蛋白质组学研究中的无标记定量方法

蛋白质定量是探索疾病发生发展状况和寻找新药靶标的重要手段.该领域最常用的技术是比较染色后的二维凝胶上蛋白点的光密度值或综合同位素标记后的质谱峰强度方法.但此二者的样品处理方法都比较麻烦,不利于进行大规模蛋白质组的定量研究.最近几年出现了利用质谱数据进行无标记定量的方法,根据数据类型这些方法可以分为2类基于鉴定蛋白的肽段数的方法和基于质谱峰强度的方法,在高通量大规模蛋白组定量研究中有很大优势.本综述主要介绍了这2类无标记定量方法的模型及优缺点,并比较了2类方法的灵敏度和准确度.肽段计数方法在检测蛋白丰度变化时更灵敏,而峰面积强度在评估蛋白比率时更准确.

用EM算法改进鸟枪法蛋白质鉴定中的无标记定量方法

蛋白质定量是探索疾病发生发展状况和寻找新药靶标的重要手段。在shotgun蛋白组学中,目前常用定量方法包括综合同位素标记后的质谱峰强度方法和无标记定量方法。根据数据类型无标记定量方法可以分为两类:基于鉴定蛋白的质谱数的方法和基于质谱峰强度的方法。本研究主要用EM算法改进基于鉴定蛋白质谱数的定量方法,并用免疫印迹实验获得的酵母全蛋白的丰度来验证EM算法改进后定量的有效性结果表明,改进后的质谱数和蛋白丰度的相关性比改进前有一定的提高。同时,利用这些数据对主要的几种基于鉴定蛋白的质谱数的模型进行了比较,发现PAI模型最好,SpS模型次之,emPAI模型最不适合于蛋白质定量。

Triterpenoid Saponins from Eclipta prostrata L.

Five triterpenoid saponins were isolated from the Chinese traditional medicine Eclipta prostrata L.. On the basis of their chemical properties and spectral data, they were identified as eclalbasaponins II(1), I(2), III(3), 3-O-[b-D-glucopyranosyl(12)-b-D-glucopyranosyl]-16a-ethoxy-olean-12-ene-28-oic acid-28-O-b-D-glu-copyranoside(4) and 3-O-[(2-O-sulfuryl-b-D-glucopyranosyl)(12)-b-D-glucopyranosyl]-echinocystic acid-28-O-b-D-glucopyranoside(5). Compounds 4 and 5 are new compounds and named eclalbasaponins XI and XII, respectively. Compounds 1 and 5 induced morphological deformation of Pyricularia oryzae mycelia.

Investigation on Non-covalent Complexes of Cyclodextrins with Li＋ in Gas Phase by Mass Spectrometry

To investigate the non-covalent interaction between cyclodextrins （CD） and lithium ion, a stoichiometry of α-CD, β-CD, heptakis（2,6-di-O-methyl）-β-CD （DM-β-CD）, or heptakis（2,3,6-tri-O-methyl）-β-CD （TM-β-CD） was mixed with lithium salt, respectively, and then incubated at room temperature for 10 min to reach the equilibrium. In posi- tive mode, the electrospray ionization mass spectrometry （ESI-MS） results demonstrated that lithium ion can conjugate to α-, β-, DM-β- or TM-β-CD and form 1：1 stoichiometric non-covalent complexes. The binding of the complexes was further confirmed by collision- induced dissociation. The dissociation constants Kdl of four complexes （Li＋α-CD, Li＋β- CD, Li＋DM-β-CD, and Li＋TM-β-CD） were determined by mass spectrometric titration. The results showed Kdl were 18.7, 26.7, 33.6, 30.5 μmol/L for the complexes of Li＋ with α-CD, β-CD, DM-β-CD, and TM-β-CD, respectively. Kdl for the Li＋ complexes of/3-CD is smaller than that of DM-β-CD due to its steric effect of the partial substituted -CH3. The Kdl for the Li＋ complexes of DM-β-CD is nearly in agreement with that of TM-β-CD, indicating Li＋ is more likely to locate in the small rim of DM-β-CD＇s hydrophobic cavity. The DFT results showed through electrostatic interaction, one Li＋ can strongly conjugate to four neighboring oxygen atoms. For the （α-CD＋Li）＋ complex, one Li＋ may also situate the small rim of α-CD＇s hydrophobic cavity to form a non-specific host-guest complex.

