

Ketoconazole, an imidazole-piperazine compound, is an orally active antimycotic agent. In addition, ketoconazole is a specific inhibitor of cytochrome P450 3A4. As about 60% of oxidized drugs are biotransformed by this isoform, the potential effect of a concomitant administration of ketoconazole on drug disposition may be of interest during drug development. The present paper describes three different approaches (methods A, B, and C) to attain high-throughput sample preparation and analysis in the quantification of ketoconazole in human plasma. Method A consisted of acetonitrile precipitation in a 96-well plate, transfer of the supernatant via a Tomtec Quadra 96 Model 320, and subsequent injection onto a 50 x 4.6 mm (i.d.) Develosil Combi-RP-5 column (packed with C30 bonded silica particles). Method B consisted of an identical sample preparation to method A with the exception that a Michrom Magic Bullet(trade mark) column, 2.0 --> 0.50 mm (i.d., tapered bore) x25 mm length, was used. Lastly, in method C, a turbulent-flow chromatography (TurboFlow LC/APCI-MS/MS) module was used for the direct analysis of ketoconazole in human plasma. A Sciex API 3000 was used in methods A and B, while a Micromass Quattro LC was employed in method C. Based on the values obtained for the calibrator (standard) and quality control samples, all three protocols yielded satisfactory accuracy, precision, and reduced manual sample preparation time.

Antifungal Agents↗
PubMed2003

The application of HPLC-F and GC-MS to the analysis of selected hydroxy polycyclic hydrocarbons in two certified fish bile reference materials.

Four selected hydroxy polycyclic aromatic hydrocarbons (OH-PAHs), 2-hydroxy-naphthalene (2-OH-NPH), 1-hydroxy-phenanthrene (1-OH-PHE), 1-hydroxy-pyrene (1-OH-PYR) and 3-hydroxy-benzo[a]pyrene (3-OH-BaP) have been analysed in two certified fish bile reference materials (CRMs) for exposure monitoring of PAHs in the aquatic environment. The two materials, BCR 720 and BCR 721, consist of bile from fish exposed to contaminated sediment and dispersed crude oil, respectively. Both bile samples have been analysed by two different analytical techniques, gas chromatography-mass spectrometry (GC-MS) and high performance liquid chromatography-fluorescence detection (HPLC-F), and the separation performance, detection limits, recoveries and reproducibility for the four target compounds were evaluated. HPLC-F requires a simple sample preparation and the separation capacity is adequate for quantification of 1-OH-PYR and 3-OH-BaP. Detection limits are excellent for 1-OH-PYR (6 pg injected) and 3-OH-BaP (3 pg injected) and generally improved with increasing molecular size. Recoveries ranged from 48 to 99% for the four selected compounds, depending on compound and concentration. Sample preparation prior to GC-MS analysis was more demanding, as reflected by the obtained recoveries for 2-OH-NPH, 1-OH-PHE and 1-OH-PYR (35 to 61%). The sensitivity improved with decreasing molecular size, 2-OH-NPH (1.2 pg injected), 1-OH-PHE (2.4 pg injected) and 1-OH-PYR (6 pg injected). Because of the superior separation power of GC and the extra selectivity of MS detection, GC-MS was the method of choice for the determination of 2-OH-NPH and 1-OH-PHE in both CRMs. In fish bile samples these two compounds are more likely to suffer from chromatographic overlap, and HPLC-F was not sufficiently selective. Determination of 1-OH-PYR was performed with success by both methods, but HPLC-F would be preferred because of the simpler and less time-consuming sample preparation. Detectable concentrations of 3-OH-BaP were present in BCR 720 and could only be determined by HPLC-F. The present work aims to present HPLC-F and GC-MS as complementary methods for the quantitative analysis of OH-PAHs in fish bile.

Animals↗
PubMed1989

Manual and automated enrichment procedures for biological samples using lipophilic gels.

