Tissue proteomics using chemical immobilization and mass spectrometry

Proteomics analysis is important for characterizing tissues to gain biological and pathological insights, which could lead to the identification of disease-associated proteins for disease diagnostics or targeted therapy. However, tissues are commonly embedded in optimal cutting temperature medium (OCT) or are formalin-fixed and paraffin-embedded (FFPE) in order to maintain tissue morphology for histology evaluation. Although several tissue proteomic analyses have been performed on FFPE tissues using advanced mass spectrometry (MS) technologies, high-throughput proteomic analysis of OCT-embedded tissues has been difficult due to the interference of OCT in the MS analysis. In addition, molecules other than proteins present in tissues further complicate tissue proteomic analysis. Here, we report the development of a method using chemical immobilization of proteins for peptide extraction (CIPPE). In this method, proteins are chemically immobilized onto a solid support; interferences from tissues and OCT embedding are removed by extensive washing of proteins conjugated on the solid support. Peptides are then released from the solid phase by proteolysis, enabling MS analysis. This method was first validated by eliminating OCT interference from a standard protein, human serum albumin, where all of the unique peaks contributed by OCT contamination were eradicated. Finally, this method was applied for the proteomic analysis of frozen and OCT-embedded tissues using iTRAQ (isobaric tag for relative and absolute quantitation) labeling and two-dimensional liquid chromatography tandem mass spectrometry. The data showed reproducible extraction and quantitation of 10,284 proteins from 3996 protein groups and a minimal impact of OCT embedding on the analysis of the global proteome of the stored tissue samples.     

Determination of pyridoxal 5′-phosphate as the semicarbazone derivative using high-performance liquid chromatography

A high-performance liquid chromatographic (hplc) procedure is described for the determination of pyridoxal 5′-phosphate (PLP) in animal tissues. The procedure is based on extraction with perchloric acid and treatment with semicarbazide to form PLP-semicarbazone. This derivative is quantitatively determined using hplc with an octylsilica column, an acidic phosphate mobile phase buffer, and fluorometric detection. The validity of the method was confirmed by inspection of the fluorescence spectra of the PLP-semicarbazone hplc peaks of semicarbazide-treated standards and tissue extracts. Preparative chromatography for extract purification is not required because of the hplc efficiency and detection specificity. This method provides a simple technique for the rapid, direct assay of PLP in animal tissues.     

High-performance liquid chromatographic determination of biotin in biological materials after crown ether-catalyzed fluorescence derivatization with panacyl bromide.

This paper reports a high-performance liquid chromatographic (HPLC) technique to determine biotin in biological samples. Biotin and the internal standard dethiobiotin are converted into fluorescent derivatives by using panacyl bromide [p-(9-anthroyloxy)phenacyl bromide] as a fluorescence label. Biotin is extracted from biological tissue with trichloroacetic acid and the extract is purified by a combination of solid-phase extraction on C18 cartridges, ion-exchange chromatography on DOWEX formate resin, and thin-layer chromatography. The purified sample extract is derivatized in the presence of a crown ether. The resulting panacyl esters can be separated on reversed-phase as well as on normal-phase HPLC. Normal phase HPLC is preferable because it provides higher sensitivity and demands less sample pretreatment. Analysis of rat intestinal tissue revealed that only about 13% of the biotin is present in free form whereas 87% is bound in proteins from which it can be released by hydrolysis. Biotin values determined by this method are comparable to those obtained by other techniques.     

Efficient extraction of RNA from mammalian tissue

RNA extraction from mammalian tissue has been compared using the different deproteinizing agents: a) guanidine-HCl, b) guanidinium-thiocyanate, c) buffer-saturated phenol, or d) buffer-saturated phenol followed by a proteinase K digestion of the aqueous phase. Both solid tissues (first, second, and third trimester fetal bovine pancreas), and human white blood cell populations were studied. Degradation, as seen in citric acid-urea agarose gels, and the ability to serve as templates for cell-free protein synthesis were used as criteria to assess the efficiency of the different methods. We conclude that employing buffer-saturated phenol with proteinase K digestion is a superior method for consistent extraction of relatively undegraded RNA in quantitative amounts from mammalian tissue.     

