Efficient extraction of proteins from recalcitrant plant tissue for subsequent analysis by two‐dimensional gel electrophoresis

Protein extraction for two‐dimensional electrophoresis from tissues of recalcitrant species is quite problematic and challenging due to the low protein content and high abundance of contaminants. Proteomics in Shorea robusta is scarcely conducted due to the lack of a suitable protein preparation procedure. To establish an effective protein extraction protocol suitable for two‐dimensional electrophoresis in Shorea robusta, four procedures (borate buffer/trichloroacetic acid extraction, organic solvent/trichloroacetic acid precipitation, sucrose/Tris/phenol, and organic solvent/phenol/sodium dodecyl sulfate) were evaluated. Following these, proteins were isolated from mature leaves and were analyzed for proteomics, and also for potential contaminants, widely reported to hinder proteomics. The borate buffer/trichloroacetic acid extraction had the lowest protein yield and did not result in any banding even in one‐dimensional electrophoresis. In contrast, organic solvent/phenol/sodium dodecyl sulfate extraction allowed the highest protein yield. Moreover, during proteomics, organic solvent/phenol/sodium dodecyl sulfate extracted protein resolved the maximum number (144) of spots. Further, when proteins were evaluated for contaminants, significant (77–95%) reductions in the nucleic acids, phenol, and sugars were discernible with refinement in extraction procedure. Accumulated data suggested that the organic solvent/phenol/sodium dodecyl sulfate extraction was the most effective protocol for protein isolation for proteomics of Shorea robusta and can be used for plants that have a similar set of contaminants.     

Analytical methods for pesticide residues in rice

Rice consumption has increased worldwide over recent decades, as it has become one of the most common foods. Although the analysis of environmental samples coming from rice areas has been well documented, there is less information regarding the analysis of pesticide residues in rice-grain samples.Rice (paddy, brown and white) can be considered a complex matrix, leading to difficulties in the application of the different multiresidue methods described in the literature. This review addresses and compares the principal extraction and clean-up methodologies [e.g., liquid-liquid extraction, solid-phase extraction, pressurized-liquid extraction, QuEChERS (quick, easy, cheap, effective, rugged and safe), gel-permeation chromatography and supercritical-fluid extraction - with QuEChERS-based methods being the most frequently employed].Traditionally, the determination of pesticide residues in rice has been based on gas chromatography with mass spectrometry (MS). But the application of new classes of pesticides has driven laboratories to increase the use of liquid chromatography with tandem MS. The limits of detection and quantification are in the ranges 0.09-90 μg/kg and 1-297 μg/kg, respectively, for the methodologies reported. These values agree with the current internationally-accepted maximum residue limits (MRLs).Based on the European Union (EU) database, more than 3000 analyses of pesticide residues in rice have been performed by official EU laboratories over the past decade. Of these, 6% reported pesticide residues above the MRLs.Physico-chemical properties can explain the occurrence of pesticides in rice commodities: lipophilic pesticides are frequently found in brown rice, whereas fungicides are mainly found in milled rice. Carbendazim, malathion, iprodione, tebuconazole, quinclorac and tricyclazole are the pesticides most frequently found in white rice, while buprofezin, hexaconazole, chlorpyrifos and edifenphos are most commonly found in paddy rice.Pesticide-residue concentrations can be affected during rice processing - with concentrations generally lower in the final products. However, few studies focusing on primary processing have addressed the setting of precise values applicable for the processing factors.     