Aspects of the use of lipophilic gels in manual sample preparation procedures are reviewed. Neutral gels with a controlled hydrophobicity are used for sorbent extraction of non-polar and medium polarity compounds from biological fluids. Acidic amphiphilic compounds can be extracted as ion-pairs with decyltrimethylammonium ions. Solvent or detergent extracts of tissues or faeces can be mixed with hydrophobic gels for transfer of analytes from a solvent to a gel phase, permitting subsequent sample preparation in gel bed systems. Hydrophobic gels, alkyl-bonded silica and polystyrene matrices can be used in series for extraction of compounds with a wide range of polarities. Group fractionations are performed on neutral and ion-exchanging lipophilic gels to yield fractions of neutral, basic and acidic metabolites within selected polarity ranges. Selective isolation of phenolic acids on a strong anion exchanger, of ethynylic steroids on a strong cation exchanger in silver form and of oximes of ketonic steroids on a strong cation exchanger in hydrogen form is possible. A computerized system for automatic sample preparation is also described. It consists of an extraction bed, a cation-exchange column and an anion-exchange column. The pumps and switching valves are arranged so that the columns can operate in series or parallel for isolation of neutral, basic and acidic metabolites of amphiphilic compounds and for regeneration of the column beds. Fractions can be collected, or the effluent from the column beds can be diluted with water to permit sorption on a solid phase. The applicability of the automated method to the analysis of bile acids and metabolites of mono(2-ethylhexyl) phthalate is demonstrated.

Animals↗
PubMed1999

Liquid-liquid extraction in the 96-well plate format with SRM LC/MS quantitative determination of methotrexate and its major metabolite in human plasma.

A method involving the semirobotic liquid-liquid extraction (LLE) in deep-well 96-well plates was developed for the quantitation of the anti-cancer/antiinflammatory drug methotrexate (MTX) and its major metabolite, 7-hydroxymethotrexate (7OH-MTX) in human plasma. The extraction time for the sample preparation was relatively short with four 96-well plates (384 samples) prepared in approximately 90 min by one person. The sample extracts were each analyzed within 1.2 min using a positive ion turbo-ionspray selected reaction monitoring liquid chromatography/mass spectrometric (SRM LC/MS) method in which 768 samples were easily analyzed within 22 h (maximum of 820 samples in 24 h). Deuterated internal standards, MTX-d3 and 7OH-MTX-d3, were used. The calibration curves for MTX and 7OH-MTX were linear (R2 > 0.997) and ranged from 0.5 to 250 and 0.75 to 100 ng/mL, respectively. The limit of quantitation (LOQ) for MTX and 7OH-MTX was 0.5 and 0.75 ng/mL, respectively; persistent carryover from the autosampler limited the LOQ achievable. The limit of detection (LOD) was 0.05 ng/mL for MTX and 0.1 ng/mL for 7OH-MTX. The intra- and inter-assay precision and accuracy did not exceed 15% for both MTX and 7OH-MTX. The recoveries were 61% for MTX and 47% for 7OH-MTX. The method was validated and demonstrated to be robust with high precision and accuracy.

Chromatography, High Pressure Liquid↗
PubMed1996

Immunomagnetic separation and solid-phase detection of Bordetella pertussis.

In the present study, novel solid-phase methods were used for both sample preparation and PCR detection of Bordetella pertussis. The sample preparation was performed by immunomagnetic separation with paramagnetic beads coated with polyclonal antibodies directed toward the surface antigens of the bacteria. The precoated immunobeads were directly used on nasopharyngeal aspirates to capture the bacteria on the solid support and were subsequently transferred to the PCR tube with no further manipulations. The region encompassing the pertussis toxin promoter was analyzed to allow direct discrimination between the three major Bordetella species (B. pertussis, B. parapertussis, and B. bronchiseptica). The resulting amplicons were captured on a second magnetic solid phase, allowing detection and restriction analysis of the target sequence. A colorimetric detection system based on a DNA binding fusion protein enabled the use of standardized enzyme-linked immunosorbent format tests both for the detection of Bordetella spp. and for species evaluation. When the optimized system was evaluated on 55 clinical aspirate samples, 21 of 22 (95%) culture-positive samples were positive by the system that we developed. In addition, two samples were positive by the PCR-based assay, while the culture assay was negative. The implications of these results are discussed.