Analysis of a Class of Logical Functions over Galois and Z_m Rings

In this paper, the author analyzed some cryptographic properties of a class of logical functions, f(x,y)=(q(x),...,q(x))·y+h(x),over Galois rings and residue rings, presented the relationship between the character spectrum of f(x,y) and the character speetrum of q(x),h(x) and the relationship between the cryptographic properties of f(x,y) and the cryptographic properties of h(x).

Low polar volatile constituents from Isodon excisa by GC-MS

An attempt had been made to isolate and identify the low polar volatile constituents from Isodon excisa. The dried plants were heat extracted with ethanol and then extracted with petroleum ether. The constituents were isolated and analyzed by GC-MS and then we retrieved them on NIST08 mass spectrometry database to determine their structures. Finally, successful results were achieved, 111 compounds were obtained and identified. 105 of them were reported for the first time in lsodon excisa and 22 of them were first found in natural products. Thus, the main constituents of it were found to be Sitosterol （33.28%）, 3-Amino-4-pyrazolecarbonitrile （9.55%）

Q estimation based on logarithmic spectral areas with different high and low frequencies

When a seismic wave propagates through subsurface viscoelastic media,the formation absorbs the high-frequency energy of the seismic wave more strongly than the low-frequency energy.As the depth and the off set increase,the diff erence between the logarithmic spectral areas with high and low frequencies gradually increases.Based on this seismic wave characteristic,we have developed a novel Q-estimation method based on logarithmic spectral area diff erence of high and low frequencies(referred to as the LSAD_LH method).In this paper,we derive the theoretical relationship between the Q value and difference of logarithmic spectral areas with high and low frequencies and prove the applicability of the LSAD_LH method using a single-layer medium numerical model.To verify the sensitivity of the LSAD_LH method to bandwidth selection and noise,we compare the LSAD_LH method with two credible methods—the logarithmic spectral ratio(LSR)and logarithmic spectral area diff erence(LSAD)methods using a synthetic model containing the random noise.The results demonstrate that the LSAD_LH method is not highly dependent on bandwidth,and in terms of noise immunity,it is signifi cantly better than the LSR method and has the same advantages as the LSAD method.To further highlight the advantages of the LSAD_LH method,we apply the LSAD_LH and LSAD methods to the vertical seismic profi ling(VSP)numerical simulation of the multilayer media and the fi eld zero-off set VSP data.The application of the two cases proves the applicability of the LSAD_LH method and the accuracy of the high Q-value estimation relative to the LSAD method.Moreover,via the transmission coeffi cient,the LSAD_LH method overcomes the weakness of the LSAD method.

New Software for the Identification and Characterization of Peptides Generated during Fontina Cheese Ripening Using Mass Spectrometry Data

The aim of this work was to design and implement a new bioinformatics software which is able to identify the protein peptides from the peaks which arise from in-source or MS/MS fragmentation. The oligopeptide fraction was extracted from Fontina cheese at different ages of ripening and subsequently analyzed by LC/MS/MS. On the resulting total ion chromatograms, the peptides were identified by a method based both on the in-source fragmentation detectable with a single-quadrupole mass analyzer and by a new software which was developed. This software performs an in-silieo digestion of the major milk proteins, it calculates all the possible peptide fragments which are generated by the loss of the first N- or C-terminal amino acids, and finally, it matches the experimental ion chromatogram with the in-silico which generated theoretical spectrum to identify the exact amino-acid protein sequence of the unknown oligopeptide. With this tool, the useful insights into the proteolytic processes which occur during Fontina cheese aging are obtained, which leads to a better knowledge about the functional features of the proteolysis end product.

