Ultrasound-assisted digestion: A useful alternative in sample preparation

Ultrasound-assisted digestion is a promising alternative in the analysis of solid samples when either simple dissolution or direct analysis is not applicable. However, the field of application of ultrasonic sample digestion is still small in comparison with classical digestion alternatives and, particularly, with microwave-assisted digestion. This fact can be justified by the scant knowledge analytical chemists have about the advantages ultrasonic energy provides to digestion. Among these, the strict control at low temperatures of ultrasound applications allows the implementation of ultrasonic-assisted steps in biochemical analyses. In this connection, two specific biological applications, ultrasonic enzymatic digestion and assistance of ultrasound for cell disruption, are also reviewed.     

Benchmarking sample preparation/digestion protocols reveals tube‐gel being a fast and repeatable method for quantitative proteomics

Sample preparation, typically by in‐solution or in‐gel approaches, has a strong influence on the accuracy and robustness of quantitative proteomics workflows. The major benefit of in‐gel procedures is their compatibility with detergents (such as SDS) for protein solubilization. However, SDS‐PAGE is a time‐consuming approach. Tube‐gel (TG) preparation circumvents this drawback as it involves directly trapping the sample in a polyacrylamide gel matrix without electrophoresis. We report here the first global label‐free quantitative comparison between TG, stacking gel (SG), and basic liquid digestion (LD). A series of UPS1 standard mixtures (at 0.5, 1, 2.5, 5, 10, and 25 fmol) were spiked in a complex yeast lysate background. TG preparation allowed more yeast proteins to be identified than did the SG and LD approaches, with mean numbers of 1979, 1788, and 1323 proteins identified, respectively. Furthermore, the TG method proved equivalent to SG and superior to LD in terms of the repeatability of the subsequent experiments, with mean CV for yeast protein label‐free quantifications of 7, 9, and 10%. Finally, known variant UPS1 proteins were successfully detected in the TG‐prepared sample within a complex background with high sensitivity. All the data from this study are accessible on ProteomeXchange (PXD003841).     

Determination of nitrie in human blood by combination of a specific sample preparation with high-performance anion-exchange chromatography and electrochemical detection

All photometric or HPLC methods described to date have been unable to detect nitrite, a reliable marker of NO synthase activity, in human blood because of its rapid metabolism within the erythrocytes. We now elaborate on method to prevent nitrite degradation during sample preparation which in combination with high-performance anion-exchange chromatography and electrochemical detection allows a sensitive measurement of nitrite. A linear current response in the concentration range of 10–1000 nmol/l nitrite was observed yielding a correlation coefficient of 0.99. In addition, the combination of the electrochemical with a UV detector allowed us to simultaneously quantify nitrate one analytical run, which is the end product of NO/nitrite metabolism. Basal levels for nitrate and nitrite in human blood were determined with 25±4 μmol/l and 578±116 nmol/l (n=8), respectively and thus were in the same concentration range as expected from NO measurement in saline perfused isolated organs or cultured endothelial cells. Therefore, the presented method may be used to assess activity of endothelial constitutive NO synthase in humans under physiological and pathophysiological conditions.     

Sample preparation and digestion for proteomic analyses using spin filters

We describe the use of commercially available microcentrifugation devices (spin filters) for cleanup and digestion of protein samples for mass spectrometry analyses. The protein sample is added to the upper chamber of a spin filter with a > or = 3000 molecular weight cutoff membrane and then washed prior to resuspension in ammonium bicarbonate. The protein is then reduced, alkylated, and digested with trypsin in the upper chamber and the peptides are recovered by centrifugation through the membrane. The method provides digestion efficiencies comparable to standard in-solution digests, avoids lengthy dialysis steps, and allows rapid cleanup of samples containing salts, some detergents, and acidic or basic buffers.     

Recent advances in DNA sequencing methods - general principles of sample preparation

DNA sequencing has revolutionized biomedicine, and progress in the field has been unrelenting since it was invented over 30 years ago. The complete DNA sequence of the human genome was obtained as the culmination of a decade of work by a large number of scientists. Less than ten years later, so-called ‘next-generation’ instruments now make it possible for a single lab to produce the same amount of data in a week. But while the instruments are increasingly automated, upstream sample processing remains a challenge. Here I review the current state of the art in preparing genomic and RNA samples for high throughput sequencing.     

