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.     

Combination of FASP and fully automated 2D‐LC‐MS/MS allows in‐depth proteomic characterization of mouse zymogen granules

Zymogen granule (ZG) constituents play important roles in pancreatic injury and disease. In previous studies, proteomic analyses with rat zymogen granules were separated by two‐dimensional gel electrophoresis or one‐dimensional SDS–PAGE, followed by in‐gel tryptic digestion. In order to overcome the disadvantage of in‐gel digestion and to carry out further in‐depth proteomic analysis of the zymogen granules, in this study, by combining a filter‐aided sample preparation method and fully automated 2D‐LC‐MS/MS technique, 800 ZG proteins were identified with at least two unique peptides for each protein, 75% of which have not been previously reported. The identified proteins revealed broad diversity in protein identity and function. This is the largest dataset of ZG proteome, and also the first dataset of the mouse ZG proteome, which may help elucidate on the molecular architecture of ZGs and their functions. Copyright © 2012 John Wiley & Sons, Ltd.     

丙酮+环己烷+甲醇组成的最低共沸混合物热力学性质的研究

Molar heat capacities of the pure samples of acetone,methanol and the azeotropic mixture composed of acetone,cyclohexane and methanol were measured by an adiabatic calorimeter from 78 to 320 K.The solid-solid andsolid-liquid phase transitions of the pure samples and the mixture were determined based on the curve of the heatcapacity with respect to temperature.The phase transitions took place at(126.16±0.68)and(178.96±1.47)K forthe sample of acetone,(157.79±0.95)and(175.93±0.95)K for methanol,which were corresponding to thesolid-solid and the solid-liquid phase transitions of the acetone and the methanol,respectively.And the phase tran-sitions occurred in the temperature ranges of 120 to 190 K and 278 to 280 K corresponding to the solid-solid andthe solid-liquid phase transitions of mixture of acetone,cyclohexane and methanol,respectively.The thermody-namic functions and the excess thermodynamic functions of the mixture relative to standard temperature of 298.15K were derived based on the relationships of the thermodynamic functions and the function of the measured heatcapacity with respect to temperature.     

Knowledge-based proteome profiling: considering identified proteins to evaluate separation efficiency by 2-D PAGE

Proteome profiling techniques rely on the separation of proteins or peptides and their subsequent quantification. The reliability of this technique is still limited because a proteome profiling result does not necessarily represent the true protein composition of the analysed sample, thus seriously hampering proper data interpretation. Many experimentally observed proteome alterations are biologically not significant. It was the aim of this study to use the knowledge of the biological context of proteins in order to establish optimised proteome profiling protocols. While 2-D spot patterns of total cell protein fractions were found to poorly represent the true protein composition, purified subcellular protein fractions were found to better represent the protein composition of the analysed sample. The application of a standardised protocol to different kinds of cells revealed several striking observations. Firstly, the protein composition of cultured cells of various origins is very similar. Secondly, proteome alterations observed with the described protocols do make sense from a biologic point of view and may thus be considered as truly representative for the analysed samples. Thirdly, primary white blood cells isolated from different donors were found to show minor, but reproducible and significant individual differences. We designate the consideration of known properties of identified proteins in proteome profiles as a knowledge-based approach. The present data suggest that this approach may tremendously help to improve the applied techniques and assess the results. We demonstrate that the fulfilment of well-defined criteria of proteome profiles eventually results in reliable and biologically relevant data.     

Evaluation of sample extraction methods for proteomics analysis of green algae Chlorella vulgaris

Many protein extraction methods have been developed for plant proteome analysis but information is limited on the optimal protein extraction method from algae species. This study evaluated four protein extraction methods, i.e. direct lysis buffer method, TCA‐acetone method, phenol method, and phenol/TCA‐acetone method, using green algae Chlorella vulgaris for proteome analysis. The data presented showed that phenol/TCA‐acetone method was superior to the other three tested methods with regards to shotgun proteomics. Proteins identified using shotgun proteomics were validated using sequential window acquisition of all theoretical fragment‐ion spectra (SWATH) technique. Additionally, SWATH provides protein quantitation information from different methods and protein abundance using different protein extraction methods was evaluated. These results highlight the importance of green algae protein extraction method for subsequent MS analysis and identification.     