Spectral Response of Different Eroded Soils in Subtropical China: A Case Study in Changting County, China

Hyper-spectral data is widely used to determine soil properties. However, few studies have explored the soil spectral characteristics as response to soil erosion. This study analysed the spectral response of different eroded soils in subtropical China, and then identify the spectral characteristics and soil properties that better discriminate softs with different erosion degrees. Two methods were compared： direct identification by inherent spectral characteristics and indirect identification by predictions of critical soft properties. Results showed that the spectral curves for different degrees of erosion were similar in morphology, while overall reflectance and characteristics of specific absorption peaks were different. When the first method is applied, some differences among different eroded groups were found by integration of associated indicators. However, the index of such indicators showed apparent mixing and crossover among different groups, which reduced the accuracy of identification. For the second method, the correlation between critical soil properties, such as soil organic matter （SOM）, iron and aluminium oxides and reflectance spectra, was analysed. The correlation coefficients for the moderate eroded group were primarily between -0.3 to -0.5, which were worse than the other twogroups. However, the maximum value of R2 was obtained as 0.86 and 0.94 for the non-apparent eroded and the severe group. Furthermore, these two groups also showed some differences in the spectral response of iron complex state （Fep）, Aluminium amorphous state （Alo） and the modelling results for soil organic matter （SOM）. The study proved that it is feasible to identify different degrees of soil erosion by hyperspectral data, and that indirect identification by modelling critical soil properties and reflectance spectra is much better than direct identification. These results indicate that hyper-spectral data may represent a promising tool in monitoring and modelling soil erosion.

Analysis of influence of water temperature on milk powder proteins using MALDI-TOF MS

The influence of water temperature on protein composition in the reconstitution of milk powder was evaluated using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry （MALDI-TOF MS）. 11 ion peaks in the matrix-assisted laser desorption/ionization （MALDI） spectra were examined to study the alteration of relative quantities of milk proteins when water at different temperature was employed in the reconstitution of milk powder. A discrepancy factor Dij was implemented to represent the degree of milk proteins＇ denaturation. Data obtained indicated that Dij value increased with rising water temperature, and thermal damage to milk proteins became evidently when the water temperature exceeded 60℃. The results confirmed that nutrient loss occurred when milk proteins denatured in water at high temperatures.

Chemical component and antimicrobial activity of volatile oil of Calycopteris floribunda

The volatile oil of leaves and barks of Calycopteris floribunda was examined by gas chromatography-mass spectrometry (GC-MS). 52 volatile chemical components in leaves were identified. The antimicrobial assay of oils in the leaves and barks was carried out by disk diffusion method in vitro. The major components (mass fraction) in leaves are caryophyllene oxide (13.79%),n-hexadecanoic acid (11.91%) and β-caryophyllene (10.45%). Ten constituents are identified accounting for about 99.98% of the total volatile oil in the bark. Among these components,n-hexadecanoic acid (59.18%),linolic acid (12.70%) and butyl octyl phthalate (8.21%) are the major constituents. The oils exhibit strong antimicrobial activity and display more potent against bacteria than fungi.

Magnetic Properties of a Mixed Spin-2 and Spin-5/2 Heisenberg Ferrimagnetic System on a Two-Dimensional Honeycomb Lattice： Green＇s Function Approach

The multisublattice Green＇s function technique is applied to study the magnetic properties of a mixed spin-2 and spin-5/2 Heisenberg ferrimagnetic system on a two-dimensional honeycomb lattice. The role of the different interactions in the Hamiltonian is explored. When only the nearest-neighbor interaction and the single-ion anisotropy are included, our results indicate that there are compensation points at finite temperatures. When the next-nearest-neighbor interaction exceeds a minimum value that depends on the other parameters in the Hamiltonian, the compensation point disappears. The next-nearest-neighbor interaction has the effect of changing the compensation temperature.