Determination of 8:2 fluorotelomer alcohol in animal plasma and tissues by gas chromatography-mass spectrometry

Fluorotelomer alcohols (FTOHs) constitute an important group of compounds among the perfluoroalkyl substances (PFAS). The PFAS have recently been a focus of many environmental and biological studies. This generated a strong need for analytical methods for analysis of PFAS at trace levels in various environmental and biological matrices. A quantitative analytical method for analysis of 8:2 FTOH in rat plasma and rat liver, kidney, and adipose tissue using GC-MS with electron impact (EI) ionization was developed and validated. Extraction of water-diluted plasma with methyl tert-butyl ether (MTBE) was used for rat plasma. The analysis of rat liver or kidney tissues required homogenization of tissue on ice, extraction with hexane, and clean up of the extract by silica (Si) normal-phase solid phase extraction (SPE). Similarly, the adipose tissue was dissolved in n-heptane and cleaned up by Si SPE. The methods were validated by performing spike recovery experiments for each type of matrix investigated and tested on authentic samples originating from 8:2 FTOH toxicological studies.     

HPLC analysis of asymmetric dimethylarginine,symmetric dimethylarginine,homoarginine and arginine in small plasma volumes using a Gemini-NX column at high pH

There is increasing recognition of the clinical importance of endogenous nitric oxide synthase inhibitors in critical illness. This has highlighted the need for an accurate high performance liquid chromatography (HPLC) method for detection of asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA) in small volumes of blood. Here, the validation of an accurate, precise HPLC method for the determination of ADMA, SDMA, homoarginine and arginine concentrations in plasma is described. Solid phase extraction is followed by derivatisation with AccQ-Fluor™ and reversed phase separation on a Gemini-NX column at pH 9. Simultaneous detection by both UV–vis and fluorescence detectors affords extra validation. This solid phase extraction method gives absolute recoveries of more than 85% for ADMA and SDMA and relative recoveries of 102% for ADMA and 101% for SDMA. The intra-assay relative standard deviations are 2.1% and 2.3% for ADMA and SDMA, respectively, with inter-assay relative standard deviations of 2.7% and 3.1%, respectively. Advantages of this method include improved recovery of all analytes using isopropanol in the solid phase extraction; sharp, well-resolved chromatographic peaks using a high pH mobile phase; a non-endogenous internal standard, n-propyl l-arginine; and accurate and precise determination of methylated arginine concentrations from only 100 μL of plasma.     

Optimization of a solid phase extraction procedure for prostaglandin E2, F2 alpha and their tissue metabolites

The primary prostaglandins PGE(2) and PGF(2 alpha) are metabolized in tissues by a series of enzymatic and non-enzymatic reactions. To measure metabolic rates and individual reaction rates it is necessary to extract the parent prostaglandins and metabolites before the separation and quantification of each compound is achieved. Here we have established and optimized a solid phase extraction (SPE) procedure to recover PGE(2), PGF(2 alpha) and their six enzymatic and non-enzymatic tissue metabolites from aqueous solutions including urine, plasma and tissue homogenate. We have used octadecyl-bonded silica gel as the stationary phase and methanol-water mixtures as binary mobile phases. The volumes and concentrations of the washing and elution solutions were optimized individually for each PG. Recoveries of all PG standards were quantitative except for PGEM, which was recovered at 80% efficiency. Biological matrix components interfered with the extraction in a PG- and matrix-specific fashion. Inclusion of 1% formic acid in the loading mixture raised recoveries from urine, plasma and tissue homogenate to >or=90%. This SPE method is the first that has been optimized by systematic elution studies for PGE(2), PGF(2 alpha) and the complement of their tissue metabolites. The procedure is simple, robust and can serve as an effective pre-purification step before downstream separation and quantification of each tissue metabolite of PGE(2) and PGF(2 alpha) from complex biological matrices.     

