“Stainomics”: Identification of mitotracker labeled proteins in mammalian cells

Organelle‐specific cell‐permeable fluorescent dyes are invaluable tools in cell biology as they reveal intracellular dynamics in living cells. Mitrotracker is a family of dyes that strongly label the mitochondrion, a key organelle associated with many crucial cellular functions. Despite the popularity of these dyes, little is known about the molecular mechanism behind their staining specificity. Here, we aimed to identify the protein targets of one member of this dye family, mitotracker red (MTR), by 2DE and MS. MTR bound to cellular proteins covalently, and its fluorescence persisted even after cell lysis, protein solubilization, denaturation, and electrophoresis. This enabled us to display MTR‐labeled proteins by 2DE. The MTR‐specific fluorescent signals on the gel revealed the spots that contained MTR‐conjugated proteins. These spots were analyzed by MS, resulting into the identification of ten proteins. We discovered that one major target is the mitochondrial protein HSP60 and that MTR staining could induce production of HSP60, predisposing cells to heat shock‐like responses. The identification of the molecular targets of biological dyes, or “stainomics,” can help correlate their intracellular staining properties with biochemical affinities. We believe this approach can be applied to a wide range of fluorescent probes.     

Identification of avocado (Persea americana) pulp proteins by nano‐LC‐MS/MS via combinatorial peptide ligand libraries

Avocado (Persea americana) proteins have been scarcely studied despite their importance, especially in food related allergies. The proteome of avocado pulp was explored in depth by extracting proteins with capture by combinatorial peptide ligand libraries at pH 7.4 and under conditions mimicking reverse‐phase capture at pH 2.2. The total number of unique gene products identified amounts to 1012 proteins, of which 174 are in common with the control, untreated sample, 190 are present only in the control and 648 represent the new species detected via combinatorial peptide ligand libraries of all combined eluates and likely represent low‐abundance proteins. Among the 1012 proteins, it was possible to identify the already known avocado allergen Pers a 1 and different proteins susceptible to be allergens such as a profilin, a polygalacturonase, a thaumatin‐like protein, a glucanase, and an isoflavone reductase like protein.     

Analysis of E. coli soluble proteins by non‐denaturing micro 2‐DE/3‐DE and MALDI‐MS‐PMF

Escherichia coli (strain K‐12)‐soluble proteins were analyzed by nondenaturing micro 2‐DE and MALDI‐MS‐PMF. The reported conditions of nondenaturing IEF in agarose column gels [Jin, Y., Manabe, T., Electrophoresis 2009, 30, 939–948] were modified to optimize the resolution of cellular soluble proteins. About 300 CBB‐stained spots, the apparent molecular masses of which ranged from ca. 6000 to 10 kDa, were detected. All the spots on two reference 2‐DE gels (one for wide mass range and one for low‐molecular‐mass range) were numbered and subjected to MALDI‐MS‐PMF for the assignment of constituting polypeptides. Most of the spots (310 spots out of 329) provided significant match (p<0.05) with polypeptides in Swiss‐Prot database and totally 228 polypeptide species were assigned. Activity staining of enzymes such as alkaline phosphatase and catalases was performed on the 2‐DE gels and the locations of the activity spots matched well with those of the MS‐assigned polypeptides of the enzymes. Most of the polypeptides with subunit information in Swiss‐Prot (119 polypeptides as homo‐multimers and 25 as hetero‐multimers out of the 228), such as pyruvate dehydrogenase complex which is composed of three enzymatic components, were detected at the apparent mass positions of their polymers, suggesting that the proteins were separated retaining their subunit structures. When a nondenaturing 2‐DE gel was vertically cut into 2 mm strips and one of the strips was subjected to a third‐dimension micro SDS‐PAGE (micro 3‐DE), about 190 CBB‐stained spots were detected. The assignment of the polypeptides separated on the 3‐DE gel would further provide information on protein/polypeptide interactions.     

