Mass spectrometry in the analysis of grape and wine proteins

Wine proteins play an important role in the quality of wine, because they affect taste, clarity and stability of product. The majority of wine proteins are in the range of 20-30 kDa. Different mass spectrometry (MS) techniques have been successfully applied to study the grape and wine proteins. By liquid chromatography (LC) electrospray ionization (ESI) MS and nano-LC/MS, nine dipeptides and 80 peptides were unambiguously identified in Champagne and Sauvignon Blanc wines, respectively. Using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) and surface-enhanced laser desorption/ionization TOF, the protein and peptide fingerprints in Chardonnay, Sauvignon Blanc and Muscat of Alexandria wines were determined. MALDI-TOF identified the mesocarp proteome of six Vitis grape varieties. Proteins in different grape tissue extracts were also studied. The major grape pathogenic-related proteins are chitinases and thaumatin-like proteins, which both persist through the vinification process and cause hazes and sediments in bottled wines. ESI-MS, LC/ESI-MS and MALDI-TOF analysis of these proteins in grape and wine were also used to characterize different grape varieties.     

野生葡萄及葡萄酒抗氧化活性和抗菌性研究

选取广西、湖南等地野生葡萄,与经典酿酒葡萄比较,研究抗氧化活性和活性物质,同时监测葡萄酒发酵过程中各指标的动态变化,并对不同品种葡萄酒的抗菌性进行研究。结果表明:赤霞珠的酚类含量和抗氧化活性高于野生葡萄和玫瑰香葡萄,但野生葡萄酒的抗菌性能显著优于赤霞珠和玫瑰香葡萄酒。葡萄酒在发酵过程中其抗氧化活性和酚类物质含量均随发酵过程的进行而升高;总抗氧化活性与总酚含量、氧自由基清除能力与原花青素含量成显著正相关,相关系数均大于0.989;总花色苷含量在发酵初期上升,后期下降,葡萄酒颜色变浅。     

河西干旱区酿酒葡萄生长的气象条件

按照平行观测的原则,利用2002、2003年两年田间试验资料,采用数理统计方法分析了河西内陆干旱区目前国内广泛种植的8个不同熟性酿酒品种的生长发育规律及其气象影响因子。结果表明：（1）新梢、果实生长呈抛物线型,生长关键期分别出现在5月上旬～6月中旬、7月上旬～8月上旬;糖分累积呈“S”型,积累关键期出现在8月中旬～9月上旬。枝条、果实、含糖量增长峰值点位相出现时间按中早熟、中晚熟、晚熟品种依次推后。（2）中早熟品种需≥10℃积温2800～2900℃,中晚熟种2900～3100℃,晚熟种3000～3200℃;新梢生长期35～50d,需≥10℃积温620～750℃。花期7～15d,需≥10℃积温130～320℃。浆果生长期50～65d,需≥10℃积温1100～1400℃。浆果成熟期35～50d,需≥10℃积温640～940％。（3）新梢生长量与日平均气温、日照时间和土壤湿度呈正相关。气温低于11～12℃时,新梢停止生长;果粒增长速度与平均气温、最高气温呈负相关,与相对湿度、降水量呈正相关。果粒增长适宜气温为20～21℃,超过21℃,增速明显变缓;含糖量积累与光、热因子均呈正相关,与水分因子呈负相关。品种熟性越晚,对气象条件反映越敏感。气温低于7～7．9℃时,糖分停止积累。通过酿酒葡萄适生气候条件分析,为区域化布局、产业化发展提供理论依据。     

Characterization and analysis of posttranslational modifications of the human large cytoplasmic ribosomal subunit proteins by mass spectrometry and Edman sequencing

The 60S ribosomal proteins were isolated from ribosomes of human placenta and separated by reversed phase HPLC. The fractions obtained were subjected to trypsin and Glu-C digestion and analyzed by mass fingerprinting (MALDI-TOF), MS/MS (ESI), and Edman sequencing. Forty-six large subunit proteins were found, 22 of which showed masses in accordance with the SwissProt database (June 2002) masses (proteins L6, L7, L9, L13, L15, L17, L18, L21, L22, L24, L26, L27, L30, L32, L34, L35, L36, L37, L37A, L38, L39, L41). Eleven (proteins L7, L10A, L11, L12, L13A, L23, L23A, L27A, L28, L29, and P0) resulted in mass changes that are consistent with N-terminal loss of methionine, acetylation, internal methylation, or hydroxylation. A loss of methionine without acetylation was found for protein L8 and L17. For nine proteins (L3, L4, L5, L7A, L10, L14, L19, L31, and L40), the molecular masses could not be determined. Proteins P1 and protein L3-like were not identified by the methods applied.     

南亚热带酿酒葡萄品种(系)引种研究

1998～1999年,对8804、真芳德(Zinfandel)、梅尔诺(Merlot Noir)、赤霞珠(Cabernet Sauvignon)等4个欧亚种优良酿酒葡萄品种(系)在我国南亚热带季风气候下的栽培适应性做了初步观察.结果表明,8804具有较强的抗病性和早期丰产性;真芳德早期丰产性突出,但抗真菌病害能力较差;梅尔诺和赤霞珠早期丰产性较差,抗病性一般,能获得较好的成熟度.     

