Universal Pretreatment Development for Low-input Proteomics Using Lauryl Maltose Neopentyl Glycol.

In recent years, there has been a growing demand for low-input proteomics, particularly in the context of single-cell proteomics (SCP). In this study, we have developed a lauryl maltose neopentyl glycol (LMNG)-assisted sample preparation (LASP) method. This method effectively reduces protein and peptide loss in samples by incorporating LMNG, a surfactant, into the digestion solution and subsequently removing the LMNG simply via reversed phase solid-phase extraction. The advantage of removing LMNG during sample preparation for general proteomic analysis is the prevention of mass spectrometry (MS) contamination. When we applied the LASP method to the low-input SP3 method and on-bead digestion in coimmunoprecipitation-MS, we observed a significant improvement in the recovery of the digested peptides. Furthermore, we have established a simple and easy sample preparation method for SCP based on the LASP method and identified a median of 1175 proteins from a single HEK239F cell using liquid chromatography (LC)-MS/MS with a throughput of 80 samples per day.

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.

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.

Isolation of extracellular vesicles from human plasma samples: The importance of controls.

BACKGROUND: Extracellular vesicles (EV) are enriched with proteins and RNA cargo, promoting cell-to-cell communication. Biofluid derived EV cargo is used for discovering disease specific markers for diagnosis and disease monitoring. RATIONAL: Blood is a complex fluid with an abundance of protiens and thus isolation of EVs is challenging. Therefore, methods for EV isolation, including commercial kits use thromboplastin D (TP-D) for pretreatment of plasma to increase EV purity and yield. This pretreatment can introduce contaminants. METHOD AND RESULTS: We performed a comparative study to evaluate the effect of EV isolation methods focusing on (a) pretreatment of plasma with additives, which include: rabbit TP (rTP) versus human recombinant thromboplastin (huTP), to increase purity and yield (b) an additional centrifugation step prior to freezing plasma and (c) comparison of frozen versus fresh plasma EV isolations. Pretreatment with rTP generated a dynamic range of proteins, however, most of these proteins were contaminants, introduced from the rTP (99.1% purity). As an alternative, huTP was used, which did not introduce any significant contaminants, however, this did not increase yield or purity. Additionally, an extra 10,000 g centrifugation did not improve either EV yield or purity. Finally, comparison of fresh or frozen plasma showed no significant difference, an important factor when sourcing plasma from biobanks. CONCLUSION: Appropriate controlsare required when adding any additives during EV isolation as even a small percentage of contaminants can have a major effect on results. Furthermore, biobanked plasma can be used with no major changes to processing.

An optimized method of extracting and quantifying active Neutrophil serine proteases from human whole blood cells.

PURPOSE: Neutrophil serine proteases (NSPs) are implicated in numerous inflammatory diseases. Thus, a robust methodology to monitor and quantify NSPs is important to study disease progression and evaluate the effect of pharmacological interventions. A comparison of the various methods used to extract NSPs from neutrophil granulocytes has not been published, providing the impetus to conduct this method optimization and comparison study. METHODS: Two NSP recovery methodologies were evaluated on samples from five human donors: zymosan stimulation and cell pellet extraction. For the zymosan stimulation method, 1 mL donor blood was added to zymosan and samples were incubated at 37°C for 30 min while shaking. Samples were then centrifuged, and the plasma was collected for quantitation of NSP activity. For the cell pellet extraction procedure, 2 mL whole blood samples were centrifuged into white blood cell pellets following red blood cell lysis. To each pellet, three sequential lysis steps were performed using either 0.05% Nonidet P-40 Substitute (NP40) or 0.02% Triton X-100 lysis buffers under agitation followed by centrifugation. NSP activities were quantified using an exogenous peptide substrate specific to each of the three NSPs being analyzed: neutrophil elastase, cathepsin G, and proteinase 3. RESULTS AND DISCUSSION: The zymosan stimulation method resulted in lower recovery of active NSPs and was unable to stimulate significant release of active cathepsin G. In contrast, the NP40 pellet extraction method showed consistent inter-donor NSP release with greater recoveries of active NSPs than the Triton method or the zymosan stimulation method. Overall, the pellet extraction procedure provided 13.3-fold greater recovery of active neutrophil elastase, 283-fold greater recovery of active cathepsin G, and 2.9-fold greater recovery of active proteinase 3 than the zymosan method. CONCLUSION: The NP40 cell pellet extraction method resulted in greater extraction of active NSPs compared to the other methods investigated here, which may allow for a more accurate and complete biomarker profile when evaluating human clinical samples.