Improved resolution in the acidic and basic region of 2‐DE of insect antennae proteins using hydroxyethyl disulfide

Olfaction is essential for processing chemical signals in insects, but characterizing the proteins implicated in this process has proved challenging. We optimized 2‐DE gel resolution of insect proteins by using a buffer containing two reducing agents, DTT and hydroxyethyl disulfide. This buffer clearly improved resolution and decreased spot streaking and spot trains of 2‐DE in comparison to DTT alone. We described for the first time that the buffer with DTT and hydroxyethyl disulfide further to reducing streaking in the basic part of the gel eliminates false spots in the acidic gel regions that appeared when only DTT was used as reducing agent.     

Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC‐MS/MS. 2. Similarity search between protein maps for the analysis of protein complexes

Human bronchial smooth muscle cell soluble proteins were analyzed by a combined method of nondenaturing micro 2DE, grid gel‐cutting, and quantitative LC‐MS/MS and a native protein map was prepared for each of the identified 4323 proteins [1]. A method to evaluate the degree of similarity between the protein maps was developed since we expected the proteins comprising a protein complex would be separated together under nondenaturing conditions. The following procedure was employed using Excel macros; (i) maps that have three or more squares with protein quantity data were selected (2328 maps), (ii) within each map, the quantity values of the squares were normalized setting the highest value to be 1.0, (iii) in comparing a map with another map, the smaller normalized quantity in two corresponding squares was taken and summed throughout the map to give an “overlap score,” (iv) each map was compared against all the 2328 maps and the largest overlap score, obtained when a map was compared with itself, was set to be 1.0 thus providing 2328 “overlap factors,” (v) step (iv) was repeated for all maps providing 2328 × 2328 matrix of overlap factors. From the matrix, protein pairs that showed overlap factors above 0.65 from both protein sides were selected (431 protein pairs). Each protein pair was searched in a database (UniProtKB) on complex formation and 301 protein pairs, which comprise 35 protein complexes, were found to be documented. These results demonstrated that native protein maps and their similarity search would enable simultaneous analysis of multiple protein complexes in cells.     

2DE‐based approach for estimation of number of protein species in a cell

Insufficient sensitivity of methods for detection of proteins at a single molecule level does not yet allow obtaining the whole image of human proteome. But to go further, we need at least to know the proteome size, or how many different protein species compose this proteome. This is the task that could be at least partially realized by the method described in this article. The approach used in our study is based on detection of protein spots in 2DE after staining by protein dyes with various sensitivities. As the different protein spots contain different protein species, counting the spots opens a way for estimation of number of protein species. The function representing the dependence of the number of protein spots on sensitivity or LOD of protein dyes was generated. And extrapolation of this function curve to theoretical point of the maximum sensitivity (detection of a single smallest polypeptide) allowed to counting the number of different molecules (polypeptide species) at the concentration level of a single polypeptide per proteome. Using this approach, it was estimated that the minimal numbers of protein species for model objects, Escherichia coli and Pirococcus furiosus, are 6200 and 3400, respectively. We expect a single human cell (HepG2) to contain minimum 70 000 protein species.     

An optimized method to extract poplar leaf proteins for two‐dimensional gel electrophoresis guided by analysis of polysaccharides and phenolic compounds

Commonly used methods for protein extraction from plant leaves, such as extraction with phenol or a combination of trichloroacetic acid and acetone, were ineffective for four tested cultivars of poplar. Moreover, multiple protocols for 2DE of the extracted proteins gave different results when protein profiles of relatively closely related plants were compared. Given that polycyclic compounds strongly hinder 2DE, we analyzed the impact of polyphenols and polysaccharides present in the plant tissues used for protein extraction, on the quality of 2DE protein profiles. Analysis of content of polyphenols and polysaccharides in leaves of poplar cultivars showed that even small differences in concentrations of analyzed metabolites accompany large differences between poplar cultivars when considering the susceptibility of samples to protein extraction for 2DE. High‐quality 2DE results were correlated with decreased amounts of polyphenols. Additional analysis using MS/MS suggested that only levels of total phenolics affected the results of 2DE. Soluble total nonstructural carbohydrates also had a negative effect, but the level of starch was not important. Finally, we present an optimized method for extraction of proteins from poplar leaves, which enables reliable comparative analysis of four different poplar cultivars, that is, “Eridano,” “Villafranca,” “NE‐42,” and “Luisa Avanzo,” which have not yet been used for the proteomic studies.     