Simple and sensitive determination of five quinolones in food by liquid chromatography with fluorescence detection

A simple and sensitive high-performance liquid chromatographic (HPLC) method has been developed for the determination of five different quinolones: enrofloxacin, ciprofloxacin, sarafloxacin, oxolinic acid and flumequine in pork and salmon muscle. The method includes one extraction and clean-up step for the five quinolones together which are detected in two separated HPLC runs by means of their fluorescence. The proposed analytical method involves homogenizing of the tissue sample with 0.05 M phosphate buffer, pH 7.4 and clean-up by Discovery DS-18 cartridges. For chromatographic separation a Symmetry C(18) column is used in two different runs: (1) ciprofloxacin, enrofloxacin and sarafloxacin with acetonitrile-0.02 M phosphate buffer pH 3.0 (18:82) as mobile phase and the detector at excitation wavelength: 280 nm and emission wavelength 450 nm; and (2) oxolinic acid and flumequine with acetonitrile-0.02 M phosphate buffer pH 3.0 (34:66) as mobile phase and excitation wavelength: 312 nm and emission wavelength: 366 nm. Detection limit was as low as 5 ng g(-1), except for sarafloxacin which had a limit of 10 ng g(-1). Standard curves using blank muscle tissues spiked at different levels showed a good linear correlation coefficient, r(2) higher than 0.999 for all quinolones.     

A rapid protocol for purification of total RNA for tissues collected from pigs at a slaughterhouse

Since RNA extraction is a crucial step in many molecular techniques, the protocols for sample collection and RNA purification need to be adapted to optimize their performance when samples are collected from animals at commercial facilities. Here we provide an RNA purification protocol for animal tissues collected from slaughterhouses. This protocol, modified from other techniques, uses TRIzol Reagent. Sample collection was performed wearing sterile gloves and facemasks, using sterile surgical instruments, and no longer than 8 min spent for each sample. A 0.9% sterile sodium chloride solution was used to wash the tissue before each sample collection. The whole process of RNA extraction was performed under cold environment and sterile conditions. This protocol produced good RNA yields (50 μg RNA per 100 mg tissue), good integrity and purity (Abs(260/280) from 1.8 to 2.0), from tissues such as liver, muscle, hypophysis, adipose tissue, and intestinal mucosa, in less than 2 h.     

SPE-HPLC法快速检测发酵液中紫杉醇的含量

针对红豆杉内生真菌发酵液中紫杉醇的含量测定进行探讨,以建立快速高效低耗的检测方法.采用C_(18)固相萃取柱对紫杉醇进行吸附,用不同浓度的甲醇-乙酸铵和甲醇分别作为洗脱剂对其进行洗脱,比较两者的洗脱效果,洗脱液用HPLC进行检测;色谱条件为:流动相甲醇(v):水(v):乙腈(v)=20: 45: 35,流速:0.70 ml/min,检测波长:227 nm.结果表明,浓度为80%的甲醇溶液洗脱效果较好,紫杉醇的回收率为87.6%.     

Effects of friction on the unconfined compressive response of articular cartilage: a finite element analysis

A finite element analysis is used to study a previously unresolved issue of the effects of platen-specimen friction on the response of the unconfined compression test; effects of platen permeability are also determined. The finite element formulation is based on the linear KLM biphasic model for articular cartilage and other hydrated soft tissues. A Galerkin weighted residual method is applied to both the solid phase and the fluid phase, and the continuity equation for the intrinsically incompressible binary mixture is introduced via a penalty method. The solid phase displacements and fluid phase velocities are interpolated for each element in terms of unknown nodal values, producing a system of first order differential equations which are solved using a standard numerical finite difference technique. An axisymmetric element of quadrilateral cross-section is developed and applied to the mechanical test problem of a cylindrical specimen of soft tissue in unconfined compression. These studies show that interfacial friction plays a major role in the unconfined compression response of articular cartilage specimens with small thickness to diameter ratios.     

Methods for detecting and identifying retinoids in tissue

Methods for retinoid analysis in tissue include direct spectrophotometry or fluorometry and retinoid responsive reporter constructs in the form of cell reporter assays or transgenic reporter animals, but chromatographic methods dominate and posses several superior features in quantitative analysis. The multitude of extraction protocols used can coarsely be divided into manual liquid-liquid extraction protocols and semi- or fully automated solid phase extraction-based protocols. Liquid chromatographic separation in reversed phase dominates although normal phase is also used. Detection is mainly performed with UV detectors although electrochemical and fluorescence detection is also used. Mass spectrometry in combination with LC is more often used in retinoid analysis and is likely to dominate in the future.     

