Optimization of mRNA extraction from human nasal mucosa biopsies for gene expression profile analysis by qRT-PCR

Quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) is the gold-standard method for analyzing modifications in gene expression in cells and tissues. However, large quantities of high-quality RNA samples are needed for analyzing the expression of multiple genes from one human tissue sample. Here, we provide an optimized protocol for extracting large amounts of RNA from human nasal mucosal biopsies. The quality and quantity of samples were sufficient for qRT-PCR analyses of the expressions of various genes, in duplicate. In contrast to other protocols, we optimized RNA isolation to increase the amount from nasal biopsy samples for analyses of multiple genes. In most previous publications, expressions of only one or a few genes, including housekeeping genes, were analyzed because the amount of biological material was small. We were able to improve our protocol with respect to the yield and quality of RNA. This is likely to produce better results from molecular analyses of very small biopsy samples of human nasal mucosa.

Increasing the coverage of the N-terminome with LysN amino terminal enrichment (LATE)

The field of N-terminomics has been advancing with the development of novel methods that provide a comprehensive and unbiased view of the N-terminome. Negative selection N-terminomics enables the identification of free and naturally modified protein N-termini. Here, we present a streamlined protocol that combines two negative selection N-terminomics methods, LATE and HYTANE, to increase N-terminome coverage by 1.5-fold compared to using a single methodology. Our protocol includes sample preparation and data analysis of both methods and can be applied to studying the N-terminome of diverse samples. The suggested approach enables researchers to achieve a more detailed and accurate understanding of the N-terminome.

GdClean: removal of Gadolinium contamination in mass cytometry data

MOTIVATION

Mass cytometry (Cytometry by Time-Of-Flight, CyTOF) is a single-cell technology that is able to quantify multiplex biomarker expressions and is commonly used in basic life science and translational research. However, the widely used Gadolinium (Gd)-based contrast agents (GBCAs) in magnetic resonance imaging (MRI) scanning in clinical practice can lead to signal contamination on the Gd channels in the CyTOF analysis. This Gd contamination greatly affects the characterization of the real signal from Gd-isotope-conjugated antibodies, severely impairing the CyTOF data quality and ruining downstream single-cell data interpretation.

RESULTS

We first in-depth characterized the signals of Gd isotopes from a control sample that was not stained with Gd-labeled antibodies but was contaminated by Gd isotopes from GBCAs, and revealed the collinear intensity relationship across Gd contamination signals. We also found that the intensity ratios of detected Gd contamination signals to the reference Gd signal were highly correlated with the natural abundance ratios of corresponding Gd isotopes. We then developed a computational method named by GdClean to remove the Gd contamination signal at the single-cell level in the CyTOF data. We further demonstrated that the GdClean effectively cleaned up the Gd contamination signal while preserving the real Gd-labeled antibodies signal in Gd channels. All of these shed lights on the promising applications of the GdClean method in preprocessing CyTOF datasets for revealing the true single-cell information.

AVAILABILITY AND IMPLEMENTATION

The R package GdClean is available on GitHub at https://github.com/JunweiLiu0208/GdClean.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Challenges in sample preparation and structure determination of amyloids by cryo-EM

Amyloids share a common architecture but play disparate biological roles in processes ranging from bacterial defense mechanisms to protein misfolding diseases. Their structures are highly polymorphic, which makes them difficult to study by X-ray diffraction or NMR spectroscopy. Our understanding of amyloid structures is due in large part to recent advances in the field of cryo-EM, which allows for determining the polymorphs separately. In this review, we highlight the main stepping stones leading to the substantial number of high-resolution amyloid fibril structures known today as well as recent developments regarding automation and software in cryo-EM. We discuss that sample preparation should move closer to physiological conditions to understand how amyloid aggregation and disease are linked. We further highlight new approaches to address heterogeneity and polymorphism of amyloid fibrils in EM image processing and give an outlook to the upcoming challenges in researching the structural biology of amyloids.

Sample Preparation of Secreted Mammalian Host Cell Proteins and Their Characterization by Two-Dimensional Electrophoresis and Western Blotting

The manufacturing and purification of therapeutic recombinant proteins expressed by cultivated mammalian cells into the cell culture medium leaves the potential for contamination by host cell proteins (HCPs). Validation and quality control testing of any therapeutic protein needs to include a test to show that HCP contamination is at a minimal level. The presence of residual mammalian HCPs during purification and in the final drug product is typically determined using enzyme linked immunosorbent assay (ELISA), which is regarded as the gold standard. The complexity and heterogeneity of HCPs, which include proteins with significant differences in molecular weight (MW), isoelectric point (pI) and hydrophobicity, poses a challenge to detection and quantitation. Two-dimensional gel electrophoresis (2-DE) is one of the most powerful technologies for studying complex protein profiles and is a valuable analytical method in biologics manufacturing. In the purification process, it is very important to know the nature and composition of HCPs, and this information can be used in a rational process design in order to minimize HCPs from the product. Additionally, 2-DE in combination with western blotting can support ELISA development and quality control for the comprehensive immunochemical detection of HCPs by estimating the recognition capacity of the polyclonal serum used in those assays. Here, we present a standardized 2-DE western blotting protocol which takes into account the latest developments in sample preparation of HCPs, protein electrophoresis, protein transfer, immunostaining, and imaging.

Bead-Based Multiplex Immunoassays: Procedures, Tips, and Tricks

Multiplex immunoassays enable the measurement of multiple proteins in a small volume of sample in a single well, enhancing discovery and profiling of multiple biomarkers when compared to singleplex immunoassays. In order to ensure optimal results are generated, it is important to know what critical actions and assay steps can adversely affect results. This chapter covers best practices for sample collection and storage, to important considerations during the assay run, and ways to ensure optimal data generation and efficient data analysis. When these practices are applied, the potential to generate actionable and quality results accelerates the research and discovery process.

Released N-Glycan Analysis for Biotherapeutic Development Using Liquid Chromatography and Mass Spectrometry

In this chapter, we describe an LC-fluorescence (FLR)/MS-based method for released N-glycan analysis in the development of biotherapeutic proteins. The method includes enzymatic release and labeling of N-glycans with a signal-enhancing tag, LC-MS data collection, and data interpretation. Using the given protocol, up to 24 glycan samples can be prepared within 1 h, while the LC-FLR/MS data can be collected and analyzed using an established data processing method in a semi-automated manner.