Identification of Volatile Compounds in Codfish(Gadus) by a Combination of Two Extraction Methods Coupled with GC-MS Analysis

Codfish is a kind of abyssal fish species with a great value in food industry. However, the flavor of codfish, especially the unpleasant odor, has caused serious problems in its processing. To accurately identify the volatile compounds in codfish, a combination of solid phase micro-extraction(SPME) method and simultaneous distillation extraction(SDE) method was used to extract the volatiles. Gas chromatography-mass spectrometry(GC-MS) along with Kovats indices(KI) and authentic standard compounds were used to identify the volatiles. The results showed that a total of 86 volatile compounds were identified in codfish, of them 24 were extracted by SDE, 69 compounds by SPME, and 10 compounds by both SDE and SPME. Seventy volatile compounds were found to have specific odors, of them 7 typical compounds contributed significantly to the flavor of codfish. Alcohols(i.e.,(E)-2-penten-1-ol and 2-octanol), esters(i.e., ethyl butyrate and methyl geranate), aldehydes(i.e., 2-dodecenal and pentadecanal) contributed the most to fresh flavor while nitrogen compounds, sulphur compounds, furans, as well as some ketones(i.e., 2-hydroxy-3-pentanone) brought unpleasant odor, such as fishy and earthy odor. It was indicated that the combination of multiple extraction methods and GC-MS analysis can enhance the accuracy of identification, and provide a reference for the further study on flavor of aquatic products.

Properties of Bio-oil from Fast Pyrolysis of Rice Husk

Physicochemical properties of bio-oil obtained from fast pyrolysis of rice husk were studied in the present work.Molecular distillation was used to separate the crude bio-oil into three fractions viz.light fraction,middle fraction and heavy fraction.Their chemical composition was analyzed by gas chromatograph and mass spectrometer（GC-MS）.The thermal behavior,including evaporation and decomposition,was investigated using thermogravimetric analyzer coupled with Fourier transform infrared spectrometer（TG-FTIR）.The product distribution was significantly affected by contents of cellulose,hemicellulose and lignin.The bio-oil yield was 46.36%（by mass） and the yield of gaseous products was 27%（by mass）.The chemicals in the bio-oil included acids,aldehydes,ketones,alcohols,phenols,sugars,etc.The light fraction was mainly composed of acids and compounds with lower boiling point temperature,the middle and heavy fractions were consisted of phenols and levoglucosan.The thermal stability of the bio-oil was determined by the interactions and intersolubility of compounds.It was found that the thermal stability of bio-oil was better than the light fraction,but worse than the middle and heavy fractions.

Data organization and management of mine typical object spectral libraries

With the development of mining industry,people have obtained profits from it,but they are facing environmental damages.In order to monitor these environmental changes,a spectral library is set up for the spectrum data organization and management of mine typical objects.Most of the spectrum data come from the long-term field measuring in mining area and other spectral libraries.For the data quality control and error detection in the measuring data,an inner precision calculation method is presented and a series of interactive graphical controls are developed for the spectrum visualization and analysis.Through extracting and saving spectrum characters for the mine typical objects,realizs spectrum matching and classification for new measured spectrum samples are realized by using Euclidean distance,Aitchison distance,Pearson correlation coefficient and vector angular cosine methods.Based on the matching result,this work is able to gather dynamically physicochemical environment parameters from the library and gives an early warning for the mine environmental changes.

Hyper-spectrum models for monitoring water quality in Dianshan Lake,China

The correlation between water quality parameters and hyper-spectral reflectance is studied with models established for each parameter and applied in Dianshan Lake, in the upstream of the Huangpu River running through Shanghai, China. Models are for dissolved oxygen (DO in mg/L): R720/R680 = 20.362×(R720/R680)2?31.438×(R720/R680)+19.156; for turbidity (NTU): R*714.5 = 206.07× (R*714.5)2?582.5×R*714.5 + 423.24; and for total phosphorus (TP in mg/L): R*509.5 = 16.661× (R*509.5)2?32.646×R*509.5+16.116. The R2 values are 0.770 8, 0.660 4 and 0.738 7, respectively, showing strong positive relationships. The models were then applied to assess water quality of different times. Results are quite satisfactory for some samples.

