Profiling of hydroxyurea-treated β-thalassemia/ serum proteome through nano-LC–ESI–MS/ MS in combination with microsol-isoelectric focusing

Advancements in proteomic tools offer a comprehensive solution to studying the complexity of diseases at molecular level. This study focusses on the clinical proteomic profiling of pre- and post-hydroxyurea (HU)-treated β-thalassemia patients in parallel with healthy individuals to better understand the role of HU in the treatment of β-thalassemia. The strategy encompasses sequential high-resolution protein fractionation using MicroSol-isoelectric focusing (ZOOM- IEF) followed by one-dimensional SDS-PAGE before nano-RP-LC–MS/ MS analysis of tryptic peptides. Protein identification was performed through Mascot search using NCBInr and SwissProt databases. Several different proteins were observed in pool serum samples of each of the three study groups. Approximately, 1250 proteins exclusive to each group were identified, and after removing the redundant and low sequence coverage proteins, the number was reduced to 576 (201 in healthy, 187 in HU-untreated and 188 in HU-treated group). Uniquely identified proteins in the HU-treated group regulate the focal adhesion, ECM-receptor interaction, PI3K-Akt signaling, Rap1 signaling, cAMP signaling, platelet activation, and Ca²⁺ signaling pathways in the HU-treated group. The proteomic profile presented here will add to the current state of understanding of molecular mechanisms involved in hydroxyurea treatment of β-thalassemia.     

Determination of Dothiepin in Human Plasma by LC–ESI–MS and its Application to Bioequivalence Studies

An LC–MS method for the determination of dothiepin in human plasma was developed and validated. Sample preparation involved extraction with n-hexane:2-propanol (95:5). Separation was on an Ultimate XB C18 column (2.1 × 150 mm, 5 μm). A single-quadrupole mass spectrometer with an electrospray interface was operated in the selected-ion monitoring mode to detect the [M+H]⁺ ions at m/z 296 for dothiepin and at m/z 278 for the internal standard (amitriptylene). The method demonstrated good linearity from 0.78 ng mL^?1 (the LOQ) to100 ng mL^?1. The mean extraction recovery was 82.4% for dothiepin and and 84.2% for the internal standard. The intra-day and inter-day precision ranged from 8.5 to 11.4% and 9.7 to 12.1% (RSD), respectively. The method was successfully applied to bioequivalence studies of dothiepin hydrochloride tablets to obtain the pharmacokinetic parameters.     

Development of a simple spectrophotometric method to estimate uranium concentration in LiCl–KCl matrix

“Off-the-shelf” clinical linear electron accelerators (LINAC) have been suggested as alternative to research accelerators once they are no longer suitable for the medical applications. We investigated feasibility of utilising a modified LINAC for instrumental photon activation analysis (IPAA) as a tool in environmental geochemistry studies. The IPAA results were compared with those obtained using a MT-25 research accelerator at Joint Institute for Nuclear Research in Dubna, Russia. To investigate soil pollution in Antalya, Turkey, 90 surface soil samples were analysed and significant enrichments of Ni, Cr and As were found.

     

Topologic Transformation of Inorganic Salt–Oxyethylated Surfactant–Water Phase Diagrams in Response to Changing Temperature

A general topologic transformation scheme of phase diagram is proposed for inorganic salt–oxyethylated surfactant–water systems that have a lower critical solution temperature (LCST) or where the surfactant–water binary subsystem is homogeneous over the entire range of liquid temperatures for the case where the salt has the salting-out, salting-in, or salting-in-and-salting-out effect. Examples are provided to illustrate the implementation of the suggested variants of the general scheme.     

Use of a porous silicon–gold plasmonic nanostructure to enhance serum peptide signals in MALDI-TOF analysis

Small peptides in serum are potential biomarkers for the diagnosis of cancer and other diseases. The identification of peptide biomarkers in human plasma/serum has become an area of high interest in medical research. However, the direct analysis of peptides in serum samples using mass spectrometry is challenging due to the low concentration of peptides and the high abundance of high-molecular-weight proteins in serum, the latter of which causes severe signal suppression. Herein, we reported that porous semiconductor-noble metal hybrid nanostructures can both eliminate the interference from large proteins in serum samples and significantly enhance the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) yields of peptides captured on the nanostructure. Serum peptide fingerprints with high fidelity can be acquired rapidly, and successful discrimination of colorectal cancer patients based on peptide fingerprints is demonstrated.     