A Protocol for Isolation, Purification, Characterization, and Functional Dissection of Exosomes

Extracellular vesicles (EVs) are membrane-enclosed vesicles released by cells. They carry proteins, nucleic acids, and metabolites which can be transferred to a recipient cell, locally or at a distance, to elicit a functional response. Since their discovery over 30 years ago, the functional repertoire of EVs in both physiological (e.g., organ morphogenesis, embryo implantation) and pathological (e.g., cancer, neurodegeneration) conditions has cemented their crucial role in intercellular communication. Moreover, because the cargo encapsulated within circulating EVs remains protected from degradation, their diagnostic as well as therapeutic (such as drug delivery tool) applications have garnered vested interest. Global efforts have been made to purify EV subtypes from biological fluids and in vitro cell culture media using a variety of strategies and techniques, with a major focus on EVs of endocytic origin called exosomes (30-150 nm in size). Given that the secretome comprises of soluble secreted proteins, protein aggregates, RNA granules, and EV subtypes (such as exosomes, shed microvesicles, apoptotic bodies), it is imperative to purify exosomes to homogeneity if we are to perform biochemical and biophysical characterization and, importantly, functional dissection. Besides understanding the composition of EV subtypes, defining molecular bias of how they reprogram target cells also remains of paramount importance in this area of active research. Here, we outline a systematic "how to" protocol (along with useful insights/tips) to obtain highly purified exosomes and perform their biophysical and biochemical characterization. This protocol employs a mass spectrometry-based proteomics approach to characterize the protein composition of exosomes. We also provide insights on different isolation strategies and their usefulness in various downstream applications. We outline protocols for lipophilic labeling of exosomes to study uptake by a recipient cell, investigating cellular reprogramming using proteomics and studying functional response to exosomes in the Transwell-Matrigel™ Invasion assay.

Improved Immunoprecipitation to Mass Spectrometry Method for the Enrichment of Low-Abundant Protein Targets

Immunoprecipitation (IP) is commonly used upstream of mass spectrometry (MS) as an enrichment tool for low-abundant protein targets. However, several aspects of the classical IP procedure such as nonspecific protein binding to the isolation matrix, detergents or high salt concentrations in wash and elution buffers, and antibody chain contamination in elution fractions render it incompatible with downstream mass spectrometry analysis. Here, we discuss an improved IP-MS workflow that is designed to minimize sample prep time and these contaminants. The method employs biotinylated antibodies to the targets of interest and streptavidin magnetic beads that exhibit low background binding. In addition, alterations in the elution protocol and subsequent MS sample prep were made to reduce time and antibody leaching in the eluent, minimizing potential ion suppression effects and thereby maximizing detection of multiple target antigens and interacting proteins.

Non-chromatographic Speciation of As by HG Technique-Analysis of Samples with Different Matrices

The applicability of the hydride generation (HG) sample introduction technique combined with different spectrochemical detection methods for non-chromatographic speciation of toxic As species, i.e., As(III), As(V), dimethylarsinate (DMA) and monomethylarsonate (MMA), in waters and other environmental, food and biological matrices is presented as a promising tool to speciate As by obviating chromatographic separation. Different non-chromatographic procedures along with speciation protocols reported in the literature over the past 20 year are summarized. Basic rules ensuring species selective generation of the corresponding hydrides are presented in detail. Common strategies and alternative approaches are highlighted. Aspects of proper sample preparation before analysis and the selection of adequate strategies for speciation purposes are emphasized.

Investigations into the Effects of pH on Quantitative Measurements of Lactate in Biological Media Using ATR-FTIR Spectroscopy

Quantification of lactate/lactic acid in critical care environments is essential as lactate serves as an important biochemical marker for the adequacy of the haemodynamic circulation in shock and of cell respiration at the onset of sepsis/septic shock. Hence, in this study, ATR-FTIR was explored as a potential tool for lactate measurement, as the current techniques depend on sample preparation and fails to provide rapid response. Moreover, the effects of pH on PBS samples (7.4, 7, 6.5 and 6) and change in solution conditions (PBS to whole blood) on spectral features were also investigated. A total 189 spectra from five sets of lactate containing media were obtained. Results suggests that lactate could be measured with more than 90% accuracy in the wavenumber range of 1500–600 cm−1. The findings of this study further suggest that there exist no effects of change in pH or media, when estimating lactate concentration changes in this range of the Mid-IR spectral region.

Covalent Organic Frameworks in Sample Preparation

Covalent organic frameworks (COFs) can be classified as emerging porous crystalline polymers with extremely high porosity and surface area size, and good thermal stability. These properties have awakened the interests of many areas, opening new horizons of research and applications. In the Analytical Chemistry field, COFs have found an important application in sample preparation approaches since their inherent properties clearly match, in a good number of cases, with the ideal characteristics of any extraction or clean-up sorbent. The review article is meant to provide a detailed overview of the different COFs that have been used up to now for sample preparation (i.e., solid-phase extraction in its most relevant operational modes-conventional, dispersive, magnetic/solid-phase microextraction and stir-bar sorptive extraction); the extraction devices/formats in which they have been applied; and their performances and suitability for this task.

Biocompatible chitosan-zinc oxide nanocomposite based dispersive micro-solid phase extraction coupled with HPLC-UV for the determination of rosmarinic acid in the extracts of medical plants and water sample

In the present research, a procedure was described for the recovery of rosmarinic acid (RA) from medical extract samples using chitosan‑zinc oxide nanoparticles as a biocompatible nanocomposite (CS-ZnO-NC). The dispersive micro-solid phase extraction (D-μ-SPE) of RA from the medical extract samples was investigated by using the prepared biocompatible composite as a solid phase. The HPLC-UV method was used for measuring the extracted RA. The important variables (pH, biocompatible composite mass, contact time, and volume of eluent) associated with the extraction process were analyzed by the application of central composite design (CCD). The achieved optimum values for the mentioned variables were 7.0, 10 mg, 4 min, and 180 μL, respectively. The extraction recovery (99.68%) obtained from the predicted model was in agreement with the experimental data (98.22 ± 1.33%). In addition, under the obtained optimum conditions and over the concentration in the range of 2-3500 ng mL-1, a linear calibration curve was obtained with R2 > 0.993. The limit of detection (LOD) and quantification (LOQ) values were computed, and the obtained ranges were respectively from 0.060 to 0.089 ng mL-1 and 0.201 to 0.297 ng mL-1. In addition, the enrichment factors were obtained in the range of 93.7-110.5 with preconcentration factor of 83.3. Therefore, the D-μ-SPE-HPLC-UV method could be used for analyzing RA in the samples of the extracts obtained from the medical plants and water with the recovery values of the analyte in the range of 96.6%-105.4% and the precision with relative standard deviation <5.7%.

A novel approach to remove interference of therapeutic monoclonal antibody with serum protein electrophoresis

OBJECTIVES

Multiple myeloma (MM) is characterized by malignant growth of plasma cells, usually producing a monoclonal antibody (mAb). New treatments for MM include therapeutic monoclonal antibodies (tmAbs), but patients treated with tmAb demonstrate interference on serum electrophoresis (SPE) and immunoprecipitation electrophoresis (IEP). Evaluation of treatment efficacy and determination of MM remission include SPE and IEP which identifies mAb, but cannot differentiate between disease associated mAb and tmAb. We hypothesized that tmAb could be removed from patient sera before testing by SPE and IEP to provide accurate diagnoses for clinicians.

DESIGN AND METHODS

We developed the Antigen Specific therapeutic monoclonal Antibody Depletion Assay (ASADA), that utilizes magnetic beads coated with the cognate antigen of the tmAbs, to deplete two different tmAb (daratumumab, elotuzumab) from saline and patient sera and assessed for complete removal of tmAb by SPE and IEP.