LC–MS/MS method for simultaneous determination of serum p‐cresyl sulfate and indoxyl sulfate in patients undergoing peritoneal dialysis

p‐Cresol sulfate (pCS) and indoxyl sulfate (IS) are protein‐bound uremic toxins that accumulate in patients with chronic kidney disease (CKD). They are closely associated with the mortality rate of CKD and morbidity of cardiovascular disease. In the present study, we established a rapid method for determination of pCS and IS by HPLC‐MS/MS in serum samples from 205 CKD patients undergoing peritoneal dialysis. In brief, serum was extracted by acetonitrile and spiked with hydrochlorothiazide. The prepared sample was eluted through HPLC column (Agilent Zorbax SB‐C₁₈, 3.5 μm, 2.1 × 100 mm) with a mobile phase of acetonitrile and 10 mm ammonium acetate solution (10:90, v/v) for subsequent detection of pCS and IS by MS/MS. The linearity ranged from 50 to 10,000 ng/mL for pCS (r > 0.99), and from 500 to 10,000 ng/mL for IS (r > 0.99). The lower limit of quantification was 50 ng/mL for pCS, and 500 ng/mL for IS. Relative standard deviation (RSD) of intra‐ and inter‐day precision was within ±15%. The results showed that pCS and IS levels were partially correlated with renal function in CKD patients, and IS was directly related to serum creatinine and estimated glomerular filtration rate.     

Fragmentation features of intermolecular cross‐linked peptides using N‐hydroxy‐ succinimide esters by MALDI‐ and ESI‐MS/MS for use in structural proteomics

The use of mass spectrometry coupled with chemical cross‐linking of proteins has become one of the most useful tools for proteins structure and interactions studies. One of the challenges in these studies is the identification of the cross‐linked peptides. The interpretation of the MS/MS data generated in cross‐linking experiments using N‐hydroxy succinimide esters is not trivial once a new amide bond is formed allowing new fragmentation pathways, unlike linear peptides. Intermolecular cross‐linked peptides occur when two different peptides are connected by the cross‐linker and they yield information on the spatial proximity of different domains (within a protein) or proteins (within a complex). In this article, we report a detailed fragmentation study of intermolecular cross‐linked peptides, generated from a set of synthetic peptides, using both ESI and MALDI to generate the precursor ions. The fragmentation features observed here can be helpful in the interpretation and identification of cross‐linked peptides present in cross‐linking experiments and be further implemented in search engine's algorithms. Copyright © 2011 John Wiley & Sons, Ltd.     

Sugarcane proteomics: Establishment of a protein extraction method for 2‐DE in stalk tissues and initiation of sugarcane proteome reference map

Sugarcane is an important commercial crop cultivated for its stalks and sugar is a prized commodity essential in human nutrition. Proteomics of sugarcane is in its infancy, especially when dealing with the stalk tissues, where there is no study to date. A systematic proteome analysis of stalk tissue yet remains to be investigated in sugarcane, wherein the stalk tissue is well known for its rigidity, fibrous nature, and the presence of oxidative enzymes, phenolic compounds and extreme levels of carbohydrates, thus making the protein extraction complicated. Here, we evaluated five different protein extraction methods in sugarcane stalk tissues. These methods are as follows: direct extraction using lysis buffer (LB), TCA/acetone precipitation followed by solubilization in LB, LB containing thiourea (LBT), and LBT containing tris, and phenol extraction. Both quantitative and qualitative protein analyses were performed for each method. 2‐DE analysis of extracted total proteins revealed distinct differences in protein patterns among the methods, which might be due to their physicochemical limitations. Based on the 2‐D gel protein profiles, TCA/acetone precipitation‐LBT and phenol extraction methods showed good results. The phenol method showed a shift in pI values of proteins on 2‐D gel, which was mostly overcome by the use of 2‐D cleanup kit after protein extraction. Among all the methods tested, 2‐D cleanup‐phenol method was found to be the most suitable for producing high number of good‐quality spots and reproducibility. In total, 30 and 12 protein spots commonly present in LB, LBT and phenol methods, and LBT method were selected and subjected to eLD‐IT‐TOF‐MS/MS and nESI‐LC‐MS/MS analyses, respectively, and a reference map has been established for sugarcane stalk tissue proteome. A total of 36 nonredundant proteins were identified. This is a very first basic study on sugarcane stalk proteome analysis and will promote the unexplored areas of sugarcane proteome research.     