Murine brain tissues with human cytomegalovirus infection: a proteomic study

To establish two-dimensional electrophoresis profiles with high resolution and reproducibility from murine brain tissues by human cytomegalovirus（HCMV） infection and paired murine brain tissues and to identify the differential expression proteins. Methods： Forty Kunming mice were randomly divided into infection group （20） injected with HCMVAD169 and control group （20） injected with saline into their brain. After 30 days, the murine brain tissues by HCMV infection and paired murine brain tissues were separated by two-dimensional gel electrophoresis（2-DE）, analyzed by Image Master 2D software, and identified by peptide mass fingerprint（PMF） and database searching, and make Western blotting analyses the differential expression of individual proteins. Results： Well resolved, reproducible 2-D maps of the above tissues were obtained. Some of the different proteins identified by mass spectrometry（MS） were matched in the SWISS-2D PAGE database, Western blotting analyses were further carried out to verify the differential expression of individual proteins. Conclusion： These data will be valuable for studying the diagnosis of disease at an early stage, mechanisms of pathogenic and the key to the development of anti-HCMV medicine.

DETERMINATION OF THERMODYNAMIC AND KINETIC PARAMETERS OF LARGE SCALE CHROMATOGRAPHIC SEPARATION OF SUGAR AND REDUCING SUGAR

The parameter identification model of largr scale chromatography separation process is proposed. The Phase equilibrium constants and lumped mass transfer coefficients of sugar and reducing sugar adsorption on D1, D2 and D3 resins as well as the axial dispersion coefficients of the fluid through packed columns are determined by means of the pulse-response experiment technique with an inert substance as a tracer and the chromatography measuring technique. The elution curve calculated from these parameters is good agreement with the experimental elution curve. The sensitivity analysis of these parameters is carried out, and the ressult shows that the elation curves of chromatography separation are more sensitive to the variations Of the Phase equilibrium relationship than to the variation of the axial dispersion as well as the lumped mass transfer coefficients.

Microstructure characterization and electrochemical corrosion behavior of Zn and Zn/Mg alloys in H_2SO_4 solution

The three systems of pure Zn, Zn-0.10% Mg(mass fraction), and Zn-0.15% Mg(mass fraction) were cast under controlled atmosphere and their microstructures were characterized by SEM/EDS analysis. The electrochemical corrosion behavior of these three samples was examined in the very aggressive solution of 50% H2SO4(mass fraction) using electrochemical impedance spectroscopy(EIS) and potentiodynamic polarization measurements. The results show that magnesium improves in some extent the corrosion resistance of pure Zn in 50% H2SO4(mass fraction) confirmed by EIS test. Results of polarization measurment also demonstrate that small amount of Mg significantly improves the passivation of Zn in the test solution. Results of surface morphology of the samples and EDS analysis reveal that Mg reduced the corrosion attacks to pure Zn.

Plant Cell Wall Proteomics： Mass Spectrometry Data, a Trove for Research on Protein Structure/Function Relationships

Proteomics allows the large-scale study of protein expression either in whole organisms or in purified organelles. In particular, mass spectrometry （MS） analysis of gel-separated proteins produces data not only for protein identification, but for protein structure, location, and processing as well. An in-depth analysis was performed on MS data from etiolated hypocotyl cell wall proteomics ofArabidopsis thaliana. These analyses show that highly homologous members of multigene families can be differentiated. Two lectins presenting 93% amino acid identity were identified using peptide mass fingerprinting. Although the identification of structural proteins such as extensins or hydroxyproline/proline-rich proteins （H/PRPs） is arduous, different types of MS spectra were exploited to identify and characterize an H/PRP. Maturation events in a couple of cell wall proteins （CWPs） were analyzed using site mapping. N-glycosylation of CWPs as well as the hydroxylation or oxidation of amino acids were also explored, adding information to improve our understanding of CWP structure/function relationships. A bioinformatic tool was developed to locate by means of MS the N-terminus of mature secreted proteins and N-glycosylation.