RESULTS

We found that tmAb could be efficiently removed from saline and patient sera. ASADA demonstrated acceptable analytical specificity and sensitivity in IEP. Recovery of appropriate quantitative values by SPE was demonstrated with clinically acceptable precision. A single bead cocktail could be used to treat both daratumumab and elotuzumab.

CONCLUSIONS

This demonstrates proof of principle that ASADA can be used to remove current and future tmAb from patient sera, regardless of platform. This research provides for accurate diagnosis, disease monitoring, and remission status in MM patients being treated with tmAb.

Investigating pre-analytical requirements for serum and plasma based infrared spectro-diagnostic

Infrared spectroscopy is a rapid, easy-to-operate, label-free and therefore cost-effective technique. Many studies performed on biofluids (eg, serum, plasma, urine, sputum, bile and cerebrospinal fluid) have demonstrated its promising application as a clinical diagnostic tool. Given all these characteristics, infrared spectroscopy appears to be an ideal candidate to be implemented into the clinics. However, before considering its translation, a clear effort is needed to standardise protocols for biofluid spectroscopic analysis. To reach this goal, careful investigations to identify and track errors that can occur during the pre-analytical phase is a crucial step. Here, we report for the first time, results of investigations into pre-analytical factors that can affect the quality of the spectral data acquired on serum and plasma, such as the impact of long-term freezing time storage of samples as well as the month-to-month reproducibility of the spectroscopic analysis. The spectral data discrimination has revealed to be majorly impacted by a residual water content variation in serum and plasma dried samples.

High-throughput quantification of carboxymethyl lysine in serum and plasma using high-resolution accurate mass Orbitrap mass spectrometry

BACKGROUND

Carboxymethyl lysine is an advanced glycation end product of interest as a potential biomarker of cardiovascular and other diseases. Available methods involve ELISA, with potential interference, or isotope dilution mass spectrometry (IDMS), with low-throughput sample preparation.

METHODS

A high-throughput sample preparation method based on 96-well plates was developed. Protein-bound carboxymethyl lysine and lysine were quantified by IDMS using reversed phase chromatography coupled to a high-resolution accurate mass Orbitrap Exactive mass spectrometer. The carboxymethyl lysine concentration (normalized to lysine concentration) was measured in 1714 plasma samples from the British Regional Heart Study (BRHS).

RESULTS

For carboxymethyl lysine, the lower limit of quantification (LLOQ) was estimated at 0.16 μM and the assay was linear between 0.25 and 10 μM. For lysine, the LLOQ was estimated at 3.79 mM, and the assay was linear between 2.5 and 100 mM. The intra-assay coefficient of variation was 17.2% for carboxymethyl lysine, 9.3% for lysine and 10.5% for normalized carboxymethyl lysine. The inter-assay coefficient of variation was 18.1% for carboxymethyl lysine, 14.8 for lysine and 16.2% for normalized carboxymethyl lysine. The median and inter-quartile range of all study samples in each batch were monitored. A mean carboxymethyl lysine concentration of 2.7 μM (IQR 2.0-3.2 μM, range 0.2-17.4 μM) and a mean normalized carboxymethyl lysine concentration of 69 μM/M lysine (IQR 54-76 μM/M, range 19-453 μM/M) were measured in the BRHS.

CONCLUSION

This high-throughput sample preparation method makes it possible to analyse large cohorts required to determine the potential of carboxymethyl lysine as a biomarker.

Detection of the tuberculosis biomarker mannose-capped lipoarabinomannan in human serum: Impact of sample pretreatment with perchloric acid

The development of an accurate and rapid diagnostic test for tuberculosis (TB) to use at point of need is vital to efforts aimed at reducing the global burden from this disease. This paper builds on our previous studies of mannose-capped lipoarabinomannan (ManLAM) as a serum biomarker for active TB infection by means of a heterogeneous immunoassay. That work found that complexation with components in serum (e.g., proteins) sterically hindered the capture and/or labeling of ManLAM in an immunoassay at levels <10 ng mL-1, compromising the clinical utility of this biomarker for detection of active TB infection. We also showed that the acidification of ManLAM-containing serum samples with perchloric acid improved the detectability of ManLAM by 250× by complex disruption when compared to measurements of untreated serum. The present study examined what effects the PCA treatment of serum samples may have on the recovery and structural integrity of ManLAM, owing to its potential susceptibility to acid hydrolysis. Recovery was assessed with an enzyme-linked immunosorbent assay (ELISA). The possible impact of acid hydrolysis on the ManLAM structure was investigated by gas chromatography-mass spectrometry and carbohydrate chemical degradation methods. The ELISA study indicated that while the signal strength for ManLAM in the serum spike-in experiments was significantly stronger after PCA pretreatment when compared to untreated human serum, it was only ∼20% of the ManLAM measured in physiological buffer. This loss in detectability was shown by structural analysis to arise mainly from the acid-induced degradation of the arabinan domains of ManLAM that are targeted by antibodies used for antigen capture and/or tagging. The implications of these findings in terms of the detection of this important biomarker for TB are also discussed.

Versatile exclusion-based sample preparation platform for integrated rare cell isolation and analyte extraction

Rare cell populations provide a patient-centric tool to monitor disease treatment, response, and resistance. However, understanding rare cells is a complex problem, which requires cell isolation/purification and downstream molecular interrogation - processes challenged by non-target populations, which vary patient-to-patient and change with disease. As such, cell isolation platforms must be amenable to a range of sample types while maintaining high efficiency and purity. The multiplexed technology for automated extraction (mTAE) is a versatile magnetic bead-based isolation platform that facilitates positive, negative, and combinatorial selection with integrated protein staining and nucleic acid isolation. mTAE is validated by isolating circulating tumor cells (CTCs) - a model rare cell population - from breast and prostate cancer patient samples. Negative selection yielded high efficiency capture of CTCs while positive selection yielded higher purity with an average of only 95 contaminant cells captured per milliliter of processed whole blood. With combinatorial selection, an overall increase in capture efficiency was observed, highlighting the potential significance of integrating multiple capture approaches on a single platform. Following capture (and staining), on platform nucleic acid extraction enabled the detection of androgen receptor-related transcripts from CTCs isolated from prostate cancer patients. The flexibility (e.g. negative, positive, combinatorial selection) and capabilities (e.g. isolation, protein staining, and nucleic acid extraction) of mTAE enable users to freely interrogate specific cell populations, a capability required to understand the potential of emerging rare cell populations and readily adapt to the heterogeneity presented across clinical samples.

Detection of Glyphosate in Drinking Water: A Fast and Direct Detection Method without Sample Pretreatment

Glyphosate (Gly) is one of the most problematic pesticides that repeatedly appears in drinking water. Continuous on-site detection of Gly in water supplies can provide an early warning in incidents of contamination, before the pesticide reaches the drinking water. Here, we report the first direct detection of Gly in tap water with electrochemical sensing. Gold working electrodes were used to detect the pesticide in spiked tap water without any supporting electrolyte, sample pretreatment or electrode modifications. Amperometric measurements were used to quantify Gly to a limit of detection of 2 μM, which is below the regulation limit of permitted contamination of drinking water in the United States. The quantification of Gly was linearly proportional with the measured signal. The selectivity of this method was evaluated by applying the same technique on a Gly Metabolite, AMPA, and on another pesticide, omethoate, with a chemical structure similar to Gly. The testing revealed no interfering electrochemical activity at the potential range used for Gly detection. The simple detection of Gly presented in this work may lead to direct on-site monitoring of Gly contamination at drinking water sources.