Low‐density‐solvent‐based air‐assisted liquid–liquid microextraction followed by gas chromatography with flame ionization detection for the determination of synthetic phenolic antioxidants in milk samples

A simple and rapid sample pretreatment technique termed low‐density‐solvent‐based air‐assisted liquid–liquid microextraction has been developed for the extraction and preconcentration of three synthetic phenolic antioxidants including butylated hydroxyanisole, butylated hydroxytoluene, and tert‐butyl hydroquinone from milk samples prior to their analysis by gas chromatography with flame ionization detection. In this method, initially trichloroacetic acid as a proteins precipitation agent is added to the sample, and then it is sonicated and centrifuged. The obtained aqueous phase is removed and the analytes extracted by the proposed method using a low‐density organic solvent. Some important parameters such as type and volume of extraction solvent, ionic strength, pH, and centrifugation rate and time were studied. Under the optimum conditions, enrichment factors were obtained in the range of 501–614. LODs and quantification were between 0.76–1.16 and 2.66–3.96 ng mL^–1, respectively. This method is rapid and requires less than 15 min for sample preparation.     

An optimized mixed‐mode stationary phase based on silica monolith particles for the separation of peptides and proteins in high‐performance liquid chromatography

A phase with both hydrophobic and hydrophilic functionalities has been synthesized by modification of ground silica monolith particles with C18 and 1‐[3‐(trimethoxysilyl)propyl] urea ligands. A series of phases was prepared by changing the ratio of the two ligands to determine the optimal ratio in view of separation efficiency. The resultant optimized stationary phase was packed in narrow‐bore glass‐lined stainless‐steel columns (1 × 300 mm and 2.1 × 100 mm) and used for the separation of synthetic peptides and proteins. The average numbers of theoretical plates (N) of 52 100/column (174 000/m, 5.75 µm plate height) and 35 500/column (118 000/m, 8.47 µm plate height) were achieved with the 300 mm column at a flow rate of 25 µL/min (0.86 mm/s) in 60:40 v/v acetonitrile/30 mM aqueous ammonium formate for the mixture of peptides (Thr‐Tyr‐Ser, Val‐Ala‐Pro‐Gly, angiotensin I, isotocin, and bradykinin) and for the mixture of proteins (myoglobin, human serum albumin, and insulin), respectively. Fast analysis of the peptides and proteins was also carried out at a flow rate of 0.9 mL/min (6.88 mm/s) with the 100 mm column and all the analytes were eluted within 2 min with good separation efficiency.     

Single‐drop microextraction followed by in‐syringe derivatization and GC‐MS detection for the determination of parabens in water and cosmetic products

A single‐drop microextraction (SDME) method followed by in‐syringe derivatization and GC‐MS determination has been developed for analysis of five parabens, including methyl, ethyl, isopropyl, n‐propyl and n‐butyl paraben in water samples and cosmetic products. N,O‐Bis(trimethylsilyl)acetamide (BSA) was used as derivatization reagent. Derivatization reaction was performed inside the syringe barrel using 0.4 μL of BSA. Parameters that affect the derivatization yield such as temperature and time of the reaction were studied. In addition, experimental SDME parameters such as selection of organic solvent, addition of salt, extraction time and extraction temperature were investigated and optimized. The RSD of the method for aqueous samples varied from 8.1 to 13%. The LODs ranged from 0.001 (n‐butyl paraben) to 0.015 (methyl paraben) μg/L, and the enrichment factors were between 23 and 150.     