Recent Advances in Sample Preparation for Cosmetics and Personal Care Products Analysis.

The use of cosmetics and personal care products is increasing worldwide. Their high matrix complexity, together with the wide range of products currently marketed under different forms imply a challenge for their analysis, most of them requiring a sample pre-treatment step before analysis. Classical sample preparation methodologies involve large amounts of organic solvents as well as multiple steps resulting in large time consumption. Therefore, in recent years, the trends have been moved towards the development of simple, sustainable, and environmentally friendly methodologies in two ways: (i) the miniaturization of conventional procedures allowing a reduction in the consumption of solvents and reagents; and (ii) the development and application of sorbent- and liquid-based microextraction technologies to obtain a high analyte enrichment, avoiding or significantly reducing the use of organic solvents. This review provides an overview of analytical methodology during the last ten years, placing special emphasis on sample preparation to analyse cosmetics and personal care products. The use of liquid-liquid and solid-liquid extraction (LLE, SLE), ultrasound-assisted extraction (UAE), solid-phase extraction (SPE), pressurized liquid extraction (PLE), matrix solid-phase extraction (MSPD), and liquid- and sorbent-based microextraction techniques will be reviewed. The most recent advances and future trends including the development of new materials and green solvents will be also addressed.

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.

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.

Polypyrrole monolithic extraction phase: From conventional to miniaturized sample preparation techniques.

Monolithic polymers are described as continuous and highly porous materials. They have been gaining popularity as an effective extracting phase for some sample preparation methods, due to their variety of functionalities, such as wide pH range tolerance, good permeability, and its ability to allow changes into their surface. Polypyrrole represents an interesting alternative for the modification in extraction phases due to its well related ability to perform multiple interactions, such as acid-base, π - π, ion exchange, interactions with hydrophobic affinities or polar functional groups. Among the different sample preparation techniques, solid-phase extraction (SPE) is one of the most popular and used; a miniaturized version of SPE is the disposable pipette extraction (DPX). DPX is a recent miniaturized extraction technique that usually employing silica-based sorbents inside a pipette tip (5 or 1 mL). The present study proposes the development of a monolithic extraction phase composed by styrene divinylbenzene (1:1) modified with polypyrrole for SPE and DPX techniques. The efficiency of the material was evaluated in face of the extraction of different samples and analytes, triazine herbicides in water and dexamethasone in synthetic synovial liquid by conventional and miniaturized solid-phase extraction techniques. The extractions performed by SPE and DPX presented absolute recovery values ranging from 74.8 to 105.0%, inter-day precision ranging from 0.6 to 14.0%, and limit of quantification of 0.5 and 5.0 ng.mL-1, respectively. The DPX miniaturized method exhibited results equivalent to the methods reported in the literature for extraction of dexamethasone in synovial fluid samples. Moreover, this technique proved to be quicker and cheaper than SPE, and produced fewer residual volumes, supporting the preference for green chemistry. Monolithic polymers modified with polypyrrole presented to be a feasible alternative extraction phase for miniaturized sample preparation techniques.

Extraction of Functional Mitochondria Based on Membrane Stiffness.

The abnormal functionality of mitochondria has been linked to many life-threatening diseases such as cancers, failure of cardiovascular functions, and neurodegenerative disorders. Therefore, in vitro analysis of mitochondria has garnered great interest for understanding the mechanism of mitochondrial dysfunction-related disease development and therapeutics. However, due to the intrinsic heterogeneity of cell membrane stiffness, it remains challenging to standardize the protocols for the extraction of mitochondria and adequate disruption of the cellular membrane while retaining the functionality of mitochondria. We have previously developed a microfluidics-based cell shredder capable of serving the purpose. In this protocol, we describe the step-by-step procedures to empirically identify the threshold shear stress using this microfluidics-based cell shredder for mitochondrial extraction. The optimal shear stress to disrupt human embryonic kidney cell (HEK 293) and mice muscle cell (C2C12) has been characterized at around 16.4 Pa, whereas cell lines with stiffer membrane stiffness, for example, neuroblastoma cells (SH-SY5Y), require 27.4 Pa to effectively lyse the cells. This protocol also provides detailed procedures to determine the quality of extracted mitochondria based on the membrane potential and the integrity of extracted mitochondria. A comparison with the widely employed Dounce homogenizer has shown that the proposed microscale cell shredder can yield at least 40% more functional mitochondria and retain higher integrity regarding extracted mitochondria than the counterparts extracted from Dounce homogenizer, especially for low cell concentrations (5-20 × 104 cells/mL) and small sample volume (<200 µL).