Validated UPLC-MS/MS method for the quantification of dasatinib in plasma: Application to pharmacokinetic interaction studies with nutraceuticals in Wistar rats

Dasatinib (DAS) is a tyrosine kinase inhibitor (TKI) used in the treatment of chronic myeloid leukemia and in the management of ulcerative colitis (UC). Since some nutraceuticals (e.g. curcumin, olive oil, and cocoa extract) could alter the function of ABC transporters and /or CYP450 enzymes, DAS bioavailability could potentially be affected following their co-administration. This work aims at studying the possibility of PK interaction between DAS and the selected nutraceuticals in UC rats using UPLC- MS/MS. Chromatographic analysis was carried out using BEH C 18 column (Waters) with a mobile phase consisting of acetonitrile and 50% aqueous methanol, 65:35, v/v, each with 0.1% formic acid and using erlotinib (ERL) as an internal standard (IS). DAS quantitation was carried out using multiple reaction monitoring (MRM) with positive ionization of the transitions at m/z 488.03 > 400.92 (DAS), and m/z 394.29 > 278.19 (ERL). Method validation was assessed as per the FDA guidelines for bioanalytical methods for DAS determination within the concentration range 1–500 ng/mL. No significant effect on the oral bioavailability of DAS was reported with any of the studied nutraceuticals. Thus, the concomitant administration of these nutraceuticals with DAS could be considered safe with a necessity to perform more detailed clinical investigations.

Rapid and safe one-step extraction method for the identification of Brucella strains at genus and species level by MALDI-TOF mass spectrometry

Brucellosis is essentially a disease of domesticated livestock; however, humans can also be infected via the consumption of contaminated meat or dairy products, underlying the need for rapid and accurate identification methods. Procedures for microbiological identification and typing of Brucella spp. are expensive, time-consuming, and must be conducted in biohazard containment facilities to minimize operator risk. The development of a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS)-based assay has reduced the processing time while maintaining performance standards. In this study, to improve the identification accuracy and suitability of the MALDI-TOF-based assay for routine diagnosis, we developed a new protein extraction protocol and generated a custom reference database containing Brucella strains representative of the most widespread species. The reference library was then challenged with blind-coded field samples isolated from infected animals. The results indicated that the database could be used to correctly identify 99.5% and 97% of Brucella strains at the genus and species level, respectively, indicating that the performance of the assay was not affected by the different culture conditions used for microbial isolation. Moreover, the inactivated samples were stored and shipped to reference laboratories with no ill effect on protein stability, thus confirming the reliability of our method for routine diagnosis. Finally, we evaluated the epidemiological value of the protocol by comparing the clustering analysis results of Brucella melitensis strains obtained via multiple locus variable-number tandem repeat analysis or MALDI-TOF MS. The results showed that the MALDI-TOF assay could not decipher the true phylogenetic tree, suggesting that the protein profile did not correspond with the genetic evolution of Brucella.

Assessment of Mycotoxin Exposure in Breastfeeding Mothers with Celiac Disease

OBJECTIVE

To assess the risk of mycotoxin exposure (aflatoxin M1, ochratoxin A, and zearalenone) in celiac disease (CD) breastfeeding mothers and healthy control mothers, as well as in their offspring, by quantifying these contaminants in breast milk.

STUDY DESIGN

Thirty-five breastfeeding women with CD on a gluten-free diet and 30 healthy breastfeeding controls were recruited. Milk sampling was performed three times per day for three consecutive days. Mycotoxin content was investigated by an analytical method using immunoaffinity column clean-up and high-performance liquid chromatography (HPLC) with fluorometric detection.

RESULTS

Aflatoxin M1 (AFM1) was detected in 37% of CD group samples (mean ± SD = 0.012 ± 0.011 ng/mL; range = 0.003-0.340 ng/mL). The control group showed lower mean AFM1 concentration levels in 24% of the analyzed samples (0.009 ± 0.007 ng/mL; range = 0.003-0.067 ng/mL, ANOVA on ranks, p-value < 0.01). Ochratoxin A and zearalenone did not differ in both groups.

CONCLUSION

Breast milk AFM1 contamination for both groups is lower than the European safety threshold. However, the estimated exposures of infants from CD mothers and control mothers was much higher (≃15 times and ≃11 times, respectively) than the threshold set by the joint FAO/WHO Expert Committee on Food Additives (JECFA). Since incongruities exist between JECFA and the European Union standard, a novel regulatory review of the available data on this topic is desirable. Protecting babies from a neglected risk of high AFM1 exposure requires prompt regulatory and food-control policies.

A new approach in separating microplastics from environmental samples based on their electrostatic behavior

Numerous studies on microplastics (MPs; Ø < 5 mm) in the aquatic environment have been published, but knowledge about the occurrence and ecological risks of MPs is limited. This is in part because current data on the distribution of MPs are comparable only to a limited extent, due to the many different methods of investigation. In addition, sample preparation is often difficult such that standard procedures are lacking. The aim of this work was to simplify the preparation of different kinds of MP samples. Our method makes use of the electrostatic behavior of plastic particles to facilitate their separation from sample matter, with up to 99% of the original sample mass removed without any loss of MPs. To determine the efficacy of this approach, four different materials (quartz sand, freshwater suspended particulate matter, freshwater sediment, and beach sand) were spiked with MPs (size: 0.063-5 mm from the seven most common types of plastics, one bioplastic type, polyethylene fibers, and tire wear. A modified electrostatic metal/plastic separator was used to reduce the sample mass and concentrate the plastics based on their physical separation. The recovery achieved with this method was as high as nearly 100% for each type of material. The method was then tested on plastic particles of different shapes and types isolated from the Rhine River. These were successfully electroseparated from the four materials, which demonstrated the utility of this method. Its advantages include the simplified handling and preparation of different field samples as well as a much shorter processing time, because after the last separation step there is hardly any biological material remaining in the sample fraction.

Gas chromatography-mass spectrometry determination of polycyclic aromatic hydrocarbons in baby food using QuEChERS combined with low-density solvent dispersive liquid-liquid microextraction

A sensitive GC-MS method is reported for the determination of twelve polycyclic aromatic hydrocarbons (PAHs) in baby food. The sample preparation involves QuEChERS extraction combined with low-density solvent dispersive liquid-liquid microextraction (LDS-DLLME) and ultra-low temperature (-80 °C). Plackett-Burman screening design was employed to identify the main sample preparation variables that affect the extraction efficiency, such as the volume of toluene used in LDS-DLLME. The suitability of proposed method was verified by analytical selectivity, linearity in solvent and matrix-matched calibration curves and adequate recoveries (72-112%) and precision (RSD values ≤11%), under repeatability and within-laboratory reproducibility conditions. High analytical sensitivity was achieved for the monitoring of PAHs at the strict limit of 1 µg kg^-1 fixed by the European Commission for baby foods. The validated method was applied to thirty-two commercial baby food samples, and the investigated PAHs were not detected in any sample.