Simultaneous determination of danofloxacin and N-desmethyldanofloxacin in cattle and chicken edible tissues by liquid chromatography with fluorescence detection

A rugged, simple, and selective method for the determination of danofloxacin and its primary metabolite, N-desmethyldanofloxacin, in cattle (liver, muscle, kidney, and fat) and chicken (liver and muscle) tissues was developed. The method is selective for danofloxacin and N-desmethyldanofloxacin over other veterinary important fluoroquinolones, such as enrofloxacin, ciprofloxacin, norfloxacin, and ofloxacin. Selectivity is achieved through a combination of extraction, chromatography, and fluorescence detection. The analytes were extracted from homogenized tissues using a methanolperchloric-phosphoric acid solution. After centrifugation, direct injection of extraction supernate was possible. The limit of quantitation was 20 pg on column. Separation was achieved on an Inertsil C₈ (5 μm, 100 Å) column with dimensions of 250×4.6 mm I.D. The mobile phase consisted of 0.05 M phosphate buffer (pH 3.5)-acetonitrile (88:12). A fluorescence detector was utilized with an excitation wavelenght of 280 nm and an emission wavelength of 440 nm. The assay was accurate and reproducible within the range of 10 to 500 ng/g for both danofloxacin and N-desmethyldanofloxacin. Intra-assay accuracy was between 98 and 101%, and precision was less than 4%. Inter-assay accuracy was between 99 and 102%, while precision was less than 2%. Recoveries for both analytes over the dynamic range were greater than 90% for all the tissues.     

Generating human intestinal tissue from pluripotent stem cells in vitro

Here we describe a protocol for generating 3D human intestinal tissues (called organoids) in vitro from human pluripotent stem cells (hPSCs). To generate intestinal organoids, pluripotent stem cells are first differentiated into FOXA2(+)SOX17(+) endoderm by treating the cells with activin A for 3 d. After endoderm induction, the pluripotent stem cells are patterned into CDX2(+) mid- and hindgut tissue using FGF4 and WNT3a. During this patterning step, 3D mid- or hindgut spheroids bud from the monolayer epithelium attached to the tissue culture dish. The 3D spheroids are further cultured in Matrigel along with prointestinal growth factors, and they proliferate and expand over 1-3 months to give rise to intestinal tissue, complete with intestinal mesenchyme and epithelium comprising all of the major intestinal cell types. To date, this is the only method for efficiently directing the differentiation of hPSCs into 3D human intestinal tissue in vitro.     

Determination of catechins and catechin gallates in tissues by liquid chromatography with coulometric array detection and selective solid phase extraction

Catechins levels in organ tissues, particularly liver, determined by published methods are unexpectedly low, probably due to the release of oxidative enzymes, metal ions and reactive metabolites from tissue cells during homogenization and to the pro-oxidant effects of ascorbic acid during sample processing in the presence of metal ions. We describe a new method for simultaneous analysis of eight catechins in tissue: (+)-catechin (C), (-)-epicatechin (EC), (-)-gallocatechin (GC), (-)-epigallocatechin (EGC), (-)-catechin gallate (CG), (-)-epicatechin gallate (ECG), (-)-gallocatechin gallate (GCG) and (-)-epigallocatechin gallate (EGCG) (Fig. 1). The new extraction procedure utilized a methanol/ethylacetate/dithionite (2:1:3) mixture during homogenization for simultaneous enzyme precipitation and antioxidant protection. Selective solid phase extraction was used to remove most interfering bio-matrices. Reversed phase HPLC with CoulArray detection was used to determine the eight catechins simultaneously within 25 min. Good linearity (>0.9922) was obtained in the range 20-4000 ng/g. The coefficients of variance (CV) were less than 5%. Absolute recovery ranged from 62 to 96%, accuracy 92.5 +/- 4.5 to 104.9 +/- 6%. The detection limit was 5 ng/g. This method is capable for determining catechins in rat tissues of liver, brain, spleen, and kidney. The method is robust, reproducible, with high recovery, and has been validated for both in vitro and in vivo sample analysis.     

A Review of Rapid Methods for the Analysis of Mycotoxins

An overview is presented of the analysis of mycotoxins by rapid methods such as: enzyme linked immuno-sorbent assay (ELISA); flow through membrane based immunoassay; immunochromatographic assay; fluorometric assay with immunoaffinity clean-up column or with a solid phase extraction clean-up column; and fluorescence polarization method. These methods are currently commercially available and are reliable, rapid methods. This review focuses on the basic principle of each rapid method as well as advantages and limitations of each method. Additionally, we address other emerging technologies of potential application in the analysis of mycotoxins.     