Semi-automated liquid--liquid back-extraction in a 96-well format to decrease sample preparation time for the determination of dextromethorphan and dextrorphan in human plasma

A semi-automated, 96-well based liquid-liquid back-extraction (LLE) procedure was developed and used for sample preparation of dextromethorphan (DEX), an active ingredient in many over-the-counter cough formulations, and dextrorphan (DOR), an active metabolite of DEX, in human plasma. The plasma extracts were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS-MS). The analytes were isolated from human plasma using an initial ether extraction, followed by a back extraction from the ether into a small volume of acidified water. The acidified water isolated from the back extraction was analyzed directly by LC-MS-MS, eliminating the need for a dry down step. A liquid handling system was utilized for all aspects of liquid transfers during the LLE procedure including the transfer of samples from individual tubes into a 96-well format, preparation of standards, addition of internal standard and the addition and transfer of the extraction solvents. The semi-automated, 96-well based LLE procedure reduced sample preparation time by a factor of four versus a comparable manually performed LLE procedure.     

Automated multi-dimensional liquid chromatography: sample preparation and identification of peptides from human blood filtrate

A comprehensive on-line sample clean-up with an integrated two-dimensional HPLC system was developed for the analysis of natural peptides. Samples comprised of endogenous peptides with molecular weights up to 20 kDa were generated from human hemofiltrate (HF) obtained from patients with chronic renal failure. The (poly-)peptides were separated using novel silica-based restricted access materials with strong cation-exchange functionalities (SCX-RAM). The size-selective sample fractionation step is followed by cation-exchange chromatography as the first dimension. The subsequent second dimension of separation is based on hydrophobic interaction using four parallel short reversed-phase (RP) columns implemented via a fully automated column switching technique. More than 1000 peaks were resolved within the total analysis time of 96 min. Substances of selected peaks were sampled to analyse their molecular weights by off-line MALDI-TOF mass spectrometry and to determine their amino acid sequence by Edman degradation. The potential for comprehensive peptide mapping and identification is demonstrated.     

Matrix layer sample preparation: an improved MALDI-MS peptide analysis method for proteomic studies

The analytical performance of MALDI-MS is highly influenced by sample preparation and the choice of matrix. Here we present an improved MALDI-MS sample preparation method for peptide mass mapping and peptide analysis, based on the use of the 2,5-dihydroxybenzoic acid matrix and prestructured sample supports, termed: matrix layer (ML). This sample preparation is easy to use and results in a rapid automated MALDI-MS and MS/MS with high quality spectra acquisition. The between-spot variation was investigated using standard peptides and statistical treatment of data confirmed the improvement gained with the ML method. Furthermore, the sample preparation method proved to be highly sensitive, in the lower-attomole range for peptides, and we improved the performance of MALDI-MS/MS for characterization of phosphopeptides as well. The method is versatile for the routine analysis of in-gel tryptic digests thereby allowing for an improved protein sequence coverage. Furthermore, reliable protein identification can be achieved without the need of desalting sample preparation. We demonstrate the performance and the robustness of our method using commercially available reference proteins and automated MS and MS/MS analyses of in-gel digests from lung tissue lysate proteins separated by 2-DE.     

Measurement uncertainty from physical sample preparation of moss samples: Estimation of mechanical cleaning vs. rinsing

Next to sampling, the physical sample preparation step is a second large source of uncertainty. To assess the level of uncertainty from sampling, sample preparation and analysis of moss material, 27 combined and duplicate samples of moss species Pleurozium schreberi (Brid.) Mitt were collected and prepared for analysis using two different treatment methods After sampling had been done, samples were dried at an ambient temperature and then each primary and duplicate sample was divided into two sub-samples for preparation. The first sub-sample was manually cleaned whereas the second one was triple rinsed with deionized water and left to dry. Subsequently, the samples were milled and digested in a close microwave system with 8 mL of HNO₃ (1:1) and 1 mL of 30% H₂O₂. In all samples Cu, Fe and Zn were determined using GFAAS and FAAS techniques. Each sample was analyzed twice. Sampling, sample preparation and analytical uncertainty were calculated using ANOVA, RANOVA, modified RANOVA and range statistics methods. Sampling and sample preparation uncertainty varied from 3.8 to 19.8% and from 3.6 to 11.2%, respectively. For all the elements examined analytical uncertainty was below 1.1%. The comparison of element concentrations in manually cleaned and rinsed samples showed that rinsed samples were enriched in Cu and Zn, as opposed to manually cleaned that in turn displayed raised levels of Fe. However, except for Zn, these differences were not statistically significant.     

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.     

Assessment of sample preparation methods for metaproteomics of extracellular proteins

Enzyme discovery in individual strains of microorganisms is compromised by the limitations of pure culturing. In principle, metaproteomics allows for fractionation and study of different parts of the protein complement but has hitherto mainly been used to identify intracellular proteins. However, the extracellular environment is also expected to comprise a wealth of information regarding important proteins. An absolute requirement for metaproteomic studies of protein expression, and irrespective of downstream methods for analysis, is that sample preparation methods provide clean, concentrated and representative samples of the protein complement. A battery of methods for concentration, extraction, precipitation and resolubilization of proteins in the extracellular environment of a constructed microbial community was assessed by means of 2D gel electrophoresis and image analysis to elucidate whether it is possible to make the extracellular protein complement available for metaproteomic analysis. Most methods failed to provide pure samples and therefore negatively influenced protein gel migration and gel background clarity. However, one direct precipitation method (TCA-DOC/acetone) and one extraction/precipitation method (phenol/methanol) provided complementary high quality 2D gels that allowed for high spot detection ability and thereby also spot detection of less abundant extracellular proteins.     