Dispersive liquid–liquid microextraction applied to the simultaneous derivatization and concentration of triclosan and methyltriclosan in water samples

A fast and novel sample preparation procedure for the determination of triclosan (TCS) and methyltriclosan (MTCS) in water samples is presented. Dispersive liquid–liquid microextraction, using a ternary mixture consisting of a disperser, an extractant and N-methyl-N-(tert-butyldimethylsilyl)trifluoroacetamide (MTBSTFA) as derivatization reagent, was used for the simultaneous derivatization, case of TCS, and concentration of both species in different water samples. Analytes were determined by gas chromatography with tandem mass spectrometry (GC–MS/MS). Influence of different factors on the performance of the sample preparation process is thoroughly discussed. Under final working conditions, a mixture of 1 mL of methanol, 40 μL of 1,1,1-trichloroethane and the same volume of MTBSTFA was added to 10 mL of water in a conical bottom glass tube. After centrifugation, the settled phase was injected directly in the chromatographic system. TCS was quantitatively extracted and converted into the corresponding tert-butyldimethylsilyl derivative, whereas for MTCS an extraction yield around 90% was attained. Limits of quantification between 2 and 5 ng L⁻¹ and reproducibility values below 10% were achieved; moreover, the performance of the extraction process was scarcely affected by the type of water sample. Globally, these values are comparable, or even better, to those reported for other approaches applied to the determination of same compounds, with the advantage of a shorter sample preparation step. Analysis of surface and wastewater samples confirmed the ubiquitous presence of TCS in the aquatic environment at levels from 20 to 700 ng L⁻¹.     

Dispersive liquid–liquid microextraction applied to isolation and concentration of alkylphenols and their short-chained ethoxylates in water samples

Dispersive liquid–liquid microextraction (DLLME) coupled with high-performance liquid chromatography with fluorescence detector was applied for the determination of alkylphenols and their short-chained ethoxylates in water samples. Development of DLLME procedure included optimisation of some important parameters such as kind and volume of extracting and dispersing solvents. Under optimised conditions 50 μL of trichloroethylene in 1.5 mL of acetone were rapidly injected into 5 mL of a water sample. After centrifuging the organic phase containing the analytes was taken for evaporation with a gentle nitrogen purge and reconstituted to 50 μL of acetonitrile. The aliquot of this solution was analysed with the use of HPLC. For octylphenol (OP) and octylphenol ethoxylates (OPEOs) linearity was satisfactory in the range 8–1000 μg L⁻¹ and for nonylphenol (NP) and nonylphenol ethoxylates (NPEOs) linearity was in the range from 50 to about 3000 μg L⁻¹. Limit of quantitation was 0.1 μg L⁻¹ for OP and OPEOs and 0.3 μg L⁻¹ for NP and NPEOs. Satisfactory recoveries between 66 and 79% were obtained for environmental samples. The results showed that DLLME is a simple, rapid and sensitive analytical method for the preconcentration of trace amounts of alkylphenols and their ethoxylates in environmental water samples.     

Differential Proteomic Analysis of Neonatal Cardiomyocytes in Response to β-Adrenergic Receptor Stimulation

Introduction Adrenoceptors(ARs),membersofthesuperfami lyofG proteincoupledreceptors,arethemostimpor tantreceptorsinvolvedincardiacregulation[1].ARsin cardiacmuscleincludebothαARsandβARssub types,whileinmostmammalianheart,βARsarethe predominantsubtypes.…     

An in silico approach to design peptide mimetics based on docking and molecular dynamics simulation of EGFR–matuzumab complex

Epidermal growth factor receptor (EGFR) plays an essential role in anticancer therapy. Matuzumab is an antibody for the treatment of colorectal, lung and stomach cancer. Matuzumab binds efficiently to EGFR and blocks its phosphorylation. The recent clinical successes have established application of peptides for cancer treatment. The present contribution introduces an in silico approach to design peptides based on molecular dynamics simulation (MDs) of the matuzumab-EGFR complex in water environment. Moreover, principal component analysis has been used to select multiple conformations of the complex in MDs for designing the peptides. The paratope and epitope in each conformation of the complex were determined, and the alanine scanning was used to identify the hot spots of EGFR conformers. The conformations of the peptides were optimized using PEP-FOLD server and MDs. The selected conformations were analyzed in a docking study to realize the binding site of the EGFR. Finally, pharmokinetics properties of the peptides were calculated. The designed oligopeptides were EWRSYYYWH, YYYWHNEWN, YYYWHNEWS and HNHSRNYGS with a higher affinity to the EGFR relative to the previously reported peptides. The newly designed peptides were investigated for their in vivo toxicities on rats, and all of them were non-toxic.     

