Impact Of Sample Preparation Research Articles

Recovery rates of selected body odor substances in different textiles applying various work-up and storage conditions measured by gas chromatography-mass spectrometry

BackgroundBody odor is an important aspect in interpersonal communication. For psychological and chemical research on body odors, suitable procedures for sampling and application, and analysis of body odors are essential. In this study, different textile fabrics (polyester, cotton, and Gazin gauze) were comparatively evaluated in view of their potential suitability for body odor sampling by determining recovery rates of selected body odor substances. In addition, the impact of sample preparation and storage conditions on the recovery rates was determined. ResultsThe recovery rates of dimethyl disulfide, (E)-non-2-enal, 5α-androst-16-en-3-one, 6-methylhept-5-en-2-one, heptanal and 3-sulfanylhexan-1-ol were determined under different conditions of storage (storage for 30 min at room temperature or storage for 30 min at room temperature followed by freezing at – 80 °C for 4 weeks) and sample work-up (solvent extraction with and without solvent-assisted flavour evaporation, in the following: SAFE). SAFE led to overall lower recovery rates with a significant effect for (E)-non-2-enal and 5α-androst-16-en-3-one. Nevertheless, the results showed that SAFE can be an essential step when working with a complex matrix. When comparing the different fabrics, except for (E)-non-2-enal no difference between the recovery rates obtained for cotton and polyester became evident. Gazin gauze showed lower recovery rates for all compounds. Finally, our results showed that the here investigated target compounds are stable during storage for four weeks at – 80 °C. Significance and NoveltyThe results show on the one hand that the here investigated compounds were stable during storage and that the fiber type had limited influence on overall recovery rates. On the other hand, they highlight the limitations of using textile materials for sampling of volatile substances, especially with regard to low recovery rates for certain substances and the necessity of material pre-treatment or distillation steps for enabling GC-MS analysis after solvent extraction.

Drained deformation characteristics of granular soil under pure principal stress axis rotation: impact of sample preparation

The distinct initial fabrics of sand may give rise to dramatically different responses to the applied loading, as evidenced by numerous laboratory tests reported in the literature. In this study, both dry deposition (DD) and moist tamping (MT) methods were employed to prepare sand specimens to generate different initial fabrics. Drained tests were conducted on these specimens under pure principal stress axis rotation while keeping the principal stress components constant. The factors that may influence the deformation characteristics of sand, such as deviatoric stress q, coefficient of intermediate principal stress b, and mean principal stress p, were also taken into consideration in the tests. Test results show that the developments of three normal strain components with number of cycles are very different between DD and MT specimens, which is also closely related to the factors of q, b, and p. It is seen that DD specimen tends to generate larger contractive volumetric strains than MT specimen, which is more significant when q and b increase or p decreases. The shear stiffness of DD specimen is greater than that of MT specimen. The shear modulus ratio, Gj/G1, increases with the increase of q and b or the decrease of p, which is more prominent in DD specimen than in MT specimen. It is also shown that DD specimen appears to exhibit stronger non-coaxiality than MT specimen, in which such difference of non-coaxiality tends to decrease with the increase in number of cycles.

Study on Molecular Profiles of Staphylococcus aureus Strains: Spectrometric Approach.

Staphylococcus aureus remains a major health problem responsible for many epidemic outbreaks. Therefore, the development of efficient and rapid methods for studying molecular profiles of S. aureus strains for its further typing is in high demand. Among many techniques, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI TOF MS) represents a timely, cost-effective, and reliable strain typing approach, which is still rarely used due to insufficient knowledge about the impact of sample preparation and analysis conditions on the molecular profiles and strain classification efficiency of S. aureus. The aim of this study was to evaluate the effect of the culture conditions and matrix type on the differentiation of molecular profiles of various S. aureus strains via the MALDI TOF MS analysis and different computational methods. The analysis revealed that by changing the culture conditions, matrix type, as well as a statistical method, the differentiation of S. aureus strains can be significantly improved. Therefore, to accelerate the incorporation of the MALDI-based strain typing in routine laboratories, further studies on the standardization and searching of optimal conditions on a larger number of isolates and bacterial species are of great need.