Gas chromatography-mass spectrometry and high-performance liquid chromatography-tandem mass spectrometry in quantifying fatty acids

This critical overview covers current analytical methods and future developments in quantitative determination of fatty acids (FAs), emphasizing sample extraction, derivatization and instrumental analysis with gas chromatography/mass spectrometry (GC/MS) and high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS²). We compare the benefits and the drawbacks of these two analytical techniques.We consider the well-established GC/MS method with pre-derivatization to be a traditional technique in terms of highly standardized sample-preparation procedures, affordability and readily available library searching for compound identification. However, the complicated derivatization steps required prior to instrumental analysis with GC/MS take a long time, with loss and transformation of FAs, low recovery and poor reproducibility.HPLC/MS² without derivatization shows the benefits of simple, mild sample-processing conditions, satisfactory recovery, short running time and high selectivity and sensitivity, which may allow it to become a viable alternative to GC/MS for the analysis of FAs in the years ahead.     

Analytical challenges and the development of biomarkers to measure and to monitor the effects of ocean acidification

Changing ocean-carbonate chemistry caused by oceanic uptake of anthropogenic atmospheric carbon dioxide leads to the formation of carbonic acid, thus lowering the pH of the sea with predictions of a decrease from current levels at 8.15 to 7.82 by the end of the century. The exact measurement of subtle pH changes in seawater over time presents significant analytical challenges, as the equilibrium constants are governed by water temperature and pressure, salinity effects, and the existence of other ionic species in seawater.Here, we review these challenges and how pH also affects dissolved inorganic and organic chemicals that affect biological systems. This includes toxic compounds (xenobiotics) as well as chemicals that are beneficial for marine organisms, such as the chemical signals (i.e. pheromones) that are utilized to coordinate animal behavior. We review how combining analytical, molecular and biochemical tools can lead to the development of biosensors to detect pH effects to enable predictive modeling of the ecological consequences of ocean acidification.     

Centrifugally-driven sample extraction, preconcentration and purification in microfluidic compact discs

Centrifugally-driven microfluidic compact discs (μ-CDs) have attracted significant interest within the analytical science community in the past decade, with the primary focus on the potential of such platforms for performing parallel and/or multiplex biological assays and further application in biomedical diagnostics. More recently, μ-CD-based devices were also applied to environmental analysis as platforms for multi-sample extraction and transportation, prior to off-disc analysis in the laboratory. This review critically summarizes recent developments in μ-CD platforms for sample extraction, preconcentration, fractionation and purification in bioanalytical and environmental applications. We also summarize the common methods employed in the fabrication of μ-CD platforms. Further, we discuss preparation of stationary phases in microfluidic channels embedded in μ-CDs, as applications of μ-CDs in sample extraction are generally based on enclosed series of extraction phases and microcolumns.     

Characterization of poly(2,6-diphenyl-p-phenylene oxide) films as adsorbent for microfabricated preconcentrators

This work aims at evaluating poly(2,6-diphenyl-p-phenylene oxide) (Tenax TA), in the form of thin films, as an adsorbent material for various analytical applications. The physical properties of the polymer were studied with regard to surface topography, crystal structure, and thermal stability. Films deposited from solution at different substrate temperatures were studied and compared to the granular form of the polymer. It was found that Tenax TA deposited from solution have a different topography compared to their granular counterpart. The films possess a complex phase composition that includes crystalline and amorphous phases. The films showed high thermal stability (400 °C) similar to the granular form. The adsorption performance of the polymer compared to other possible adsorbent films such as polydimethylsiloxane (PDMS) and layer-by-layer assembled gold nanoparticles (GNPs) were also investigated. Representative volatile organic compound samples were used to compare the adsorption properties of Tenax TA films to that of the granules.     

Development of a new microextraction method based on a dynamic single drop in a narrow-bore tube: application in extraction and preconcentration of some organic pollutants in well water and grape juice samples

A novel sample preparation technique, the microextraction method based on a dynamic single drop in a narrow-bore tube, coupled with gas chromatography-flame ionization detection (GC-FID) is presented in this paper. The most important features of this method are simplicity and high enrichment factors. In this method, a microdrop of an extraction solvent assisted by an air bubble was repeatedly passed through a narrow-bore closed end tube containing aqueous sample. It has been successfully used for the analysis of some pesticides as model analytes in aqueous samples. Parameters affecting the method's performance such as selection of extraction solvent type and volume, number of extractions, volume of aqueous sample (tube length), and salt effect were studied and optimized. Under the optimal conditions, the enrichment factors (EFs) for triazole pesticides were in the range of 141-214 and the limits of detection (LODs) were between 2 and 112 μg L⁻¹. The relative standard deviations (C = 1000 μg L⁻¹, n = 6) were obtained in the range of 2.9-4.5%. The recoveries obtained for the spiked well water and grape juice samples were between 71 and 106%. Low cost, relatively short sample preparation time and less solvent consumption are other advantages of the proposed method.     