Base Sequence↗
PubMed2006

High throughput screening for spores and vegetative forms of pathogenic B. anthracis by an internally controlled real-time PCR assay with automated DNA preparation.

Human infections with Bacillus anthracis have become rare but in cases of intentional release, masses of samples would have to be expected. Current PCR assays for anthrax are appropriate for use in single cases, but they have not been formulated for high throughput screening. This article describes a high throughput real-time PCR for anthrax, including automated sample preparation without the need for pre-culturing of samples. The assay detects single copies of target gene. An internal control monitors the whole assay including sample preparation. The limit of detection in blood was 1,066 (95%CI, 741-1,739) copies/ml, corresponding to 4.4-32.3 organisms/ml. Using spore preparations, 20 colony-forming units (CFU) per sample could be detected reliably (0.8 CFU per PCR). The extraction procedures depleted viable spores from solution by factors of 10,000 (automated procedure) and >100,000 (conventional column procedure). One hundred and ten clinical and environmental specimens were retested, 50 of them sampled during a period of heightened anthrax awareness in 2001. A widely used assay yielded two false positive results (cross-reaction with B. cereus), while the new assay tested all samples negative. The internal control operated stable in all clinical samples. The assay is capable of testing for anthrax in the high throughput mode.

Automation↗
PubMed1997

Determination of ethylenediaminetetraacetic acid as the nickel chelate in environmental water by solid-phase extraction and capillary electrophoresis/tandem mass spectrometry.

An automated extraction procedure using solid-phase extraction (SPE) disk technology was developed for the qualitative and quantitative determination of ethylenediaminetetraacetic acid (EDTA) in water samples. The procedure involves conversion of all free and chelated EDTA present into the nickel EDTA chelate followed by extraction on strong anion exchange extraction disks, A 5 mL water sample is extracted and concentrated to 30 microL. This extract is then analyzed by capillary electrophoresis (CE) using ion spray-tandem mass spectrometry (MS) for selective detection. An amine-coated capillary column is used to separate anions using negative voltage and high electroosmotic flow. A self-aligning liquid junction is used as the CE/MS interface. The sample is injected using field amplification for enhanced concentration detection limits down to 0.15 microgram/L. This detection limit is about five times lower than any report we have found in the literature and provides the unique specificity afforded by mass spectrometry. Total sample preparation and run time was forty minutes per sample, including evaporation steps and capillary rinsing between runs. A tray of 24 vials, including samples and standards, was analyzed for these experiments and was easily finished within one day. These experiments demonstrate that CE/MS can be a rugged, quantitative technique, which, with proper sample preparation and focusing techniques, can compete with the concentration sensitivity of established analytical methods.

Chelating Agents↗
PubMed2004

Matrix-dependent cationization in MALDI mass spectrometry.

The matrix dependence in cationization processes, the competition between cationization and protonation and the question of whether gas-phase cation transfer or attachment of free cations dominates in matrix-assisted laser desorption/ionization mass spectrometry were studied. Two different sample preparation methods were employed, the dried-droplet sample preparation and a mixture of solid matrix, analyte and salt. The latter ensures that the formation of cation adducts takes place in the gas phase. By monitoring the suppression of matrix signals for different matrices, it was found that matrices with high gas-phase metal ion binding energies require high analyte concentrations for matrix suppression to occur. By comparing the mass spectra obtained using sinapinic acid or sinapinic methyl ester as a matrix, a correlation between cationization and deprotonation of matrix molecules was found. It is also demonstrated that attachment of free gas-phase cations, rather than cation transfer from the cationized matrix, is the predominant process in cationization.