Influence of forage particle size and residual moisture on near infrared reflectance spectroscopy (NIRS) calibration accuracy for macro-mineral determination

Near infrared reflectance spectroscopy (NIRS) is routinely used for the determination of nutrient components of forages. However, little is known about the impact of sample preparation on the accuracy of the calibration to predict minerals. Three types of forages, hay (n = 117), grass (n = 109) and haylage (n = 119) were used to determine the impact of different sample preparation procedures: particle size (1.0 mm and 0.5 mm) and presence or absence of residual moisture (dried and re-dried) on resultant NIRS prediction statistics. All forages were scanned using a total of four combinations of sample pre-treatments (1 mm dried, 1 mm re-dried, 0.5 mm dried and 0.5 mm re-dried). Each sample preparation combination was subjected to spectra pre-processing methods such as standard normal variate (SNV), detrending (DT), combination of SNV and DT (SNV&DT) and None (log1/R) together with mathematical treatments (1,4,4,1; 2,4,4,1; 2,6,4,1; 3,5,5,1 and 2,4,4,2). Reduction of particle size from 1 mm to 0.5 mm slightly improved calibration statistics for the prediction of macro-minerals in hay and haylage samples. However, for the grass samples, improved calibration statistics was observed at a particle size of 1 mm for most of the minerals studied. Furthermore, the removal of residual moisture through additional oven drying improved calibration statistics for all minerals examined in the hay, haylage and grass samples. These results highlight the importance of the reduction in particle sizes for the improvement of calibration statistics for the determination of macro-minerals. In addition, re-drying of samples will improve calibration statistics for macro-minerals at particle sizes of 1 mm and/or 0.5 mm.

Investigating the Impact of Sample Preparation on Mass Spectrometry-Based Drug-To-Antibody Ratio Determination for Cysteine- and Lysine-Linked Antibody-Drug Conjugates.

Antibody–drug conjugates (ADCs) are heterogeneous biotherapeutics and differ vastly in their physicochemical properties depending on their design. The number of small drug molecules covalently attached to each antibody molecule is commonly referred to as the drug-to-antibody ratio (DAR). Established analytical protocols for mass spectrometry (MS)-investigation of antibodies and ADCs often require sample treatment such as desalting or interchain disulfide bond reduction prior to analysis. Herein, the impact of the desalting and reduction steps—as well as the sample concentration and elapsed time between synthesis and analysis of DAR-values (as acquired by reversed phase liquid chromatography MS (RPLC–MS))—was investigated. It was found that the apparent DAR-values could fluctuate by up to 0.6 DAR units due to changes in the sample preparation workflow. For methods involving disulfide reduction by means of dithiothreitol (DTT), an acidic quench is recommended in order to increase DAR reliability. Furthermore, the addition of a desalting step was shown to benefit the ionization efficiencies in RPLC–MS. Finally, in the case of delayed analyses, samples can be stored at four degrees Celsius for up to one week but are better stored at −20 °C for longer periods of time. In conclusion, the results demonstrate that commonly used sample preparation procedures and storage conditions themselves may impact MS-derived DAR-values, which should be taken into account when evaluating analytical procedures.

Transmembrane protein western blotting: Impact of sample preparation on detection of SLC11A2 (DMT1) and SLC40A1 (ferroportin).

Western blotting has been widely used for investigation of protein expression, posttranslational modifications, and interactions. Because western blotting usually involves heat-denaturation of samples prior to gel loading, clarification of detailed procedures for sample preparation have been omitted or neglected in many publications. We show here the case that even excellent primary antibodies failed to detect a specific protein of interest due to a routine heating practice of protein samples. We performed western blotting for transmembrane iron transporter proteins; SLC11A2 (divalent metal transporter 1, DMT1), SLC40A1 (ferroportin 1, Fpn1), and transferrin receptor-1 (TfR1), along with cytoplasmic iron storage protein ferritin H. Our results in 12 human culture cell lysates indicated that only unheated samples prior to gel loading gave rise to clear resolution of DMT1 protein, while heated samples (95°C, 5min) caused the loss of resolution due to DMT1 protein aggregates. Unheated samples also resulted in better resolution for Fpn1 and TfR1 western blots. Conversely, only heated samples allowed to detect ferritin H, otherwise ferritin polymers failed to get into the gel. Neither different lysis/sample loading buffers nor sonication improved the resolution of DMT1 and Fpn1 western blots. Thus, heating samples most critically affected the outcome of western blotting, suggesting the similar cases for thousands of other transmembrane and heat-sensitive proteins.