Application of ultrasonically modified cloud point extraction method for simultaneous enrichment of cadmium and lead in sera of different types of gallstone patients

A novel and greener ultrasonically assisted/modified cloud point extraction procedure for the simultaneous preconcentration of lead and cadmium in serum samples of different types of gallstone patients was developed. The chelates of the under study metals, formerly formed with 8-hydroxyquinoline, were extracted in the micelles of a nonionic surfactant prior to analysis by flame atomic absorption spectrometer (FAAS). After the arrival of the cloud point, the critical micellar mass produced was homogenously dispersed in the aqueous phase with the help of ultrasound energy. The reliability of the developed procedure was tested by relative standard deviation (% RSD), which was found to be <5%. The performance of the proposed procedure was checked by applying to certified reference material and spiking standard in real samples. All the experimental parameters were optimized. The developed procedure of Um-CPE was applied successfully for the analysis of the target heavy metals in serum samples of different types of gallstone patients and referents. The higher levels of the understudy metals were observed in the patients as compared to the referents but the levels of the both metal were found to be considerably higher in patients with pigmented gallstones.

Screening and identification of steroidal saponins from Anemarrhena asphodeloides employing UPLC tandem triple quadrupole linear ion trap mass spectrometry

This study presents a practical and valid strategy for the screening and structural characterization of Anemarrhena asphodeloides Bge steroidal saponins (SSs) using ultra-high performance liquid chromatography coupled with triple quadrupole linear ion trap mass spectrometry. The whole analytical protocols integrate four-step procedures in the positive mode: (1) rational deduction of mass fragmentation pathways of A. asphodeloides SSs; (2) untargeted screening of potential A. asphodeloides SSs by multiple-ion monitoring-information-dependent-acquiring-enhanced product ion (MIM-IDA-EPI) scan through reverse phase liquid chromatography; (3) comprehensive construction of an ammoniated precursor ion database by combining untargeted MIM-IDA-EPI scans and data literature; and (4) structural interpretation of targeted A. asphodeloides SSs using MIM-IDA-EPI and multiple reaction monitoring (MRM)-IDA-EPI with an energy-resolved technique. The protocols were used to analyze SSs in A. asphodeloides; of the 87 detected SSs that were unambiguously characterized or tentatively identified, 19 compounds were the first to be reported from A. asphodeloides and 13 ones were characterized as potential new compounds. Accuracy of the analytical procedure was demonstrated by structural identification of three SSs by NMR spectroscopy. The proposed schemes hold an excellent promise in the structural prediction and interpretation of complex SSs from plant medicines by mass spectrometry.

A Prototype Ice-Melting Probe for Collecting Biological Samples from Cryogenic Ice at Low Pressure

In the Solar System, the surface of an icy moon is composed of irregular ice formations at cryogenic temperatures (<200 K), with an oxidized surface layer and a tenuous atmosphere at very low pressure (<10^-6 atm). A lander mission, whose aim is to collect and analyze biological samples from the surface ice, must contain a device that collects samples without refreezing liquid and without sublimation of ice. In addition, if the samples are biological in nature, then precautions must be taken to ensure the samples do not overheat or mix with the oxidized layer. To achieve these conditions, the collector must maintain temperatures close to maintenance or growth conditions of the organism (<293 K), and it must separate or neutralize the oxidized layer and be physically gentle. Here, we describe a device that addresses these requirements and is compatible with low atmospheric pressure while using no pumps. The device contains a heated conical probe with a central orifice, which is forced into surface ice and directs the meltwater upward into a reservoir. The force on the probe is proportional to the height of meltwater (pressure) obtained in the system and allows regulation of the melt rate and temperature of the sample. The device can collect 5-50 mL of meltwater from the surface of an ice block at 233-208 K with an environmental pressure of less than 10^-2 atm while maintaining a sample temperature between 273 and 293 K. These conditions maintain most biological samples in a pristine state and maintain the integrity of most organisms' structure and function. Key Words: Europa-Icy moon-Microbe-Eukaryote-Spacecraft. Astrobiology 17, 709-720.

Transmission electron microscopy artifacts in characterization of the nanomaterial-cell interactions

We investigated transmission electron microscopy artifacts obtained using standard sample preparation protocols applied to the investigation of Escherichia coli cells exposed to common nanomaterials, such as TiO₂, Ag, ZnO, and MgO. While the common protocols for some nanomaterials result only in known issues of nanomaterial-independent generation of anomalous deposits due to fixation and staining, for others, there are reactions between the nanomaterial and chemicals used for post-fixation or staining. Only in the case of TiO₂ do we observe only the known issues of nanomaterial-independent generation of anomalous deposits due to exceptional chemical stability of this material. For the other three nanomaterials, different artifacts are observed. For each of those, we identify causes of the observed problems and suggest alternative sample preparation protocols to avoid artifacts arising from the sample preparation, which is essential for correct interpretation of the obtained images and drawing correct conclusions on cell-nanomaterial interactions. Finally, we propose modified sample preparation and characterization protocols for comprehensive and conclusive investigations of nanomaterial-cell interactions using electron microscopy and for obtaining clear and unambiguous revelation whether the nanomaterials studied penetrate the cells or accumulate at the cell membranes. In only the case of MgO and ZnO, the unambiguous presence of Zn and Mg could be observed inside the cells.

Speciation of mercury in water and fish samples by HPLC-ICP-MS after magnetic solid phase extraction

In this paper, Fe₃O₄@SiO₂@γ-mercaptopropyltrimethoxysilane (γ-MPTS) magnetic nanoparticles was prepared and a new method of magnetic solid phase extraction (MSPE)-high performance liquid chromatography (HPLC)-inductively coupled plasma mass spectrometry (ICP-MS) was developed for the speciation of mercury including inorganic mercury (Hg²⁺), methylmercury (MeHg⁺) and phenylmercury (PhHg⁺) in environmental water, wastewater, tap water and fish samples. A rapid separation of three target mercury species was achieved in 8min by employing relatively high ratio of methanol in HPLC mobile phase. Various parameters affecting Fe₃O₄@SiO₂@γ-MPTS-based MSPE of target mercury species have been investigated. Under the optimized conditions, the limits of detection for Hg²⁺, MeHg⁺ and PhHg⁺ were in the range of 0.49-0.74ngL^-1. The intra- and inter-day relative standard deviations (n=5) were less than 9.0% and 12%, respectively. The developed MSPE-HPLC-ICP-MS method was validated by the speciation of mercury in the Certified Reference Material of DORM-2 dogfish as well as real-world samples including environmental water, wastewater, tap water and fish samples, and it has the advantages of simple operation, rapid separation, high sensitivity, high enrichment factor and is suitable for the analysis of mercury species in samples with complex matrix.

Food safety in Thailand. 3: Pesticide residues detected in mangosteen (Garcinia mangostana L.), queen of fruits

BACKGROUND

For developing countries like Thailand, regulation of pesticide usage exists, but it is not fully enforced. Therefore, pesticide residues in vegetables and fruits have not been well monitored. This study aimed to determine the pesticide residues in mangosteen fruits sold in Thailand. The mangosteen samples (n = 111) were purchased and the contents of 28 pesticides were analysed by GC-MS/MS method.