Development of an HPTLC‐based diagnostic method for invasive aspergillosis

A rapid, sensitive and specific high‐performance thin‐layer chromatographic (HPTLC) method was developed and validated for determination of gliotoxin in Aspergillus infected immunocompromised patients with invasive aspergillosis (IA). Densitometric analysis of gliotoxin was carried out in the absorbance mode at 254 nm after single‐step extraction with chloroform. The method uses TLC aluminum plates pre‐coated with silica gel 60F‐254 as a stationary phase and toluene–isoamyl alcohol–methanol (10:0.5:0.5, v/v/v) as mobile phase, which gives compact spot of gliotoxin (R_f = 0.51). The calibration curve was linear (r² ≥ 0.994) between peak area and concentration in the tested range of 100–1000 ng spot^?1 with minimum detectable range 0.025 ng μ^?1 of serum sample. The mean ± SD value of slope and intercept of the standard chromatogram of gliotoxin were found to be 523.2 ± 1.555635 and 915.8 ± 30.68843, respectively. The developed method is simple, rapid, precise and less costly than earlier diagnostic methods, and different serum samples can be run on a single TLC plate for comparative analysis. The proposed method can be used to analyze gliotoxin in patient serum for easy, rapid and cost‐effective diagnosis of IA. Copyright © 2009 John Wiley & Sons, Ltd.     

How many proteins can be identified in a 2DE gel spot within an analysis of a complex human cancer tissue proteome?

Two‐dimensional gel electrophoresis (2DE) in proteomics is traditionally assumed to contain only one or two proteins in each 2DE spot. However, 2DE resolution is being complemented by the rapid development of high sensitivity mass spectrometers. Here we compared MALDI‐MS, LC‐Q‐TOF MS and LC‐Orbitrap Velos MS for the identification of proteins within one spot. With LC‐Orbitrap Velos MS each Coomassie Blue‐stained 2DE spot contained an average of at least 42 and 63 proteins/spot in an analysis of a human glioblastoma proteome and a human pituitary adenoma proteome, respectively, if a single gel spot was analyzed. If a pool of three matched gel spots was analyzed this number further increased up to an average of 230 and 118 proteins/spot for glioblastoma and pituitary adenoma proteome, respectively. Multiple proteins per spot confirm the necessity of isotopic labeling in large‐scale quantification of different protein species in a proteome. Furthermore, a protein abundance analysis revealed that most of the identified proteins in each analyzed 2DE spot were low‐abundance proteins. Many proteins were present in several of the analyzed spots showing the ability of 2DE‐MS to separate at the protein species level. Therefore, 2DE coupled with high‐sensitivity LC‐MS has a clearly higher sensitivity as expected until now to detect, identify and quantify low abundance proteins in a complex human proteome with an estimated resolution of about 500 000 protein species. This clearly exceeds the resolution power of bottom‐up LC‐MS investigations.     

Deciphering key proteins of oil palm (Elaeis guineensis Jacq.) fruit mesocarp development by proteomics and chemometrics