色谱保留时间在蛋白质组研究中的应用

液相色谱与串联质谱联用(LC-MS/MS)技术是蛋白质组学研究中的常见方法。保留时间作为独立于质谱信息的参数已经被用于蛋白质的鉴定和定量工作中。在多肽鉴定领域,多肽的色谱保留时间预测与常规的二级串联质谱数据库搜索算法结合可以提高鉴定的可信度。鉴定的灵敏度也可以通过匹配多次LC-MS实验中具有相同精确质量数和保留时间的峰而提高。另一方面,由于色谱条件的微小改变即会引起保留时间的变化,因此对多次实验结果进行保留时间比对是进行非标记定量的不可或缺的步骤。另外,联合保留时间偏移和质量数信息还可以进行蛋白质翻译后修饰(post-translational modification, PTM)的鉴定。     

光照强度和掺杂浓度对n-PS形貌和电化学行为影响

测试分析了光照强度和掺杂浓度对n型硅电极电化学特性的影响。采用电化学阳极腐蚀法在光照辅助下制备多孔硅(PS),通过扫描电镜研究掺杂浓度对PS表面微观形貌的影响,通过积分球测试仪测试研究了PS对光的反射率。结果表明,对于n型硅,光照是激发空穴的必要手段,光照强度越强,硅/电解液界面的电荷转移阻抗越小,更利于反应的进行;掺杂浓度越高,电化学极化阻力越小,促进PS孔密度增加。本实验条件下,形成的PS是微米级孔,随着掺杂浓度的增加,形成的PS孔径越小,孔深存在一个极值;电阻率为0.35Ω·cm的硅片拥有最大的孔深13μm;PS的孔结构大大提升了硅基对光子的捕获能力,相比于单晶硅,在可见-近红外范围,电阻率为0.0047Ω·cm的硅片制备的n-PS对光的反射率已经从30%降低到了5%。     

The critical aggregation concentration of peptide surfactants is predictable from dynamic hydrophobic property

Peptide surfactants are a kind of newly emerged functional materials, which have a variety of applications such as building nanoarchitecture, stabilizing membrane proteins and controlling drug release. In the present study, we report the modelling and prediction of critical aggregation concentration (CAC), an important parameter that characterizes the self-assembling behaviour of peptide surfactants through the use of statistical modelling and quantitative structure–property relationship (QSPR) approaches. In order to accurately describe the structural and physicochemical properties of the highly flexible peptide molecules, a new method called molecular dynamics-based hydrophobic cross-field (MD-HCF) is proposed to capture both the hydrophobic profile and dynamic feature of 32 surface-activity, structure-known peptides. A number of statistical models are then developed using partial least squares (PLS) regression with or without improvement by genetic algorithm (GA). We demonstrate that MD-HCF performs much better than the widely used CODESSA method in both its predictability and interpretability. We also highlight the importance of dynamic hydrophobic property in accurate prediction and reasonable explanation of peptide self-assembling behaviour in solution, albeit which is exhaustive to compute compared with those derived directly from peptide static structure. To the best of our knowledge, this study is the first to computationally model and predict the self-assembling behaviour of peptide surfactants.     

Removal of isobaric interference using pseudo-multiple reaction monitoring and energy-resolved mass spectrometry for the isotope dilution quantification of a tryptic peptide

Energy-resolved mass spectrometry (ERMS) and an isotopically labelled internal standard were successfully combined to accurately quantify a tryptic peptide despite the presence of an isobaric interference. For this purpose, electrospray ionisation tandem mass spectrometry (ESI-MS/MS) experiments were conducted into an ion trap instrument using an unconventional 8 m/z broadband isolation window, which encompassed both the tryptic peptide and its internal standard. Interference removal was assessed by determining an excitation voltage that was high enough to maintain a constant value for the analyte/internal standard peaks intensity ratio, thus ensuring accurate quantification even in the presence of isobaric contamination. Pseudo-multiple reaction monitoring (MRM) was employed above this excitation voltage to quantify the trypic peptide. The internal standard calibration model showed no lack of fit and exhibited a linear dynamic range from 0.5 μM up to 2.5 μM. The detection limit was 0.08 μM. The accuracy of the method was evaluated by quantifying the tryptic peptide of three reference samples intentionally contaminated with the isobaric interference. All the reference samples were accurately quantified with ∼1% deviation despite the isobaric contamination. Furthermore, we have demonstrated that this methodology can also be applied to quantify the isobaric peptide by standard additions down to 0.2 μM. Finally, liquid chromatography ERMS (LC ERMS) experiments yielded similar results, suggesting the potential of the proposed methodology for analysing complex samples.     

Investigation of the interaction between HIV-1 DNA and cyclic peptides by electrospray ionization mass spectrometry

The interaction between HIV-I DNA and five cyclic peptides (CPI-CP5) was investigated using electrospray ionization mass spectrometry (ESI-MS). It revealed that CPI [c(Ala-Tyr-Leu-Ala-Gly)] and CP4 [c(Pro-D-Tyr-Leu-D-Ala-Gly)] have the higher binding affinity with the duplex DNA among the five cyclic peptides.     