Anti-Bacterial Agents↗
PubMed2002

Speciation of mercury, tin, and lead compounds by gas chromatography with microwave-induced plasma and atomic-emission detection (GC-MIP-AED).

Because of their high toxicity and widespread distribution, the reliable selective quantification of alkyl and aryl species containing mercury, tin, or lead has been one of the goals of speciation analysis in recent years. Since becoming commercially available, GC-MIP-AED has been one of the most-used tools in this work. In this paper, the value and limitations of GC-MIP-AED for the speciation of Hg, Sn, and Pb compounds in environmental samples are reviewed and compared with the analytical characteristics of other hyphenated GC-based techniques. Because quantification of Hg, Sn, and Pb species by GC techniques normally requires complex sample preparation involving several steps, the effect of sample-preparation methods on the accuracy and precision of the results is discussed. Finally, we describe the current status of a rapid, low-cost GC-MIP-PED system specifically designed for routine quantification of Hg, Sn, and Pb species in environmental control laboratories.

Journal Article↗
PubMed2004

Transmission electron microscopy of fluorapatite-gelatine composite particles prepared using focused ion beam milling.

In this paper, synthetic fluorapatite-gelatine composite particles are prepared for transmission electron microscopy (TEM) studies using two methods based on focused ion beam (FIB) milling. TEM studies on the FIB-prepared specimens are compared with TEM observations on samples prepared using an ultramicrotome. The results show that ultramicrotome slicing causes significant cracking of the apatite, whereas the ion beam can be used to make high-quality, crack-free specimens with no apparent ion beam-induced damage. The TEM observations on the FIB-prepared samples confirm that the fluorapatite composite particles are composed of elongated, preferentially orientated grains and reveal that the grain boundaries contain many small interstices filled with an amorphous phase.

Journal Article↗
PubMed2005

Metabolic profiling of laser microdissected vascular bundles of Arabidopsis thaliana.

BACKGROUND: Laser microdissection is a useful tool for collecting tissue-specific samples or even single cells from animal and plant tissue sections. This technique has been successfully employed to study cell type-specific expression at the RNA, and more recently also at the protein level. However, metabolites were not amenable to analysis after laser microdissection, due to the procedures routinely applied for sample preparation. Using standard tissue fixation and embedding protocols to prepare histological sections, metabolites are either efficiently extracted by dehydrating solvents, or washed out by embedding agents. RESULTS: In this study, we used cryosectioning as an alternative method that preserves sufficient cellular structure while minimizing metabolite loss by excluding any solute exchange steps. Using this pre-treatment procedure, Arabidopsis thaliana stem sections were prepared for laser microdissection of vascular bundles. Collected samples were subsequently analyzed by gas chromatography-time of flight mass spectrometry (GC-TOF MS) to obtain metabolite profiles. From 100 collected vascular bundles (approximately 5,000 cells), 68 metabolites could be identified. More than half of the identified metabolites could be shown to be enriched or depleted in vascular bundles as compared to the surrounding tissues. CONCLUSION: This study uses the example of vascular bundles to demonstrate for the first time that it is possible to analyze a comprehensive set of metabolites from laser microdissected samples at a tissue-specific level, given that a suitable sample preparation procedure is used.

Journal Article↗
PubMed2004

Technical note: comparison of Raman, mid, and near infrared spectroscopy for predicting the amino acid content in animal meals.