Determination of cortisol in hair using liquid chromatography-tandem mass spectrometry: a short review.

Cortisol is considered a particularly relevant biomarker in the context of stress evaluation. This study aims to review of the available literature on the determination of cortisol in hair using LC-MS/MS. Currently, there is no standardized procedure for the measurement of cortisol concentrations in hair, and different sample preparation, chromatographic separation and mass spectrometric detection conditions were described. Simple methanolic extraction, reversed-phase separation and MRM detection in negative ion mode are the most common employed analytical approaches. Reported assays presented acceptable sensitivity for clinical purposes. The increasing use of mass spectrometry in clinical laboratories may contribute to the establishment of LC-MS/MS as the method of choice for the determination of cortisol concentrations in hair.

Development of a syringe membrane-based microextraction method based on metal-organic framework mixed-matrix membranes for preconcentration/extraction of polycyclic aromatic hydrocarbons in tea infusion.

Inevitably, the residues of polycyclic aromatic hydrocarbons (PAHs) in tea leaves will be transferred to hot tea infusion, constituting a certain drinking risk; consequently, it is imperative to develop rapid, sensitive, and robust approaches for their trace-level detection. Herein, we developed a syringe membrane-based microextraction (SMME) method for preconcentration/extraction of PAHs in tea infusions. This method utilized metal-organic framework-mixed matrix membranes (MOF-MMMs) as adsorbents, which anchored the nanoparticles of MOFs onto the surface of PVDF membrane. The UiO-66 (Zr)-based MMM possessed high Brunauer-Emmett-Teller (BET) surface area (320.5 m2 g-1) and pore volume (0.18 cm3 g-1), thus enhancing extraction/adsorption efficiency. Under optimized conditions, the limits of detection for PAHs reached as low as 0.02-0.08 µg L-1 with extraction recoveries of 85.5-102.1%, and the inter-day and intra-day precision was lower than 8.4% in tea infusions. Consequently, the SMME/HPLC-DAD method shows a great potential in conventional monitoring of PAHs in tea samples.

Detection of insulins in postmortem tissues: an optimized workflow based on immunopurification and LC-MS/HRMS detection.

Diabetes is a worldwide disease in perpetual expansion. Type 1 and sometimes type 2 diabetic patients require daily human insulin (HI) or analog administration. Easy access to insulins for insulin-treated diabetics, their relatives, and medical professionals can enable abuse for suicidal or homicidal purpose. However, demonstrating insulin overdose in postmortem blood is challenging. Tissue analyses are contributive, as insulins can accumulate before death or undergo only limited degradation. The present study describes an assay for HI and synthetic analogs (lispro, aspart, glulisine, detemir and degludec, glargine and its main metabolite (M1)) in liver, kidney, muscle, and injection site samples. It is based on a 5-step sample preparation (reduction of tissue sample size, homogenization, extraction, concentration, and immunopurification) associated with liquid chromatography coupled to high-resolution mass spectrometry (LC-MS/HRMS). Selectivity and limit of detection (LOD) for all target analogs were assessed in the above matrices. LOD was determined at 25 ng/g for HI and for analogs except detemir and degludec, where LOD was 50 ng/g in kidney and injection site samples and 80 ng/g in the liver and muscle. The method was applied to13 forensic cases in which insulin use was suspected.

Effect of different sample treatment methods on Low Endotoxin Recovery Phenomenon.

Endotoxin is a kind of lipopolysaccharide that exits on the cell wall of Gram-negative bacteria. It can cause fever, shock or even death when is delivered into human body. So, it is necessary to control the endotoxin contamination for biopharmaceutical products that are mainly administered by intravenous route. Limulus Amebocyte Lysate (LAL)-based tests are usually used to detect endotoxin content in biologics formulations. However, an undesirable phenomenon called "Low Endotoxin Recovery (LER)" often occurs in formulation buffers that usually contain chelating component, such as sodium citrate, and amphiphilic surfactant, such as Tween-20. The occurrence of this LER phenomenon may interfere with endotoxin detection and cause false negative results. In this study, we compared the effect of different sample treatment methods on endotoxin detection and found that the LER phenomenon was better controlled under the conditions of low pH (pH = 5.0), low temperature (2-8 °C) and in the presence of divalent cations in the solution. In addition, although the endotoxin activity was found to have decreased due to LER phenomenon, the particle size distribution of endotoxin determined by dynamic light scattering (DLS) in LER solution did not change obviously, which is different from previous hypothesis about LER phenomenon in literature that the particle size of endotoxin aggregates would decrease under LER conditions. These findings provide some insights into different sample treatment methods for endotoxin detection and give a better understanding and solution on minimizing the LER phenomenon.