Microfunnel‐filter‐based emulsification microextraction followed by gas chromatography for simple determination of organophosphorus pesticides in environmental water samples

A simple and fast method named microfunnel‐filter‐based emulsification microextraction is introduced for an efficient determination of some organophosphorus pesticides including diazinon, malathion, and chlorpyrifos in the environmental samples including the river, sea, and well water. This method is based upon the dispersion of a low‐toxicity organic solvent (dihexyl ether), as the extractant, in a high volume of an aqueous sample solution (45 mL). It is implemented without a centrifugation step, and using a syringe filter and a micro‐funnel, the phase separation and transfer of the enriched analytes to the gas chromatograph are simply achieved. By filtration of the extractant phase, a suitable sample clean‐up is obtained, and the total extraction time is just a few minutes. The factors influencing the extraction efficiency are optimized, and under the optimal conditions, the proposed method provides a good linearity (in the range of 15–1500 ng/mL (R² > 0.996). A high enrichment factor is obtained (in the range of 306–342), and the method provides low limits of detection and quantification (in the ranges of 4–8 and 15–25 ng/mL, respectively).     

Rapid pretreatment and determination of bisphenol A in water samples based on vortex‐assisted liquid–liquid microextraction followed by high‐performance liquid chromatography with fluorescence detection

A method for the rapid pretreatment and determination of bisphenol A in water samples based on vortex‐assisted liquid–liquid microextraction followed by high‐performance liquid chromatography with fluorescence detection was proposed in this paper. A simple apparatus consisting of a test tube and a cut‐glass dropper was designed and applied to collect the floating extraction drop in liquid–liquid microextraction when low‐density organic solvent was used as the extraction solvent. Solidification and melting steps that were tedious but necessary once the low‐density organic solvent used as extraction solvent could be avoided by using this apparatus. Bisphenol A was selected as model pollutant and vortex‐assisted liquid–liquid microextraction was employed to investigate the usefulness of the apparatus. High‐performance liquid chromatography with fluorescence detection was selected as the analytical tool for the detection of bisphenol A. The linear dynamic range was from 0.10 to 100 μg/L for bisphenol A, with good squared regression coefficient (r² = 0.9990). The relative standard deviation (n = 7) was 4.7% and the limit of detection was 0.02 μg/L. The proposed method had been applied to the determination of bisphenol A in natural water samples and was shown to be economical, fast, and convenient.     

Graphene‐coated magnetic‐sheet solid‐phase extraction followed by high‐performance liquid chromatography with fluorescence detection for the determination of aflatoxins B1, B2, G1, and G2 in soy‐based samples

A new method named graphene‐coated magnetic‐sheet solid‐phase extraction based on a magnetic three‐dimensional graphene sorbent was developed for the extraction of aflatoxins prior to high‐performance liquid chromatography with fluorescence detection. The use of a perforated magnetic‐sheet for fixing the magnetic nanoparticles is a new feature of the method. Hence, the adsorbent particles can be separated from sample solution without using an external magnetic field. This made the procedure very simple and easy to operate so that all steps of the extraction process (sample loading, washing, and desorption) were carried out continuously using two lab‐made syringe pumps. The factors affecting the performance of extraction procedure such as the extraction solvent, adsorbent dose, sample loading flow rate, ionic strength, pH, and desorption parameters were investigated and optimized. Under the optimal conditions, the obtained enrichment factors and limits of detection were in the range of 205–236 and 0.09–0.15 μg/kg, respectively. The relative standard deviations were <3.4 and 7.5% for the intraday (n = 6) and interday (n = 4) precisions, respectively. The developed method was successfully applied to determine aflatoxins B₁, B₂, G₁, and G₂ in different soy‐based food samples.     