RESULTS

Of the pesticides tested, eight were found in 100% of the mangosteen samples. However, in 97% of these samples, either chlorothalonil, chlorpyrifos, diazinon, dimethoate, metalaxyl or profenofos was detected exceeding their maximum residue limits (MRLs), representing a 97% rate of pesticide detection above the MRL. This rate is much higher than those found in other fruits sold in developed countries. However, this conclusion excludes the fresh Thai mangosteens grown for export, as these are generally cultivated and harvested to GAP standards. Since the edible part of the mangosteen is the pulp, washing the fruits with running water can reduce the risk of pesticide residues contaminating the pulp which would be eaten by the consumer.

CONCLUSION

The findings strongly suggest that routine monitoring of pesticide residues in fruits and vegetables is required to reduce the health risks associated with consuming contaminated food. © 2016 Society of Chemical Industry.

An overview of renal metabolomics

The high-throughput, high-resolution phenotyping enabled by metabolomics has been applied increasingly to a variety of questions in nephrology research. This article provides an overview of current metabolomics methodologies and nomenclature, citing specific considerations in sample preparation, metabolite measurement, and data analysis that investigators should understand when examining the literature or designing a study. Furthermore, we review several notable findings that have emerged in the literature that both highlight some of the limitations of current profiling approaches, as well as outline specific strengths unique to metabolomics. More specifically, we review data on the following: (i) tryptophan metabolites and chronic kidney disease onset, illustrating the interpretation of metabolite data in the context of established biochemical pathways; (ii) trimethylamine-N-oxide and cardiovascular disease in chronic kidney disease, illustrating the integration of exogenous and endogenous inputs to the blood metabolome; and (iii) renal mitochondrial function in diabetic kidney disease and acute kidney injury, illustrating the potential for rapid translation of metabolite data for diagnostic or therapeutic aims. Finally, we review future directions, including the need to better characterize interperson and intraperson variation in the metabolome, pool existing data sets to identify the most robust signals, and capitalize on the discovery potential of emerging nontargeted methods.

Antioxidant Capacity Determination in Plants and Plant-Derived Products: A Review

The present paper aims at reviewing and commenting on the analytical methods applied to antioxidant and antioxidant capacity assessment in plant-derived products. Aspects related to oxidative stress, reactive oxidative species' influence on key biomolecules, and antioxidant benefits and modalities of action are discussed. Also, the oxidant-antioxidant balance is critically discussed. The conventional and nonconventional extraction procedures applied prior to analysis are also presented, as the extraction step is of pivotal importance for isolation and concentration of the compound(s) of interest before analysis. Then, the chromatographic, spectrometric, and electrochemical methods for antioxidant and antioxidant capacity determination in plant-derived products are detailed with respect to their principles, characteristics, and specific applications. Peculiarities related to the matrix characteristics and other factors influencing the method's performances are discussed. Health benefits of plants and derived products are described, as indicated in the original source. Finally, critical and conclusive aspects are given when it comes to the choice of a particular extraction procedure and detection method, which should consider the nature of the sample, prevalent antioxidant/antioxidant class, and the mechanism underlying each technique. Advantages and disadvantages are discussed for each method.

Study of aroma formation and transformation during the manufacturing process of Biluochun green tea in Yunnan Province by HS-SPME and GC-MS

BACKGROUND

Biluochun is a typical non-fermented tea and is also famous for its unique aroma in China. Few studies have been performed to evaluate the effect of the manufacturing process on the formation and content of its aroma.

RESULTS

The volatile components were extracted at different manufacturing process steps of Biluochun green tea using fully automated headspace solid-phase microextraction (HS-SPME) and further characterised by gas chromatography-mass spectrometry (GC-MS). Among 67 volatile components collected, the fractions of linalool oxides, β-ionone, phenylacetaldehyde, aldehydes, ketones, and nitrogen compounds were increased while alcohols and hydrocarbons declined during the manufacturing process. The aroma compounds decreased the most during the drying steps.

CONCLUSION

We identified a number of significantly changed components that can be used as markers and quality control during the producing process of Biluochun. The drying step played a major role in the aroma formation of green tea products and should be the most important step for quality control. © 2016 Society of Chemical Industry.

Development of an SPME-GC-MS method for the specific quantification of dimethylamine and trimethylamine: use of a new ratio for the freshness monitoring of cod fillets

BACKGROUND

Fish is a highly perishable food, so it is important to be able to estimate its freshness to ensure optimum quality for consumers. The present study describes the development of an SPME-GC-MS technique capable of quantifying both trimethylamine (TMA) and dimethylamine (DMA), components of what has been defined as partial volatile basic nitrogen (PVB-N). This method was used, together with other reference methods, to monitor the storage of cod fillets (Gadus morhua) conserved under melting ice.

RESULTS

Careful optimisation enabled definition of the best parameters for extracting and separating targeted amines and an internal standard. The study of cod spoilage by sensory analysis and TVB-N assay led to the conclusion that the shelf-life of cod fillet was between 6 and 7 days. Throughout the study, TMA and DMA were specifically quantified by SPME-GC-MS; the first was found to be highly correlated with the values returned by steam distillation assays. Neither TMA-N nor DMA-N were able to successfully characterise the decrease in early freshness, unlike dimethylamine/trimethylamine ratio (DTR), whose evolution is closely related to the results of sensory analysis until the stage where fillets need to be rejected.

CONCLUSION

DTR was proposed as a reliable indicator for the early decrease of freshness until fish rejection. © 2015 Society of Chemical Industry.

DNA Methylation Analysis of ChIP Products at Single Nucleotide Resolution by Pyrosequencing®

Interaction and co-occurrence of protein and DNA-based epigenetic modifications have become a topic of interest for many fundamental and biomedical questions. We describe within this chapter a protocol that combines two techniques in order to determine the methylation status of the DNA specifically associated with a protein of interest. First, DNA that directly interacts with the selected protein (such as a specific histone modification, a transcription factor, or any other DNA-associated protein) is purified by standard chromatin immunoprecipitation (ChIP). Second, the level of DNA methylation of this immunoprecipitated DNA is measured by bisulfite conversion and Pyrosequencing, a quantitative sequencing-by-synthesis method. This procedure allows determining the methylation status of genomic DNA associated to a specific protein at single nucleotide resolution.