Considerations on the Laboratory Measurement of the Basic Friction Angle of Planar Rock Surfaces/Effect of Testing Methods and Surface Polishing

Over last decades, basic friction angle has been considered as one of the essential components of the developed criteria for shear strength of rock joints and thus an important input parameter in numerical modeling of the rock mass. This parameter is either measured by tilt test or by direct shear test on flat surfaces that are mostly saw-cut. While this parameter has been used in the proposed rock shear strength criteria as a constant rock property, researchers have reported a wide range for it. In this paper, the substantial impact of sample preparation and surface polishing on the obtained results of basic friction angle was shown by tilt and saw-cut tests (two common methods for evaluation the basic friction angle with two different levels of normal stresses) on two types of limestone. The results showed, based on the surface polishing, the basic friction angle measured by tilt test is approximately 10 degrees greater than the one measured by the direct shear test. Also, the results displayed that the range of variations of the basic friction angles of the tilt tests was more than the shear test results. Combining the results of this study with the other published works showed that the basic friction angle was found to vary with different factors, instead of being unique and constant.

The impact of sample preparation on the elemental composition of soft tissues assessed by laser ablation ICP-MS

Oven drying and freeze drying may alter the elemental composition of soft tissues subjected to LA-ICP-MS or ICP-MS analysis.

Impact of sample preparation on holographic imaging of leukocytes

The label-free analysis of leukocytes by holographic microscopy has the potential to overcome the extensive labeling procedures of conventional analysis by automated hematology analyzers and manual blood smear analysis. For the enrichment of leukocytes, selective lysis of erythrocytes is applied in flow cytometry to minimize the background. In the case of quantitative phase measurements, lysis procedures may affect the morphology of leukocytes inducing refractive index changes, which can deteriorate the specificity and sensitivity of the method. To study the effects of selective erythrocyte lysis on phase measurements of leukocytes, we compared two widespread methods: lysis by hypotonic shock followed by magnetic depletion of erythrocytes and lysis with a commercial lysis buffer containing ammonium chloride and potassium bicarbonate. We observed that lymphocytes were less affected than granulocytes and monocytes by both methods and that the intracellular changes increased with increasing incubation times. These findings indicate a significant effect of erythrocyte lysis on leukocytes and need to be studied for future hematology applications.

Identifying Challenges and Risks Associated with the Analysis of Major Mycotoxins in Feed and Botanicals

Abstract Changing weather conditions have heightened the risk of growth of mycotoxigenic molds on crops and various agricultural commodities. Mycotoxins, which are linked to carcinogenic and nephrotoxic effects in animals and humans, have been traditionally analyzed by immunoassays, gas, and LC techniques with spectrophotometric detectors. This review discusses the current techniques and challenges in commercial settings associated with the analysis of mycotoxins in unique matrices such as animal feeds, herbal products, and dietary supplements containing botanicals. Because of the advantages and growing acceptance of LC-tandem MS (MS/MS) over traditional approaches, discussion is mainly based on LC-MS/MS-based approaches. Considering the impact of sample preparation on accuracy of quantitative results, discussion about pros and cons of recently introduced sample preparation techniques is integrated with analytical methods. A section of the review explains the importance and availability of reference materials for mycotoxins. The present discussion provides good insight into the current challenges and developments during mycotoxin analysis of feed and botanicals and addresses the need for researchers in terms of an official MS-based method.