Palm oil is an edible vegetable oil derived from lipid‐rich fleshy mesocarp tissue of oil palm (Elaeis guineensis Jacq.) fruit and is of global economic and nutritional relevance. While the understanding of oil biosynthesis in plants is improving, the fundamentals of oil biosynthesis in oil palm still require further investigations. To gain insight into the systemic mechanisms that govern oil synthesis during oil palm fruit ripening, the proteomics approach combining gel‐based electrophoresis and mass spectrometry was used to profile protein changes and classify the patterns of protein accumulation during these complex physiological processes. Protein profiles from different stages of fruit ripening at 10, 12, 14, 15, 16, 18 and 20 weeks after anthesis (WAA) were analysed by two‐dimensional gel electrophoresis (2DE). The proteome data were then visualised using a multivariate statistical analysis of principal component analysis (PCA) to get an overview of the proteome changes during the development of oil palm mesocarp. A total of 68 differentially expressed protein spots were successfully identified by matrix‐assisted laser desorption/ionisation‐time of flight (MALDI‐TOF/TOF) and functionally classified using ontology analysis. Proteins related to lipid production, energy, secondary metabolites and amino acid metabolism are the most significantly changed proteins during fruit development representing potential candidates for oil yield improvement endeavors. Data are available via ProteomeXchange with identifier PXD009579. This study provides important proteome information for protein regulation during oil palm fruit ripening and oil synthesis.     

Evaluation of extraction procedures for 2‐DE analysis of aphid proteins

Protein sample preparation is a crucial step in a 2‐DE proteomics approach. In order to establish a routine protocol for the application of proteomics analysis to aphids, this study focuses on the specific protein extraction problems in insect tissues and evaluates four methods to bypass them. The approaches of phenol extraction methanol/ammonium acetate precipitation (PA), TCA/acetone precipitation, PEG precipitation, and no precipitation were evaluated for proteins isolation and purification from apterous adult aphids, Sitobion avenae. For 2‐DE, the PA protocol was optimal, resulting in good IEF and clear spots. PA method yielded the greatest amount of protein and displayed most protein spots in 2‐DE gels, as compared with the TCA/acetone precipitation, PEG precipitation and no precipitation protocols. Analysis of protein yield, image quality and spot numbers demonstrate that the TCA/acetone precipitation protocol is a reproducible and reliable method for extracting proteins from aphids. The PEG precipitation approach is a newly developed protein extraction protocol for aphids, from which more unique protein spots can be detected, especially for detection of acid proteins. These protocols are expected to be applicable to other insects or could be of interest to laboratories involved in insect proteomics, despite the amounts and types of interfering compounds vary considerably in different insects.     

Two-dimensional maps in soft immobilized pH gradient gels: a new approach to the proteome of the Third Millennium

Same major improvements in proteome analysis of cytosolic and membrane proteins by two-dimensional mapping are here reported. A much improved transfer of proteins from the first to the second dimensional sodium dodecyl sulfate (SDS)-gel is obtained by simply diluting the gel matrix, normally composed of 4%T polyacrylamide in all commercially available Immobiline strips down to as low as 3%T. In the analysis of total lysates of platelets, this augmented transfer has been evaluated as being 2-3 times higher than in standard 4%T gels. A second major improvement, in the case of analysis of membrane protein preparations, has been demonstrated to consist in a delipidation step in a tertiary solvent mixture composed of tri-n-butyl phosphate:acetone:methanol in a 1:12:1 ratio. By adopting this protocol, large amounts of spectrins (240-220 kDa, filamentous proteins of the red blood cell membranes) could be transferred vs. essentially none when delipidation was omitted. The present report also confirms the importance of a reduction and alkylation step of the protein sample prior to all electrophoretic steps, including focusing in the Immobiline gel, as recently reported by Herbert et al.     

Determination of Sumatriptan and Zolmitriptan in Presence of Their Corresponding Degradation Products by HPTLC Methods

Accurate, sensitive, and precise high performance thin layer chromatographic (HPTLC) methods were developed and validated for the determination of sumatriptan and zolmitriptan in presence of their degradation products. Sumatriptan was separated from its degradation products and analyzed on TLC silica gel 60 F₂₅₄ plates using chloroform–ethyl acetate–methanol–ammonia (4:3:3:0.1, v/v) as a developing system followed by densitometric measurement of the bands at 228 nm. Zolmitriptan was determined using chloroform–ethyl acetate–methanol–ammonia (3:3:3:1, v/v) as a developing system followed by densitometric measurement at 222 nm. The methods were validated over a range of 0.5–4 μg/spot for sumatriptan and 0.5–3 μg/spot for zolmitriptan. The proposed methods were successfully applied for the determination of the studied drugs in bulk powder and in their pharmaceutical formulations.     