Pretreatment and determination methods for benzimidazoles: An update since 2005.

Benzimidazoles, commonly used as pesticides and veterinary drugs, have posed a threat to human health and the environment due to unreasonable use and lack of valid regulation. Therefore, an up-to-date and comprehensive summary of the pretreatment and analytical approaches in different substrates is urgently needed. The present review consequently updates and covers various newly developed pretreatment methods (e.g., cationic micellar precipitation, magnetic-solid phase extraction, hollow fiber liquid phase microextraction, disperse liquid-liquid microextraction-solidified floating organic drop, stir cake sorptive extraction, solid phase microextraction method, QuEChERS, and molecular imprinted polymer-based methods) since 2005. The review also elaborates and discusses different determination methods (e.g., newly developed HPLC and related methods, improved spectrofluorimetry methods, capillary electrophoresis, and the electrochemical sensor). Furthermore, some critical points and prospects are highlighted, to describe the trends in this area.

Application of the Dehydration Homogeneous Liquid-Liquid Extraction (DHLLE) Sample Preparation Method for Fingerprinting of Honey Volatiles.

Recently, we proposed a new sample preparation method involving reduced solvent and sample usage, based on dehydration homogeneous liquid-liquid extraction (DHLLE) for the screening of volatiles and semi-volatiles from honey. In the present research, the method was applied to a wide range of honeys (21 different representative unifloral samples) to determine its suitability for detecting characteristic honey compounds from different chemical classes. GC-FID/MS disclosed 130 compounds from different structural and chemical groups. The DHLLE method allowed the extraction and identification of a wide range of previously reported specific and nonspecific marker compounds belonging to different chemical groups (including monoterpenes, norisoprenoids, benzene derivatives, or nitrogen compounds). For example, DHLLE allowed the detection of cornflower honey chemical markers: 3-oxo-retro-α-ionols, 3,4-dihydro-3-oxoedulan, phenyllactic acid; coffee honey markers: theobromine and caffeine; linden honey markers: 4-isopropenylcyclohexa-1,3-diene-1-carboxylic acid and 4-(2-hydroxy-2-propanyl)cyclohexa-1,3-diene-1-carboxylic acid, as well as furan derivatives from buckwheat honey. The obtained results were comparable with the previously reported data on markers of various honey varieties. Considering the application of much lower volumes of very common reagents, DHLLE may provide economical and ecological advantages as an alternative sample preparation method for routine purposes.

Assessment of brain-to-blood drug distribution using liquid chromatography.

Delivery of already existing and new drugs under development to the brain necessitates passage across the blood-brain barrier (BBB) with its tight intercellular junctions, molecular components and transporter systems. Consequently, it is critical to identify the extent of brain permeation and the partitioning across the BBB. The interpretation of brain-to-blood ratios is considered to be a significant and fundamental approach for estimating drug penetration through BBB, the brain-targeting ability and central nervous system (CNS) pharmacokinetics. Among the different bioanalytical techniques, liquid chromatography with various detectors has been widely used for determination of these ratios. This review defines the different approaches for sample preparation, extraction techniques and liquid chromatography procedures concerned with the determination of drugs in blood and brain tissues and the assessment of brain-to-blood levels. These approaches are expanded to cover the analysis of several drug classes such as CNS-acting drugs, chemotherapeutics, antidiabetics, herbal medicinal products, radiopharmaceuticals, antibiotics and antivirals. Accordingly, stability in biological matrices and matrix effects are investigated. The different administration/formulation effects and the possible deviations in these ratios are also disscussed.

Review of sample preparation methods for chromatographic analysis of neonicotinoids in agricultural and environmental matrices: From classical to state-of-the-art methods.

This review specifically examines the development of sample preparation methods for residue analyses of neonicotinoid insecticides in agricultural and environmental matrices. Pesticide residue analysis is fundamentally important to ensure the safety of foods and processed foods of plant and animal origin, and to preserve the environment, particularly soil and water. For the development of pesticide residue analysis, the sample preparation process is an important key to maximizing the analytical performance of highly sensitive and accurate chromatographic instruments and to acquiring reliable analytical results. This review outlines sample preparation methods that have been proposed to date for extraction of neonicotinoids that might remain in a complicated sample matrix in quantitatively trace amounts, and for cleaning up, to the greatest extent possible, the interfering components that coexist in the sample extract.