The importance of drying and grinding samples for determining mobile chromium fractions in polluted river sediments

A possible impact of sample preparation on the chemical fractionation results is generally underestimated in studies of forms of occurrence of heavy metals in river sediments. Our analysis of the recently published results of sequential extraction of chromium has revealed the effect of sample grinding on the result of determination of mobile chromium fractions in river sediments. This observation has been experimentally verified along with the analysation of potential effect of river sediment drying conditions on chromium distribution pattern. The studies were carried out on river sediments polluted with tannery effluents (Cr, 29.2–233 mg/kg). The determined content of chromium bound to carbonates in powdered samples was 2 to 7 times higher than those in raw river sediment samples. It was shown that the main reason was the different kinetic characteristics of chromium leaching in these sediments. Using the shrinking core model, it was found that diffusion through the “ash layer” was the rate-controlling step during the extraction of the carbonate fraction of chromium. It has been additionally confirmed that common air drying of sediment samples does not affect the results of chemical fractionation of chromium.The results of our studies are also vital for the assessment of environmental risk posed by river sediments polluted with heavy metals. In the case of sediment samples used in this study, powdering changed the risk category (RAC) from low risk to high risk. Hence, in order to achieve a realistic assessment of chromium mobility and environmental risk, it is advisable to use raw samples, despite their poorer homogeneity, and thus, lower precision of chemical fractionation results.

Identifying Challenges and Risks Associated with the Analysis of Major Mycotoxins in Feed and Botanicals.

Changing weather conditions have heightened the risk of growth of mycotoxigenic molds on crops and various agricultural commodities. Mycotoxins, which are linked to carcinogenic and nephrotoxic effects in animals and humans, have been traditionally analyzed by immunoassays, gas, and LC techniques with spectrophotometric detectors. This review discusses the current techniques and challenges in commercial settings associated with the analysis of mycotoxins in unique matrices such as animal feeds, herbal products, and dietary supplements containing botanicals. Because of the advantages and growing acceptance of LC-tandem MS (MS/MS) over traditional approaches, discussion is mainly based on LC-MS/MS-based approaches. Considering the impact of sample preparation on accuracy of quantitative results, discussion about pros and cons of recently introduced sample preparation techniques is integrated with analytical methods. A section of the review explains the importance and availability of reference materials for mycotoxins. The present discussion provides good insight into the current challenges and developments during mycotoxin analysis of feed and botanicals and addresses the need for researchers in terms of an official MS-based method.

Impact of sample preparation upon intracellular metabolite measurements in 3D cell culture systems

IntroductionInterest in cell culture metabolomics has increased greatly in recent years because of its many potential applications and advantages (e.g., in toxicology). The first critical step for exploring the cellular metabolome is sample preparation. For metabolomics studies, an ideal sample preparation would extract a maximum number of metabolites and would enable reproducible, accurate analysis of a large number of samples and replicates. In addition, it would provide consistent results across several studies over a relatively long time frame.ObjectivesThis study was conducted to evaluate the impact of sample preparation strategies on monitoring intracellular metabolite responses, highlighting the potential critical step(s) in order to finally improve the quality of metabolomics studies.MethodsThe sample preparation strategies were evaluated by calculating the sample preparation effect, matrix factor, and process efficiency (PE) for 16 tobacco exposition-related metabolites, including nicotine, nicotine-derived nitrosamine ketone, their major metabolites, and glutathione, using isotopically-labelled internal standards. Samples were analyzed by liquid chromatography (LC) coupled to high-resolution mass spectrometry (HRMS).ResultsA sample drying step increased losses or variability for some selected metabolites. By avoiding evaporation, good sample preparation recovery was obtained for these compounds. For some metabolites, the cell or culture type impacted PE and matrix factor.ConclusionIn our sample preparation protocol, the drying–reconstitution step was identified as the main cause of metabolite losses or increased data variability during metabolomics analysis by LC-HRMS. Furthermore, PE was affected by the type of matrix. Isotopologue internal standards fully compensate losses or enhancements.

(Un)targeted hair metabolomics: first considerations and systematic evaluation on the impact of sample preparation.