Systematic annotation and bioinformatics analyses of large-scale Oryza sativa proteome

Much has been now recognized on the rice (Oryza sativa L.) proteomics by using the powerful experimental tool two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). 2D-PAGE can be utilized for monitoring global changes of quantitative protein expression in specific tissues under various conditions. However, systematic annotations of the protein spots generated by 2D-PAGE are still limited for rice. In this study, a new approach for Oryza sativa proteome annotation based on the 2D-gel maps was developed. Based on the publicly available 2D-PAGE data of rice, 11,201 gel spots were annotated accounting for 87.2% of the total spots on the gel maps. Gel spot alignments were performed for the annotated gel maps belonging to 23 rice tissues or organelles. In summary, 253 alignments between 23 tissues or organelles were performed, and 26,207 co-expressed proteins were identified using our analytical strategy. Large-scale bi-cluster analysis of 23 tissues/organelles proteomes of rice was carried out to detect novel functional proteins. Function and pathway analysis identified a number of common gene products with great potential in regulating specific physiological and biochemical events within various rice tissues/organelles. It also suggested that the tissue- or organelle-specific proteins might be responsible for the functional divergence of these tissues or organelles. Taken together, this study provides us new strategies and informative resources for rice proteome research based on 2D-PAGE data.     

Optimizing protein recovery yield from serum samples treated with beads technology

Proteomics studies are often complicated by the wide dynamic range of the biological fluids, in which few highly abundant proteins obscure the signal of low abundant ones. To overcome this problem, several techniques have been developed on the basis of "depletion principles," namely immuno-subtraction with specific antibodies against the most-abundant proteins. Unfortunately, the probability of codepletion is a noteworthy drawback associated with these strategies. The ProteoMiner (PM) technology is a novel approach, consisting of a combinatorial library of hexapeptide ligands coupled to beads, that allows the capture of all species present in a proteome, but at much reduced protein concentration differences, simultaneously enhancing the concentration of the most dilute species. In this study, we evaluated the compatibility of the PM kit's elution reagent with 2-DE analysis, comparing five different purification methods on serum samples eluted from the beads: the "ReadyPrep 2-D Clean-up kit" and precipitation with organic solvents, as acetone/methanol, TCA/acetone, ACN, and chloroform/methanol. Considering protein recovery yield (quantity) and 2-DE spot pattern (quality), precipitation with ACN offered the most promising approach, showing the best spot resolution in all regions of the pH gradient and the greatest number of protein spots visualized on 2-D gels.     

Development of a highly sensitive high‐performance thin‐layer chromatography method for the screening and simultaneous determination of sofosbuvir,daclatasvir, and ledipasvir in their pure forms and their different pharmaceutical formulations

The combination of sofosbuvir and daclatasvir or sofosbuvir and ledipasvir is now widely used as an ideal treatment for hepatitis C virus infection. For this purpose, a simple, sensitive, accurate, economic, and precise high‐performance thin‐layer chromatography was developed and validated for the determination of sofosbuvir, daclatasvir, and ledipasvir in their pure form as well as their different pharmaceutical products. The method used Merck high‐performance thin‐layer chromatography aluminum plates precoated with silica gel 60 F254 as a stationary phase and mobile phase consisting of methylene chloride/methanol/ethyl acetate/ammonia (25%) (6:1:4:1, v/v/v/v). This system was found to give compact symmetric peaks of sofosbuvir, daclatasvir, and ledipasvir with retardation factors of 0.27 ± 0.01, 0.50 ± 0.007, and 0.68 ± 0.008, respectively. The densitometric scanner was set at 275 nm using a deuterium lamp. The calibration curves were linear over the range of 100–3000 ng/spot for sofosbuvir, and daclatasvir, and range of 50–3000 ng/spot for ledipasvir. The detection limits were 22.5, 31.90, and 15.80 for sofosbuvir, daclatasvir, and ledipasvir. The quantitation limits were 67.50, 95.60, and 47.50 for sofosbuvir, daclatasvir, and ledipasvir. The proposed method was validated according to International Conference on Harmonization (ICH) guidelines and the results were acceptable.     