Influence of acidification on the optical properties and molecular composition of dissolved organic matter

Acidification is a common method for preserving dissolved organic matter (DOM) in natural water samples until sophisticated laboratory analyses can be performed. However, little is known about the effects of this practice on the composition and optical properties of DOM. In this study, the effects of acidification on DOM in porewater samples collected from the RL IV bog system of the Glacial Lake Agassiz Peatlands in northern Minnesota were characterized. Molecular composition was determined by ultrahigh resolution mass spectrometry and optical properties by UV absorption and three-dimensional fluorescence spectroscopy. Excitation–emission matrix fluorescence spectroscopy results indicate that the fluorescence properties of the peatland porewater DOM were sensitive to pH and that the observed changes were fluorophore dependent. Ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry revealed the appearance of newly formed, oxygen-rich compounds upon acidification. The extent to which these oxygen-rich compounds were formed was also dependent on the composition of the DOM.     

Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry

Precise proteomic profiling of limited levels of disease tissue represents an extremely challenging task. Here, we present an effective and reproducible microproteomic workflow for sample sizes of only 10,000 cells that integrates selective sample procurement via laser capture microdissection (LCM), sample clean-up and protein level fractionation using short-range SDS-PAGE, followed by ultrasensitive LC-MS/MS analysis using a 10 μm i.d. porous layer open tubular (PLOT) column. With 10,000 LCM captured mouse hepatocytes for method development and performance assessment, only 10% of the in-gel digest, equivalent to ～1000 cells, was needed per LC-MS/MS analysis. The optimized workflow was applied to the differential proteomic analysis of 10,000 LCM collected primary and metastatic breast cancer cells from the same patient. More than 1100 proteins were identified from each injection with >1700 proteins identified from three LCM samples of 10,000 cells from the same patient (1123 with at least two unique peptides). Label free quantitation (spectral counting) was performed to identify differential protein expression between the primary and metastatic cell populations. Informatics analysis of the resulting data indicated that vesicular transport and extracellular remodeling processes were significantly altered between the two cell types. The ability to extract meaningful biological information from limited, but highly informative cell populations demonstrates the significant benefits of the described microproteomic workflow.     

Tools for analyzing the phosphoproteome and other phosphorylated biomolecules: a review

Enrichment, separation and mass spectrometric analysis of biomolecules carrying a phosphate group plays an important role in current analytical chemistry. Application areas range from the preparative enrichment of phospholipids for biotechnological purposes and the separation and purification of plasmid DNA or mRNA to the specific preconcentration of phosphoproteins and -peptides to facilitate their later identification and characterization by mass spectrometry. Most of the recent improvements in this field were triggered by the need for phosphopeptide enrichment technology for the analysis of cellular protein phosphorylation events with the help of liquid chromatography–mass spectrometry. The high sensitivity of mass spectrometry and the possibility to combine this technique with different separation modes in liquid chromatography have made it the method of choice for proteome analysis. However, in the case of phosphoprotein analysis, the low abundance of the resulting phosphopeptides and their low quality fragment spectra interfere with the identification of phosphorylation events. Recent developments in phosphopeptide enrichment and fragmentation technologies successfully helped to overcome these limitations. In this review, we will focus on sample preparation techniques in the field of phosphoproteomics, but also highlight recent advancements for the analysis of other phosphorylated biomolecules.