The interest in metabolomic studies has rapidly increased over the past few years. Changes of endogenous compounds are typically detected in plasma or urine. However, the use of hair allows for long-term monitoring of metabolomic changes and has recently started being applied to metabolomic studies. Within the proposed study, we aimed for a systematical investigation of different pre-analytical parameters on detected metabolites from different chemical classes in hair. For this purpose, three different parameters were varied: (1) multi-step decontamination (dichloromethane (DCM), acetone, H2O, acetone; H2O, acetone, DCM, acetone; and H2O, methanol/acetone), (2) homogenization (pulverization vs. cutting into snippets), and (3) extraction (acetonitrile (ACN)/buffer pH4 vs. ACN/H2O vs. ACN/buffer pH8.5). To include as many metabolites as possible, samples were analyzed by high-resolution time of flight mass spectrometry coupled to liquid chromatography (HPLC-HRMS) and additionally by gas chromatography high-resolution mass spectrometry (GC-HRMS) followed by untargeted-like data processing, respectively. The application of different decontamination procedures yielded similar results, although pointing to a trend towards increased washing-out effects if protic solvents were used as a first washing step. Pulverization of hair samples was favorable in terms of detected and tentatively identified metabolites. Evaluation of extraction solvents showed differences in extraction yield for the majority of investigated metabolites, yet, a prediction of metabolite extraction according to their pKa values was not possible. Overall, successive decontamination with DCM, acetone, H2O, and acetone; homogenization by pulverization; and extraction with ACN/H2O produced reliable results. Graphical abstract.

Piloting and implementation of quality assessment and quality control procedures in RBC-Omics: a large multi-center study of red blood cell hemolysis during storage.

The major aims of the RBC-Omics study were to evaluate the genomic and metabolomic determinants of spontaneous and stress-induced hemolysis during RBC storage. This study was unique in scale and design to allow evaluation of RBC donations from a sufficient number of donors across the spectrum of race, ethnicity, sex, and donation intensity. Study procedures were carefully piloted, optimized, and controlled to enable high-quality data collection. The enrollment goal of 14,000 RBC donors across four centers, with characterization of RBC hemolysis across two testing laboratories, required rigorous piloting and optimization and establishment of a quality assurance (QA) and quality control (QC) program. Optimization of WBC elution from leukoreduction (LR) filters, development and validation of small-volume transfer bags, impact of manufacturing and sample-handling procedures on hemolysis parameters, and testing consistency across laboratories and technicians and over time were part of this quality assurance/quality control program. LR filter elution procedures were optimized for obtaining DNA for analysis. Significant differences between standard and pediatric storage bags led to use of an alternative LR-RBC transfer bag. The impact of sample preparation and freezing methods on metabolomics analyses was evaluated. Proficiency testing monitored and documented testing consistency across laboratories and technicians. Piloting and optimization, and establishment of a robust quality assurance/quality control program documented process consistency throughout the study and was essential in executing this large-scale multicenter study. This program supports the validity of the RBC-Omics study results and a sample repository that can be used in future studies.

Drained responses of granular soil sheared under inclined principal stress axes: Impact of sample preparation

Previous studies have found that the sample preparation method and the resulting sand fabric have significant effect on sand behavior. In the present study, sand specimens were prepared in the laboratory by dry deposition (DD) method and moist tamping (MT) method to create two distinct initial fabrics of sand. Drained hollow cylinder tests were carried out on these specimens under fixed but inclined principal stress axes. Test results show that the major principal stress direction has greater influence on the development of both deviatoric and volumetric strains for DD samples than for MT. DD samples tend to have a higher stress ratio R corresponding to the characteristic state point than MT series. Moreover, the shear strength of DD samples is higher than MT, but significantly influenced by the major principal stress direction. DD samples show stronger non-coaxiality than MT samples under low stress ratio (R ≤ 0.1).

Robust measurements of electric conductivity in polyethylene based materials: measurement setup, data processing and impact of sample preparation

In this work, a measurement setup and an algorithm are introduced that allow for obtaining and processing the current data during standard measurements of electric conductivity in polymeric insulation materials. Robustness of this setup is demonstrated through dc conductivity measurements of low density polyethylene (LDPE) specimens that were prepared by two different techniques, i.e. compression molding and extrusion, at two independent laboratories (at Chalmers and KTH) from the same raw pellets. The results resented in this paper reveal that the implemented data processing algorithm allows for clear separation of the conduction current level and the external noise and thus for good differentiation between the conductivity levels in the investigated material specimens. In addition, a high reproducibility of the results is obtained for the independently manufactured specimens, suggesting the proposed measurement technique is well suitable for characterization of low conducting dielectrics.