Coloring–decoloring behavior of fluoroalkyl end‐capped 2‐acrylamido‐2‐methylpropanesulfonic acid oligomer/acetone composite in methanol

A reddish‐brown fluoroalkyl end‐capped 2‐acrylamido‐2‐methylpropanesulfonic acid (AMPS) oligomer/acetone composite was prepared by heating the white oligomer powder with acetone at 80 °C for 3 h. The color was not observed in the corresponding non‐fluorinated AMPS oligomer/acetone composite, which was prepared under similar conditions. The coloring was probably caused by the formation of acetone polyaldol condensation products in the fluorinated oligomeric gel network cores. The colored R_F‐(AMPS)_n‐R_F/acetone composite powders were stable and did not exhibit any color change after 2 years in natural light at room temperature. The colored composite powders dissolved in methanol to give a reddish‐brown solution at room temperature. However, the retro‐polyaldol condensation decolored the solution after 1 day at room temperature. This is the first example of the retro‐aldol polycondensation of acetone under mild conditions. The decoloration increased by between 38‐ and 70‐fold under UV irradiation, compared with that in dark conditions. The coloring–decoloring behavior was consistent and repeatable; therefore our fluorinated oligomer/acetone composites are promising candidates for new fluorinated coloring materials. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2555–2564     

Development and validation of TLC‐densitometric method for determination of lipid A adjuvant as a bulk and in solid fat nanoemulsions

A simple, sensitive, selective and precise high‐performance thin‐layer chromatographic method was developed for determination of lipid A (MPLA) adjuvant as a bulk and in solid fat nanoemulsions. Chromatographic separations were performed on thin‐layer chromatography aluminum plates precoated with silica gel 60 F‐254 as stationary phase and chloroform–methanol–ethyl acetate solution (10:2:4, v/v/v) as mobile phase. With this solvent system, compact spots for MPLA at R_f value 0.80 ± 0.02 were obtained. Densitometric analysis of MPLA was carried out in absorbance mode at 357 nm. Linear regression analysis for the calibration plots showed good linear relationship with r = 0.9996 in the concentration range of 20–100 ng/spot. The mean values (±SD) of slope and intercept were found to be 7.355 ± 0.006 and 109.52 ± 0.170, respectively. Limits of detection (LOD) and quantitation (LOQ) were observed at 3.096 and 9.382 ng/spot, respectively.The method was validated for precision, accuracy, robustness and recovery as per the International Conference on Harmonization guidelines. Statistical analysis proved that the developed method for quantification of MPLA as a bulk and in solid fat nanoemulsions is reproducible, selective and economical. This method could be applied for quantitative assay of MPLA in lipid‐based vaccine formulations. Copyright © 2015 John Wiley & Sons, Ltd.     

A comprehensive and non‐prefractionation on the protein level approach for the human urinary proteome: touching phosphorylation in urine