Reduction of proteins during sample preparation and two-dimensional gel electrophoresis of woody plant samples

Protein extraction procedure and the reducing agent content (DTT, dithioerythritol, tributyl phosphine and tris (2-carboxyethyl) phosphine (TCEP)) of the sample and rehydration buffers were optimised for European beech leaves and roots and Norway spruce needles. Optimal extraction was achieved with 100 mM DTT for leaves and needles and a mixture of 2 mM TCEP and 50 mM DTT for roots. Performing IEF in buffers containing hydroxyethyldisulphide significantly enhanced the quality of separation for all proteins except for acidic root proteins, which were optimally focused in the same buffer as extracted.     

Gel‐aided sample preparation (GASP)—A simplified method for gel‐assisted proteomic sample generation from protein extracts and intact cells

We describe a “gel‐assisted” proteomic sample preparation method for MS analysis. Solubilized protein extracts or intact cells are copolymerized with acrylamide, facilitating denaturation, reduction, quantitative cysteine alkylation, and matrix formation. Gel‐aided sample preparation has been optimized to be highly flexible, scalable, and to allow reproducible sample generation from 50 cells to milligrams of protein extracts. This methodology is fast, sensitive, easy‐to‐use on a wide range of sample types, and accessible to nonspecialists.     

Laboratory-scale ultrasound pre-treated digestion of sludge: Heat and energy balance

The objective of this work was to maximize the digestibility of biological sludge to elucidate the feasibility of a new sludge management strategy to recover good quality sludge for agricultural use. The combined effects of organic loading rates (from 0.7 to 2.8 g VS L⁻¹ d⁻¹) and the degree of disintegration by anaerobic digestion of sonicated activated sludge were discussed, and the thermal and energetic balances were evaluated. Despite low sonication inputs, sludge digestion performance improved in terms of solids degradation and biogas production depending on the soluble organic load. The biogas production by sonicated sludge was higher (up to 30%) with respect to the control. Filterability improved during digestion of sonicated sludge at medium OLR due to a significant abatement of the fines. Thermal balances indicated that sonication may be a proper system to guarantee self-sustaining WAS mesophilic digestion. Nevertheless, thickening is a pre-requisite to achieve a positive energy balance.     

Microwave digestion preparation and ICP determination of boron in human plasma

A microwave digestion procedure, followed by Inductively Coupled Argon Plasma Spectroscopy, is described for the determination of boron (B) in human plasma. The National Institute of Standards and Technology (NIST) currently does not certify the concentration of B in any substance. The NIST citrus leaves 1572 (CL) Standard Reference Material (SRM) and wheat flour 1567a (WF) were chosen to determine the efficacy of digestion. CL and WF values compare favorably to those obtained from an open-vessel, wet digestion followed by ICP, and by neutron activation and mass spectrometric measurements. Plasma samples were oxidized by doubled-distilled ultrapure HNO₃ in 120 mL PFA Teflon^™ vessels. An MDS-81D microwave digestion procedure allows for rapid and relatively precise determination of B in human plasma, while limiting handling hazards and sources of contamination.     

Industrial by-products from white-rot fungi production. Part II: Application in anaerobic digestion for enzymatic treatment of hay and straw

By-products of white-rot fungi cultivations are valuable resources for the production of useful enzyme cocktails. These enzymes, which act synergistically to deconstruct lignocellulose polymers, can be recovered and potentially applied in industrial processes. This study investigated the application of processed by-products from Lentinula edodes cultivations in mesophilic and thermophilic anaerobic digestions of hay and straw. Untreated and mechanically treated hay and straw were investigated in biochemical methane potential assays with or without application of enzyme-containing materials. Biomasses, inocula and processed by-product were analyzed chemically and the degradation rate of lignocellulose polymers determined.In mesophilic conditions, all of the fungus-derived enzyme treatments increased the methane yield. A newly generated enzyme preparation significantly enhanced the methane yield of chopped hay and straw, and accelerated the rate of hemicellulose degradation. In general, the degree of cellulose degradation correlated with the methane yield. The novel enzyme preparation contains a larger variety of enzymes than is commonly found in biogas enzyme preparations and is thus an attractive candidate for significant process improvement. Our new investigation further shows that enzyme preparations of L. edodes have a high potential for catalytic activity in lignocellulose-rich systems without manure as co-substrate.     