High-Resolution Mass Spectrometry as a Tool To Evaluate the Sample Preparation of Sludge.

This study explored the sample preparation steps based on QuEChERS (quick, easy, cheap, effective, rugged, and safe) of a complex matrix, such as sewage sludge, regarding their impacts on the chemical signatures of the samples obtained via high-resolution mass spectrometry (HRMS). The effects on the HRMS signal of the intrinsic parameters of the QuEChERS method, such as the extraction solvent, the buffer salt, or the purification procedure, have been evaluated. Different strategies have been used to perform these evaluations, such as a comparison of the total number of HRMS signals, a comparison of the targeted screening based on more than 100 compounds, and a comparison of a nontargeted screening based both on the study of the most discriminating couples [mass-to-charge ratio (m/z); retention time (tR)] and on the most intense peaks. Moreover, two specific methods dedicated to the extraction of surfactants and drugs have been added to this comparison to visualize the impact of specific conditions on the chemical signature. This study provides the first information on the impact of sample preparation on the HRMS analysis of sludge. It shows that acetonitrile is the most effective solvent for obtaining maximum information from sewage sludge. The comparison of the different cleanup procedures emphasizes the significance of this step and demonstrates the connection between the intrinsic physicochemical properties of molecules and the operating conditions of the extraction, particularly the pH. Moreover, the study highlights that surfactants, i.e., quaternary ammoniums in the positive ionization mode and linear alkylbenzene sulfonates in the negative mode, are the most discriminating compounds.

Impact of sample preparation on physical quantification of filling fats and oils in fresh and stored chocolate

Filling fat and oil migration in filled chocolate products often cause quality loss, such as fat bloom or changes in texture. Therefore, and due to legal restrictions, the detection and quantification of filling fats and oils in chocolate is of interest. Common methods are fatty acid or triacylglycerol (TAG) analysis by GC or HPLC. Additionally, NMR and DSC are used to evaluate migration especially in stored products. Using DSC, the melting and crystallization peak of a filling oil can be detected directly, while NMR turns the reduction of solid fat content (SFC) caused by filling fats and oils to account. However, fat and oil migration is not the only effect during storage, which might affect NMR and DSC measurements. Post‐crystallization is also of interest. Therefore, DSC and NMR methods were used to observe and to evaluate the detectable amount over time. Dark chocolate was mixed with hazelnut oil, butterfat, and coconut oil. Samples were stored and analyzed using NMR and DSC. Additionally, methods to destroy thermal history of the sample were investigated. We found that post‐crystallization, which occurs during the first 2 wk after production, has a major impact on detectability of filling fats and oils using physical methods. However, standardized sample preparation was successfully applied and amounts below 1 g per 100 g sample were detectable and amounts above 1–2 g were quantifiable with slender time and effort.Practical applications: Filling fat and oil migration during production and storage is a major problem with regards to product stability and shelf life. Especially filling migration during storage is reported to be an activator for fat bloom formation. Physical methods are a cost and time efficient way to control and adjust processing. Our results report sample preparation techniques to detect filling fats and oils in fresh and stored chocolate. This provides the possibility of large scale storage tests with focus on fat and oil migration.Fresh and stored dark chocolate was analyzed with regards to filling fat content using DSC and NMR. Impact of sample preparation on decision and determination limit was evaluated.

Impact of sample preparation on the specific surface area of synthetic ettringite

The effect of sample preparation, including degassing conditions and method to stop cement hydration, on the specific surface area (SSABET) of synthetic ettringite (AFt) was studied. Dehydration of AFt occurs even at moderate temperatures under N2 flow (0% RH). However, partial dehydration associated to a loss of up to 12 water molecules does not imply a change in SSABET. A mild degassing 16h at 40°C under N2 flow is suggested mainly to preserve the chemical composition and morphology of calcium sulfate carrier. At higher temperatures, ettringite dehydration involves a significant modification of its crystalline structure and increase of the SSABET. Typical protocols to stop cement hydration, solvent exchange and freeze-drying, lead to larger water removal from the AFt and crystallinity reduction, being significantly higher when the latter is applied. However, only freeze-drying leads to a moderate increase of the synthetic AFt SSABET.