The objective of this study was to compare three infrared spectroscopy techniques for routine evaluation of AA in animal meals. Animal meals (n = 54) with known AA contents were scanned with a near (NIRS), mid (FTIR), and Raman infrared spectrometer. For NIRS and Raman, samples were scanned "as is", whereas for FTIR, samples had to be finely ground before scanning to obtain reasonable spectra. Both FTIR and Raman data suffered from noise; for Raman, this prevented the development of calibrations. Using derivatized spectral data and a standardized outlier removal procedure, calibrations for nutritionally relevant AA could be developed that were equivalent for both NIRS and FTIR. The variation across AA tested explained (r2) by these calibrations was 70% for NIRS and 68 + 3% for FTIR. Removing spectral data between 4,000 and 2,000 cm(-1) from the FTIR data improved calibrations (P = 0.09) and explained an average of 77% of the variation with prediction errors lower than obtained with NIRS (P < 0.01). However, FTIR calibrations based on the entire or the shortened spectrum contained fewer samples than did NIRS calibrations (41 and 39 vs. 48, respectively; P < 0.01) because more samples were removed as outliers. In conclusion, Raman did not yield acceptable spectra for animal meals. For FTIR, sample preparation was more time-consuming because the samples required grinding before analysis. Using the entire mid-infrared range, FTIR calibrations were comparable to NIRS calibrations. Calibrations for FTIR were improved by eliminating wave numbers that exhibited more noise, resulting in prediction errors better than those for NIRS. Thus, FTIR has the potential to yield better calibrations for AA in animal meals than NIRS, but it requires greater care in sample preparation and scanning.

Amino Acids↗
PubMed2006

[Developments of liquid-phase microextraction based on hollow fiber].

The liquid-phase microextraction (LPME), based on disposable hollow fiber, has been developed to be a new environmentally benign sample preparation technique which incorporate sampling, extraction and concentration into a single step. The novel technique can be easily manipulated in combination with high performance liquid chromatography, gas chromatography and capillary electrophoresis, and can provide excellent sample clean-up effect and high degree of extraction recovery and enrichment. It is proved to be simple, low-cost and virtually solvent-free. The extraction set-up, extraction mode, basic principles and recent applications of the hollow fiber-based liquid-phase microextraction are reviewed.

Analytic Sample Preparation Methods↗
PubMed1985

The influence of tissue treatment on brain Na+, K+-ATPase activity and its response to vanadate inhibition.

This study has compared the effect of freezing in situ and decapitation without freezing on the Na+,K+-ATPase activity in mouse cerebral cortex homogenates under otherwise comparable conditions. The Na+,K+-ATPase activity was substantially influenced by the sample preparation; a twofold value was obtained for frozen samples as compared to that in fresh samples. Not only basal activity, but also the sensitivity of the enzyme towards vanadate inhibition depended on tissue treatment; lesser inhibition was observed in frozen samples. These findings suggest the possible implication of altered enzyme characteristics due to sample preparation while studying the influence of various other factors on enzyme activity.

Animals↗
PubMed2000

Time-weighted average sampling of volatile and semi-volatile airborne organic compounds by the solid-phase microextraction device.

The ultimate goal of the chemist is to perform sample preparation, and analysis, if possible at the place where a sample is located rather than moving the sample to laboratory, as is common practice in many cases at the present time. This approach eliminates errors and time associated with sample transport and storage and therefore it would result in more accurate, precise and faster analytical data. In addition to portability, two other important features of ideal field sample preparation technique are elimination of solvent use and integration with a sampling step. A method is developed which addresses these requirements for the determination of time-weighted average concentration of gas phase compounds using a solid-phase microextraction device. Quantification of target analytes in air using this method can be carried out without external calibration. The volatile and semi-volatile organic compounds in air diffuse into the fiber coating which is retracted a known distance into its needle housing during the sampling period. The coatings used are poly(dimethylsiloxane) and poly(dimethylsiloxane)-divinylbenzene. The sampling rate at which gas phase analytes load onto the fiber is determined for a wide range of hydrocarbons. There is a good agreement between the theoretical and experimental sampling rates. Sampling time ranges from 1 min to 24 h depending on the coating used and its retraction distance. Effect of the flow-rate on the uptake rate by the fiber is studied. The method is tested in the field and compared with National Institute of Occupational Health and Safety Method 1550. Good agreement between the results is obtained.

Chromatography↗