Optimization of human dendritic cell sample preparation for mass spectrometry-based proteomic studies

Dendritic cells (DCs) are specialized leukocytes that orchestrate the adaptive immune response. Mass spectrometry (MS)-based proteomic study of these cells presents technical challenges, especially when the DCs are human in origin due to the paucity of available biological material. Here, to maximize MS coverage of the global human DC proteome, different cell disruption methods, lysis conditions, protein precipitation, and protein pellet solubilization and denaturation methods were compared. Mechanical disruption of DC cell pellets under cryogenic conditions, coupled with the use of RIPA (radioimmunoprecipitation assay) buffer, was shown to be the method of choice based on total protein extraction and on the solubilization and identification of nuclear proteins. Precipitation by acetone was found to be more efficient than that by 10% trichloroacetic acid (TCA)/acetone, allowing in excess of 28% more protein identifications. Although being an effective strategy to eliminate the detergent residue, the acetone wash step caused a loss of protein identifications. However, this potential drawback was overcome by adding 1% sodium deoxycholate into the dissolution buffer, which enhanced both solubility of the precipitated proteins and digestion efficiency. This in turn resulted in 6 to 11% more distinct peptides and 14 to 19% more total proteins identified than using 0.5 M triethylammonium bicarbonate alone, with the greatest increase (34%) for hydrophobic proteins.     

Concentration and desalting of peptide and protein samples with a newly developed C18 membrane in a microspin column format.

Protein identification plays an important role in today's academic and industrial proteomic research. Commonly used methods for the separation of proteins from complex samples include liquid chromatography (e.g., ion exchange, reversed-phase, hydrophobic interaction), or types of gel electrophoresis (e.g., 1d and 2d PAGE). Relevant proteins separated in the latter way are often cut out, cleaved with trypsin "in gel," and the resulting peptide mixtures combined with matrix and spotted onto a target plate for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-ms) analysis. Subsequently, proteins can be identified by comparison of the resulting peptide mass fingerprints against different databases.(1) since the success of protein identification can be enhanced by the desalting and concentration of the samples, an innovative C18-membrane was incorporated into a microspin column (Vivapure C18 micro spin column, Vivascience AG, Hannover, Germany) to analyze its performance for sample preparation prior to MALDI-ToF-ms. Rapid concentration of single or multiple 200-microl volumes through an available membrane only 2 mm in diameter allowed for analysis of very dilute samples. We observed the successful and rapid desalting of urea-containing protein samples at 100 fmol/mul up to a mass of approximately 70 KDA and the concentration of digest peptides from a solution of 1 fmol/microl using C18-membrane technology.     

Tissue digestion for aluminum determination in experimental animal studies

Four different procedures for the determination of aluminum in tissues by atomic absorption spectrometry (AAS) were investigated. They consisted of conventional acid digestion carried out before and after sample drying, associated or not with fat extraction. Drying was carried out in a conventional oven at 65 °C for 24 h. For fat extraction, different solvents and solvent mixtures were investigated considering both extraction yield and sample adequacy for further AAS measurement. Acid digestion was carried out with pure HNO₃ or with its mixture with HClO₄. After digestion, aluminum was measured by graphite furnace atomic absorption spectrometry. Tissues were collected from Al-exposed and nonexposed mice. The results indicated that drying the sample prior to digestion is advantageous as the amount of acid necessary can be significantly reduced. This procedure does not contribute to increase the aluminum level in the samples providing that careful measures to avoid contamination are taken, as the same procedures carried out without taking any precautions to avoid contamination produced imprecise results. Finally, aluminum was not found in the fatty fraction of any sample, even in exposed mice, demonstrating that aluminum does not accumulate in this part of the tissues.     

An automated sample preparation system with mini-reactor to isolate and process submegabase fragments of bacterial DNA

Existing methods for extraction and processing of large fragments of bacterial genomic DNA are manual, time-consuming, and prone to variability in DNA quality and recovery. To solve these problems, we have designed and built an automated fluidic system with a mini-reactor. Balancing flows through and tangential to the ultrafiltration membrane in the reactor, cells and then released DNA can be immobilized and subjected to a series of consecutive processing steps. The steps may include enzymatic reactions, tag hybridization, buffer exchange, and selective removal of cell debris and by-products of the reactions. The system can produce long DNA fragments (up to 0.5 Mb) of bacterial genome restriction digest and perform DNA tagging with fluorescent sequence-specific probes. The DNA obtained is of high purity and floating free in solution, and it can be directly analyzed by pulsed-field gel electrophoresis (PFGE) or used in applications requiring submegabase DNA fragments. PFGE-ready samples of DNA restriction digests can be produced in as little as 2.1 h and require less than 10⁸ cells. All fluidic operations are automated except for the injection of the sample and reagents.