Increasing attention has been paid to the urinary proteome because it holds the promise of discovering various disease biomarkers. However, most of the urine proteomics studies routinely relied on protein pre‐fractionation and so far did not present characterization on phosphorylation status. Two robust approaches, integrated multidimensional liquid chromatography (IMDL) and Yin‐yang multidimensional liquid chromatography (MDLC) tandem mass spectrometry, were recently developed in our laboratory, with high‐coverage identification of peptide mixtures. In this study, we adopted a strategy without pre‐fractionation on the protein level for urinary proteome identification, using both the IMDL and the Yin‐yang MDLC methods for peptide fractionation followed by identification using a linear ion trap‐orbitrap (LTQ‐Orbitrap) mass spectrometer with high resolution and mass accuracy. A total of 1310 non‐redundant proteins were highly confidently identified from two experiments, significantly including 59 phosphorylation sites. More than half the annotated identifications were membrane‐related proteins. In addition, the lysosomal as well as kidney‐associated proteins were detected. Compared with the six largest datasets of urinary proteins published previously, we found our data included most of the reported proteins. Our study developed a robust approach for exploring the human urinary proteome, which would provide a catalogue of urine proteins on a global scale. It is the first report, to our best knowledge, to profile the urinary phosphoproteome. This work significantly extends current comprehension of urinary protein modification and its potential biological significance. Moreover, the strategy could further serve as a reference for biomarker discovery. Copyright © 2010 John Wiley & Sons, Ltd.     

Characterization of quinoa seed proteome combining different protein precipitation techniques: Improvement of knowledge of nonmodel plant proteomics

A shotgun proteomics approach was used to characterize the quinoa seed proteome. To obtain comprehensive proteomic data from quinoa seeds three different precipitation procedures were employed: MeOH/CHCl₃/double‐distilled H₂O, acetone either alone or with trichloroacetic acid; the isolated proteins were then in‐solution digested and the resulting peptides were analyzed by nano‐liquid chromatography coupled to tandem mass spectrometry. However, since quinoa is a nonmodel plant species, only a few protein sequences are included in the most widely known protein sequence databases. To improve the data reliability a UniProt subdatabase, containing only proteins of Caryophillales order, was used. A total of 352 proteins were identified and evaluated both from a qualitative and quantitative point of view. This combined approach is certainly useful to increase the final number of identifications, but no particular class of proteins was extracted and identified in spite of the different chemistries and the different precipitation protocols. However, with respect to the other two procedures, from the relative quantitative analysis, based on the number of spectral counts, the trichloroacetic acid/acetone protocol was the best procedure for sample handling and quantitative protein extraction. This study could pave the way to further high‐throughput studies on Chenopodium Quinoa.     

A New Preparation of 1,3,3‐Trimethylbicyclo[2.2.2]octan‐2,6‐dione,a Never Isolated Intermediate in a Total Synthesis of (+)‐Norpatchoulenol. Formal Total Synthesis of (±)‐Iso‐Norpatchoulenol

A new preparation and the isolation and spectroscopic characterization of 1,3,3‐trimethylbicyclo[2.2.2]octan‐2,6‐dione ( 3 ), a so far elusive key intermediate in the Liu–Ralitsch total synthesis of (+)‐norpatchoulenol ((+)‐ 1a ), is described. The preparation of 3 constitutes also a formal total synthesis of (±)‐iso‐norpatchoulenol ((±)‐ 1b ), since 3 is correlated to an intermediate in the Monti and co‐workers synthesis of (±)‐ 1b .     

Thermodynamic properties of the azeotropic mixture of acetone and methanol

The molar heat capacities of the pure samples of acetone and methanol, and the azeotropic mixture composed of acetone and methanol were measured with an adiabatic calorimeter in the temperature range 78–320 K. The solid–solid and solid–liquid phase transitions of the pure samples and the mixture were determined based on the curve of the heat capacity with respect to temperature. The phase transitions took place at 126.16±0.68 and 178.96±1.47 K for the sample of acetone, 157.79±0.95 and 175.93±0.95 K for methanol, which were corresponding to the solid–solid and the solid–liquid phase transitions of the acetone and the methanol, respectively. And the phase transitions occurred at 126.58±0.24, 157.16±0.42, 175.50±0.46 and 179.74±0.89 K corresponding to the solid–solid and the solid–liquid phase transitions of the acetone and the methanol in the mixture, respectively. The thermodynamic functions and the excess thermodynamic functions of the mixture relative to standard temperature 298.15 K were derived based on the relationships of the thermodynamic functions and the function of the measured heat capacity with respect to temperature.