Solid‐based disperser liquid–liquid microextraction for the preconcentration of phthalate esters and di‐(2‐ethylhexyl) adipate followed by gas chromatography with flame ionization detection or mass spectrometry

A new approach for the development of a dispersive liquid–liquid microextraction followed by GC with flame ionization detection was proposed for the determination of phthalate esters and di‐(2‐ethylhexyl) adipate in aqueous samples. In the proposed method, solid and liquid phases were used as the disperser and extractant, respectively, providing a simple and fast mode for the extraction of the analytes into a small volume of an organic solvent. In this method, microliter levels of an extraction solvent was added onto a sugar cube and it was transferred into the aqueous phase containing the analytes. By manual shaking, the sugar was dissolved and the extractant was released into the aqueous phase as very tiny droplets to provide a cloudy solution. Under optimized conditions, the proposed method showed good precision (RSD less than 5.2%), high enrichment factors (266–556), and low LODs (0.09–0.25 μg/L). The method was successfully applied for the determination of the target analytes in different samples, and good recoveries (71–103%) were achieved for the spiked samples. No need for a disperser solvent and higher enrichment factors compared with conventional dispersive liquid–liquid microextraction and low cost and short sample preparation time are other advantages of the method.     

Selective extraction based on poly(MAA‐VB‐EGMDA) monolith followed by HPLC for determination of hordenine in plasma and urine samples

Hordenine is an active compound found in several foods, herbs and beer. In this work, a novel sorbent was fabricated for selective solid‐phase extraction (SPE) of hordenine in biological samples. The organic polymer sorbent was synthesized in one step in the plastic barrel of a syringe by a pre‐polymerization solution consisting of methacrylic acid (MAA), 4‐vinylphenylboronic acid (VB) and ethylene glycol dimethacrylate (EGDMA). The conditions for preparation were optimized to generate a poly(MAA‐VB‐EGMDA) monolith with good permeability. The monolith exhibited good enrichment efficiency towards hordenine. By using tyramine as the internal standard, a poly(MAA‐VB‐EGMDA)‐based SPE‐HPLC method was established for analysis of hordenine. Conditions for SPE, including volume of eluting solvent, pH of sample solution, sampling rate and sample volume, were optimized. The proposed SPE‐HPLC method presented good linearity (R² = 0.9992) within 10–2000 ng/mL and the detection limits was 3 ng/mL, which is significantly more sensitive than reported methods. The method was also applied in plasma and urine samples; good capability of removing matrices was observed, while hordenine in low content was well extracted and enriched. The recoveries were from 90.6 to 94.7% and from 89.3 to 91.5% for the spiked plasma and urine samples, respectively, with the relative standard deviations <4.7%. Copyright © 2014 John Wiley & Sons, Ltd.     

Reversed‐phase single drop microextraction followed by high‐performance liquid chromatography with fluorescence detection for the quantification of synthetic phenolic antioxidants in edible oil samples

The reversed‐phase mode of single drop microextraction has been used as a preparation method for the extraction of some phenolic antioxidants from edible oil samples. Butylated hydroxyl anisole, tert‐butylhydroquinone and butylated hydroxytoluene were employed as target compounds for this study. High‐performance liquid chromatography followed by fluorescence detection was applied for final determination of target compounds. The most interesting feature of this study is the application of a disposable insulin syringe with some modification for microextraction procedure that efficiently improved the volume and stability of the solvent microdrop. Different parameters such as the type and volume of solvent, sample stirring rate, extraction temperature, and time were investigated and optimized. Analytical performances of the method were evaluated under optimized conditions. Under the optimal conditions, relative standard deviations were between 4.4 and 10.2%. Linear dynamic ranges were 20–10 000 to 2–1000 μg/g (depending on the analytes). Detection limits were 5–670 ng/g. Finally, the proposed method was successfully used for quantification of the antioxidants in some edible oil samples prepared from market. Relative recoveries were achieved from 88 to 111%. The proposed method had a simplicity of operation, low cost, and successful application for real samples.