Use of Malachite Green-Loop Mediated Isothermal Amplification for Detection of Plasmodium spp. Parasites

Malaria elimination efforts are hampered by the lack of sensitive tools to detect infections with low-level parasitemia, usually below the threshold of standard diagnostic methods, microscopy and rapid diagnostic tests. Isothermal nucleic acid amplification assays such as the loop-mediated isothermal amplification (LAMP), are well suited for field use as they do not require thermal cyclers to run the test. However, the use of specialized equipment, as described by many groups, reduces the versatility of the LAMP technique as a simple tool for use in endemic countries. In this study, the use of the malachite green (MG) dye, as a visual endpoint readout, together with a simple mini heat block was evaluated for the detection of malaria parasites. The assay was performed for 1 hour at 63°C and the results scored by 3 independent human readers. The limit of detection of the assay was determined using well-quantified Plasmodium spp. infected reference samples and its utility in testing clinical samples was determined using 190 pre-treatment specimens submitted for reference diagnosis of imported malaria in the United States. Use of a simplified boil and spin methods of DNA extraction from whole blood and filter paper was also investigated. We demonstrate the accurate and sensitive detection of malaria parasites using this assay with a detection limit ranging between 1-8 parasites/μL, supporting its applicability for the detection of infections with low parasite burden. This assay is compatible with the use of a simple boil and spin sample preparation method from both whole blood and filter papers without a loss of sensitivity. The MG-LAMP assay described here has great potential to extend the reach of molecular tools to settings where they are needed.

Development and validation of an UHPLC method for the determination of betamethasone valerate in cream, gel, ointment and lotion

An ultra high performance liquid chromatographic method has been developed and validated for the determination of betamethasone valerate (BMV) in topical dermatologic formulations. For the development of the method, response surface methodology based on a three-level full factorial design was used. The eluent composition, the column dimension and the flow rate were chosen as relevant experimental parameters to investigate. The response surface plots revealed an optimum separation by using a RP column (30 mm × 2 mm i.d., 2.2 μm particle size), at 30 °C; isocratic mobile phase consisting of acetonitrile:water (60:40) at a flow rate of 0.2 mL min(-1) and a wavelength set at 254 nm. The proposed method was validated for four types of matrices according to ICH guidelines requirements. Dexamethasone acetate (DMA) was used as internal standard. Linearity was studied in the range of 5-200 μg mL(-1) for BMV in spiked matrix samples. Recoveries were in the range of 95-105% and precision was better than 5% for both analytes, either in cream, gel, ointment, or lotion formulations, when using simple sample preparation. Retention times were 0.95 min for DMA and 1.40 min for BMV, demonstrating a short method run time. The method was successfully applied for routine analysis of dermatological formulations containing betamethasone valerate.

Challenges Associated with Sample Preparation for the Analysis of PBDEs in Human Serum

Polybrominated diphenyl ethers (PBDEs) are used as flame retardants in many applications; however, certain PBDE congeners are persistent, bioaccumulative, and toxic to both humans and the environment. PBDEs have been found in human specimens, and a variety of analytical techniques have been used for their determination in biological matrixes. Nevertheless, obtaining a relatively clean analytical blank sample during PBDE analysis is a big challenge because of the ubiquitous nature of these compounds. Thus, the present study was conducted to compare the PBDE background levels associated with the three most commonly used extraction techniques: liquid-liquid extraction (LLE), SPE, and accelerated solvent extraction (ASE). Conventionally used blank matrixes (HPLC grade water, Milli-Q water, and air) were spiked with internal standards and extracted using LLE, SPE, or ASE. The extracts were analyzed by GC/electron ionization-tandem MS. The ASE method achieved the lowest background levels for nearly all the PBDE congeners analyzed, which may be attributed to the stainless steel and closed-vessel nature of the ASE cells.

(1)H NMR Metabolomic Footprinting Analysis for the In Vitro Screening of Potential Chemopreventive Agents

Metabolomics is the quantification and analysis of the concentration profiles of low-molecular-weight compounds present in biological samples. In particular metabolic footprinting analysis, based on the monitoring of metabolites consumed from and secreted into the growth medium, is a valuable tool for the study of pharmacological and toxicological effects of drugs. Mass spectrometry and nuclear magnetic resonance (NMR) are the two main complementary techniques used in this field. Although less sensitive, NMR gives a direct fingerprint of the system, and the spectra obtained contain metabolic information that can be distilled by chemometric techniques. In this chapter, we present how metabolomic footprinting can be used to assess in vitro a potential chemopreventive molecule as metformin.

Quantitation of Aldosterone in Serum or Plasma Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)

Accurate determination of serum and plasma aldosterone is essential for screening, diagnosis, and subtype classification of primary aldosteronism (PA). Its measurement is also used in the investigation of adrenal incidentaloma, adrenal carcinoma, Addison's disease, congenital adrenal hyperplasia, renal artery stenosis, and renal tubular channelopathies. We describe a simple and robust method for the accurate and precise measurement of aldosterone in serum or plasma using liquid chromatography and tandem mass spectrometry (LC-MS/MS). After addition of internal standard, aldosterone is extracted from serum samples using supported liquid extraction (SLE) with methyl-t-butyl ether (MtBE). The MtBE is evaporated to dryness and sample is reconstituted with mobile phase before injection onto the LC-MS/MS and quantitation using an 8-point calibration curve. The assay calibration range is approximately 50-6500 pmol/L (0.16-234 ng/dL) with total imprecision between 6.8 and 4.1 % for concentrations between about 50 and 1000 pmol/L respectively.

Quantification of Metanephrine and Normetanephrine in Urine Using Liquid Chromatography-Tandem Mass Spectrometry

Measuring urinary metanephrines aides in the diagnosis of pheochromocytomas-catecholamine producing tumors. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) allows for greater sensitivity and simpler sample preparation as compared with other techniques. Here we describe a simple LC-MS/MS method for measuring metanephrines in urine. Each urine sample was treated with diphenylboronic acid to create boronate complexes, and then applied to a Bond-Elut Plexa cartridge. After solid phase extraction, samples were concentrated and analyzed on an Atlantis T3 column with chromatographic run time totaling 8.5 min. MS/MS was set in positive electrospray ionization mode with multiple reaction monitoring for data collection. The assay was linear from 0.2 to 27.4 μmol/L and 0.3 to 14.6 μmol/L for metanephrine and normetanephrine, respectively. Intra-assay and total precision at three concentration levels over 10 days were <5 % for metanephrine and <10 % for normetanephrine.

Quantification of Five Clinically Important Amino Acids by HPLC-Triple TOF™ 5600 Based on Pre-column Double Derivatization Method

Phenylalanine, tyrosine, glycine, cystine, and phosphoethanolamine are commonly measured amino acids in various physiological fluids to diagnose or follow-up various inborn errors of metabolism. The gold standard method for the amino acids quantitation has been ion exchange chromatography with ninhydrin post-column derivatization. However, this method is very laborious and time consuming. In recent years, liquid-chromatography mass spectrometry is being increasingly used for the assay of amino acids. Pre-column butyl derivatization with reverse phase chromatography has been widely used for mass spectrometry analysis of amino acids. Phosphoethanolamine is not butylated and cannot be measured by this method. Nevertheless, phosphoethanolamine can be dansyl-derivatized using dansyl chloride. We developed a double derivatization method by using butanol and dansyl chloride to derivatize carboxylic and amino groups separately, and then combining the derivatives to simultaneously measure these five amino acids using TOF-MS scan. Stable isotope-labeled internal standards were used.