Strategies to recover proteins from ocular tissues for proteomics

We present here the results of protein extraction from different ocular regions using different detergents. Extraction strategies used to determine optimal protein extraction included: pressure cycling and aqueous-organic phase extraction in combination with electrophoretic fractionation for anterior, posterior, and peripapillary sclera. Detergent extraction of proteins from freshly enucleated porcine eyes (n = 8) showed significant differences for different eye regions. Protein yield ranged from 2.3 to 50.7 mug protein/mg for different ocular tissues, with the lens yielding the most protein. ASB-14 and Triton X-100 provided the best protein yields (n = 10) for anterior and posterior sclera. The spectrophotometric measurements for ASB-14 were not consistent with SDS-PAGE densitometry. A combination of 0.5% Triton X-100, 0.5% Tween-20, and 0.1% Genapol C-100 was found optimal for extraction from sclera. Proteins from different regions of the eye are best extracted with different detergents. The pressure cycling technology provided superior extraction compared to the other methods. Additional aqueous-organic phase partitioning enables superior fractionation when compared to SDS-PAGE alone. Organic phase fractionation is compatible with MS and allowed identification of 34, 71, and 77 proteins respectively from anterior, posterior, and peripapillary sclera. The extraction strategy may affect the final outcome in protein profiling by MS or by other methods.     

Determination of paclitaxel in mouse plasma and brain tissue by liquid chromatography-mass spectrometry

Paclitaxel is an anticancer agent extracted from the bark of the yew tree and is widely used in chemotherapy for solid tumors, including non-small cell lung cancer and ovarian carcinoma. Most assays to measure paclitaxel in plasma require a large amount of sample (0.4-1 ml) to achieve the necessary sensitivity, and are not suitable when only small sample sizes are available. To circumvent this latter limitation, we developed a sensitive liquid chromatography-mass spectrometry (LC-MS) method for the determination of paclitaxel in plasma based on the use of small sample volumes (50 microl plasma). A solid phase extraction procedure was employed that enabled the eluent to be directly injected onto a reversed phase chromatographic HPLC system using positive electrospray ionization followed by mass spectrometric detection. The extraction recoveries of paclitaxel were 98 and 83% from plasma and brain tissues, respectively. The mobile phase consisted of 50% acetonitrile in 0.1% formic acid that was pumped at 0.2 ml/min to yield a retention time for paclitaxel of 6.2 and 5.4 min for cephalomannine, the internal standard. The method has been validated at paclitaxel plasma concentrations from 0.036 to 9.9 microg/ml, and from 0.054 to 1.96 microg/ml in brain homogenates. A sensitive and specific assay for paclitaxel has been developed that has the advantages of using small sample sizes, and a single extraction step without solvent evaporation.     

Optimization of ASE and SPE conditions for the HPLC‐FLD detection of piperazine in chicken tissues and pork

Accelerated solvent extraction (ASE) and solid‐phase extraction (SPE) conditions were optimized by a high‐performance liquid chromatography‐fluorescence detector (HPLC‐FLD) method for the detection of piperazine in chicken tissues and pork. Piperazine residues were determined by precolumn derivatization with trimethylamine and dansyl chloride. Samples were extracted with 2% formic acid in acetonitrile using an ASE apparatus and purified using a Strata‐X‐C SPE column. The monosubstituted product of the reaction of piperazine with dansyl chloride was 1‐dansyl piperazine (1‐DNS‐piperazine). Chromatographic separations were performed on an Athena C₁₈ column (250 × 4.6 mm, id: 5 μm) with gradient elution using ultrapure water and acetonitrile (5:95, V/V) as the mobile phase. The calibration curves showed good linearity over a concentration range of LOQ‐200.0 μg/kg with a coefficient of determination (R²) ≥ .9992. The recoveries and relative standard deviations (RSD values) ranged from 78.49% to 97.56% and 1.19% to 5.32%, respectively, across the limit of quantification (LOQ) and 0.5, 1, and 2.0 times the maximum residue limit (MRL; μg/kg). The limits of detection (LODs) and LOQs were 0.96 to 1.85 μg/kg and 3.20 to 5.50 μg/kg, respectively. The method was successfully applied for the validation of animal products in the laboratory.