Summary of ISO/TC 201 Standard: XXIII,ISO 24236:2005—surface chemical analysis—Auger electron spectroscopy—repeatability and constancy of intensity scale

This International Standard specifies a method for evaluating the constancy and repeatability of the intensity scale of Auger electron spectrometers, for general analytical purposes, using an electron gun with a beam energy of 2 keV or greater. It is only applicable to instruments that incorporate an ion gun for sputter cleaning. It is not intended to be a calibration of the intensity/energy response function. 1 , 2 That calibration may be made by the instrument manufacturer or other organization. The present procedure provides data to evaluate and confirm the accuracy with which the intensity/energy response function remains constant with instrument usage. Guidance is given to some of the instrumental settings that may affect this constancy. © Crown Copyright 2006. Reproduced with the permission of the Controller of HMSO.     

Evaluation of peptide fractionation strategies used in proteome analysis

Peptide fractionation is extremely important for the comprehensive analysis of complex protein mixtures. Although a few comparisons of the relative separation efficiencies of 2‐D methodologies using complex biological samples have appeared, a systematic evaluation was conducted in this study. Four different fractionation methods, namely strong‐cation exchange, hydrophilic interaction chromatography, alkaline‐RP and solution isoelectric focusing, which can be used prior to LC‐MS/MS analysis, were compared. Strong‐cation exchange × RPLC was used after desalting the sample; significantly more proteins were identified, compared with the nondesalted sample (1990 and 1375). We also found that the use of a combination of analytical methods resulted in a dramatic increase in the number of unique peptides that could be identified, compared with only a small increase in protein levels. The increased number of distinct peptides that can be identified is especially beneficial, not only for unequivocally identifying proteins but also for proteomic studies involving posttranslational modifications and peptide‐based quantification approaches using stable isotope labeling. The identification and quantification of more peptides per protein provide valuable information that improves both the quantification of, and confidence of protein identification.     

A simple sheathless CE-MS interface with a sub-micrometer electrical contact fracture for sensitive analysis of peptide and protein samples

Online coupling of capillary electrophoresis (CE) to electrospray ionization mass spectrometry (MS) has shown considerable potential, however, technical challenges have limited its use. In this study, we have developed a simple and sensitive sheathless CE-MS interface based on the novel concept of forming a sub-micrometer fracture directly in the capillary. The simple interface design allowed the generation of a stable ESI spray capable of ionization at low nanoliter flow-rates (45–90 nL/min) for high sensitivity MS analysis of challenging samples like those containing proteins and peptides. By analysis of a model peptide (leucine enkephalin), a limit of detection (LOD) of 0.045 pmol/μL (corresponding to 67 attomol in a sample volume of ∼15 nL) was obtained. The merit of the CE-MS approach was demonstrated by analysis of bovine serum albumin (BSA) tryptic peptides. A well-resolved separation profile was achieved and comparable sequence coverage was obtained by the CE-MS method (73%) compared to a representative UPLC-MS method (77%). The CE-MS interface was subsequently used to analyse a more complex sample of pharmaceutically relevant human proteins including insulin, tissue factor and α-synuclein. Efficient separation and protein ESI mass spectra of adequate quality could be achieved using only a small amount of sample (30 fmol). In addition, analysis of ubiquitin samples under both native and denatured conditions, indicate that the CE-MS setup can facilitate native MS applications to probe the conformational properties of proteins. Thus, the described CE-MS setup should be useful for a wide range of high-sensitivity applications in protein research.     

Summary of ISO/TC 201 Standard: XXIV,ISO 24237:2005—surface chemical analysis—X‐ray photoelectron spectroscopy—repeatability and constancy of intensity scale

This International Standard specifies a method for evaluating the repeatability and constancy of the intensity scale of X‐ray photoelectron spectrometers, for general analytical purposes, using non‐monochromated Al or Mg X‐rays or monochromated Al X‐rays. It is only applicable to instruments that incorporate an ion gun for sputter cleaning. It is not intended to be a calibration of the intensity/energy response function (Seah MP. J. Electron Spectrosc. 1995; 71: 191; http://www.npl.co.uk/nanoanalysis/a1calib.html [2006]). That calibration may be made by the instrument manufacturer or other organization. The present method provides data to evaluate and confirm the accuracy with which the intensity/energy response function remains constant with instrument usage. Guidance is given to some of the instrument settings that may affect this constancy. Copyright © 2006 John Wiley & Sons, Ltd.