Quantitation of Albumin in Urine by Liquid Chromatography Tandem Mass Spectrometry

Urinary excretion of human serum albumin (HSA), a 6.65 kDa monomeric protein, is a sensitive marker of renal damage associated with many diseases including diabetes mellitus. Albumin is synthesized by the liver and functions as a transport protein for fat-soluble hormones and drugs and for maintaining plasma colloid osmotic pressure and pH. Albumin is not filtered at the glomerulus and its presence in the urine at concentration above 30 mg/day is suggestive of glomerular damage. Early diagnosis of microalbuminuria (30-300 mg/24 h urine albumin excretion or 30-300 mg/g creatinine in random collections) has prognostic value for monitoring disease progression and early clinical management of diabetic nephropathy in prediabetic patients. Current methods for quantitation of urine albumin are based on immunoassays or size exclusion high-performance liquid chromatography coupled with UV detection (SEC-HPLC-UV). Studies have demonstrated discordance between the existing methods. It has been suggested that while immunoassays underestimate albumin in urine, SEC-HPLC-UV method overestimates albumin as it cannot separate co-eluting interferences. This chapter describes a liquid chromatography tandem mass spectrometry LC-MS/MS candidate reference method for albumin quantitation.

High-Throughput Microarray Incubations Using Multi-Well Chambers

Peptide microarrays are ideal tools for a variety of applications ranging from epitope mapping to immune monitoring. Here we present a method for high-throughput screening of biological samples using only standard microtiter plate equipment. Parallel incubation of a large number of samples with a small library of peptides is enabled by printing multiple identical mini-arrays on one microarray slide and further combining four slides to yield an incubation frame possessing the dimensions of a 96-well microtiter plate. Applying conventional lab equipment such as ELISA washers, hundreds of samples can be processed in 1 day yielding approx. 200 data points in triplicates per sample.

LC-MS-Based Metabolomic Investigation of Chemopreventive Phytochemical-Elicited Metabolic Events

Phytochemicals are under intensive investigation for their potential use as chemopreventive agents in blocking or suppressing carcinogenesis. Metabolic interactions between phytochemical and biological system play an important role in determining the efficacy and toxicity of chemopreventive phytochemicals. However, complexities of phytochemical biotransformation and intermediary metabolism pose challenges for studying phytochemical-elicited metabolic events. Metabolomics has become a highly effective technical platform to detect subtle changes in a complex metabolic system. Here, using green tea polyphenols as an example, we describe a workflow of LC-MS-based metabolomics study, covering the procedures and techniques in sample collection, preparation, LC-MS analysis, data analysis, and interpretation.

Quantitation of Parathyroid Hormone in Serum or Plasma by Liquid Chromatography-Tandem Mass Spectrometry

Parathyroid hormone (PTH), an 84 amino acid peptide hormone, is an important regulator of calcium homeostasis. Quantitation of PTH in serum is useful for the diagnosis of primary hyperparathyroidism, hypoparathyroidism, and for monitoring osteodystrophy in patients with renal failure. The biological activity of PTH arises from binding of PTH (N terminus) to its target receptor (D'Amour et al., Kidney Int 68: 998-1007, 2005). Several C-terminal and N-terminal fragments circulate in normal subjects. Recent studies have demonstrated that accurate quantitation of PTH fragments may be of clinical value. In this chapter a mass spectrometry based method for quantitation of PTH(1-84) is described. This method involves immunoaffinity capture of PTH followed by trypsinization and quantitation of PTH-specific tryptic peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The N-terminal tryptic peptide, PTH(1-13) as surrogate of 1-84 PTH, is used for quantitation.

Broadscale resolving power performance of a high precision uniform field ion mobility-mass spectrometer

An extensive study of two current ion mobility resolving power theories ("conditional" and "semi-empirical") was undertaken using a recently developed drift tube ion mobility-mass spectrometer. The current study investigates the quantitative agreement between experiment and theory at reduced pressure (4 Torr) for a wide range of initial ion gate widths (100 to 500 μs), and ion mobility values (K0 from 0.50 to 3.0 cm(2) V(-1) s(-1)) representing measurements obtained in helium, nitrogen, and carbon dioxide drift gas. Results suggest that the conditional resolving power theory deviates from experimental results for low mobility ions (e.g., high mass analytes) and for initial ion gate widths beyond 200 μs. A semi-empirical resolving power theory provided close-correlation of predicted resolving powers to experimental results across the full range of mobilities and gate widths investigated. Interpreting the results from the semi-empirical theory, the performance of the current instrumentation was found to be highly linear for a wide range of analytes, with optimal resolving powers being accessible for a narrow range of drift fields between 14 and 17 V cm(-1). While developed using singly-charged ion mobility data, preliminary results suggest that the semi-empirical theory has broader applicability to higher-charge state systems.

Seasonal and Particle Size-Dependent Variations of Hexabromocyclododecanes in Settled Dust: Implications for Sampling

Particle size is a significant parameter which determines the environmental fate and the behavior of dust particles and, implicitly, the exposure risk of humans to particle-bound contaminants. Currently, the influence of dust particle size on the occurrence and seasonal variation of hexabromocyclododecanes (HBCDs) remains unclear. While HBCDs are now restricted by the Stockholm Convention, information regarding HBCD contamination in indoor dust in China is still limited. We analyzed composite dust samples from offices (n = 22), hotels (n = 3), kindergartens (n = 2), dormitories (n = 40), and main roads (n = 10). Each composite dust sample (one per type of microenvironment) was fractionated into 9 fractions (F1-F9: 2000-900, 900-500, 500-400, 400-300, 300-200, 200-100, 100-74, 74-50, and <50 μm). Total HBCD concentrations ranged from 5.3 (road dust, F4) to 2580 ng g(-1) (dormitory dust, F4) in the 45 size-segregated samples. The seasonality of HBCDs in indoor dust was investigated in 40 samples from two offices. A consistent seasonal trend of HBCD levels was evident with dust collected in the winter being more contaminated with HBCDs than dust from the summer. Particle size-selection strategy for dust analysis has been found to be influential on the HBCD concentrations, while overestimation or underestimation would occur with improper strategies.

Minimizing technical variation during sample preparation prior to label-free quantitative mass spectrometry

Sample preparation is the crucial starting point to obtain high-quality mass spectrometry data and can be divided into two main steps in a bottom-up proteomics approach: cell/tissue lysis with or without detergents and a(n) (in-solution) digest comprising denaturation, reduction, alkylation, and digesting of the proteins. Here, some important considerations, among others, are that the reagents used for sample preparation can inhibit the digestion enzyme (e.g., 0.1% sodium dodecyl sulfate [SDS] and 0.5 M guanidine HCl), give rise to ion suppression (e.g., polyethylene glycol [PEG]), be incompatible with liquid chromatography-tandem mass spectrometry (LC-MS/MS) (e.g., SDS), and can induce additional modifications (e.g., urea). Taken together, all of these irreproducible effects are gradually becoming a problem when label-free quantitation of the samples is envisioned such as during the increasingly popular high-definition mass spectrometry (HDMS(E)) and sequential window acquisition of all theoretical fragment ion spectra (SWATH) data-independent acquisition strategies. Here, we describe the detailed validation of a reproducible method with sufficient protein yield for sample preparation without any known LC-MS/MS interfering substances by using 1% sodium deoxycholate (SDC) during both cell lysis and in-solution digest.