酿酒葡萄品质评价及其对气象条件的响应

根据2004～2005年我国北方6省酿酒葡萄主要产区葡萄取样和宁夏芦花台园艺场田间试验葡萄化验结果,运用层次分析方法（AHP）对酿酒葡萄主要品质因子总糖、糖酸比pH、单宁进行综合评价,运用主成分分析方法和因子分析法研究影响每个地区酿酒葡萄综合品质的主要气象因子和影响时段。结果表明：2004～2005年贺兰山东麓的御马、玉泉营、广夏三基地、贺东在庄园;河西走廊的高台、武威;新疆石河子酿酒葡萄品质优良,渤海湾的烟台、蓬莱、昌藜等地酿酒葡萄品质表现一般。酿酒葡萄综合品质主要受果实着色期、全生育期和7～8月的降水量和水热系数的影响,其中降水量起主导作用。果实着色期气温日较差和全生育期平均相对湿度对酿酒葡萄综合品质的形成也有重要影响,影响相对较小的是果实着色期的最低气温。采样地区的光照、温度等气象条件基本适宜酿酒葡萄品质形成,对优质酿酒葡萄形成没有大的限制作用。     

Mass spectrometry and database search in the analysis of proteins from the fungus Pleurotus ostreatus

Tandem mass spectrometry is a method of choice for rapid analysis in proteomics. Identification and characterization of proteins from organisms with sequenced genomes is today a routine procedure as will be identification of proteins from organisms with unsequenced genomes with new developing tools. Here, we report the use of isotopic labeling with electrospray ionisation (ESI)-tandem mass spectrometry for de novo sequencing in combination with database search taking advantage of different programs for identification of fungal proteins. Using this approach we could identify the proteins of interest. Nevertheless, the identification of a novel protein responsible for the conversion of testosterone into androstenedione was still a difficult task, mostly due to the low homology of steroid transforming enzymes, especially those from microorganisms. Protein p27 was identified as the vanillate O-demethylase oxidoreductase, p33 and p36 as two isoenzymes of malate dehydrogenase, and p45 as citrate synthase. By rechecking the sequences using additional programs it could be shown that the protein p36 has a higher local homology to the steroid-transforming enzyme than to the malate dehydrogenase. Therefore, we assume that p36 is a pluripotent enzyme most probably responsible for the 17beta-hydroxysteroid dehydrogenase activity.     

Profiling the effects of process changes on residual host cell proteins in biotherapeutics by mass spectrometry

An advanced liquid chromatography/mass spectrometry (MS) platform was used to identify and quantify residual Escherichia coli host cell proteins (HCPs) in the drug substance (DS) of several peptibodies (Pbs). Significantly different HCP impurity profiles were observed among different biotherapeutic Pbs as well as one Pb purified via multiple processes. The results can be rationally interpreted in terms of differences among the purification processes, and demonstrate the power of this technique to sensitively monitor both the quantity and composition of residual HCPs in DS, where these may represent a safety risk to patients. The breadth of information obtained using MS is compared to traditional multiproduct enzyme‐linked immunosorbent assay (ELISA) values for total HCP in the same samples and shows that, in this case, the ELISA failed to detect multiple HCPs. The HCP composition of two upstream samples was also analyzed and used to demonstrate that HCPs that carry through purification processes to be detectable in DS are not always among those that are the most abundant upstream. Compared to ELISA, we demonstrate that MS can provide a more comprehensive, and accurate, characterization of DS HCPs, thereby facilitating process development as well as more rationally assessing potential safety risks posed by individual, identified HCPs. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:951–957, 2013     

The MALDI mass spectrometry in the identification of new proteins in snake venoms

By MALDI MS, we searched cobra venoms for new low-content polypeptides. A number of new proteins with molecular masses 7–25 kDa, characteristic of the known snake protein toxins, were identified, with the content of one of them less than 0.02%.     

Multidimensional proteomic analysis of photosynthetic membrane proteins by liquid extraction-ultracentrifugation-liquid chromatography-mass spectrometry

The membrane protein components of photosystem I (PSI) and II (PSII) from different species were prefractionated by liquid extraction and sucrose gradient ultracentrifugation and subsequently analyzed by reversed-phase high-performance liquid chromatography-electrospray ionization-mass spectrometry (RP-HPLC-ESI-MS) using poly-(styrene-divinylbenzene)-based monolithic capillary columns. The analytical method was shown to be very flexible and enabled the identification of antenna proteins as well as most of the proteins of the reaction center from PSI and PSII in various plant species with few RP-HPLC-ESI-MS analyses necessitating only minor adaptations in the gradients of acetonitrile in 0.05% aqueous trifluoroacetic acid. The membrane proteins, ranging in molecular mass (Mr) from 4196 (I protein) to more than 80,000 (PSI A/B) as well as isoforms were identified on the basis of their intact Mr and comparison with Mr deduced from known DNA or protein sequences. High quality mass spectra enabled the identification and quantitation of the nonphosphorylated and phosphorylated reaction center subunits D1, D2, and CP43 of PSII, containing five to seven membrane-spanning alpha-helices. Because of its high flexibility and suitability for proteins having a very wide range of Mr and hydrophobicities, the method is generally applicable to the analysis of complex mixtures of membrane proteins.     

Mass spectrometry of nicotinic acetylcholine receptors and associated proteins as models for complex transmembrane proteins

Studies were conducted to optimize matrix-assisted laser desorption/ionization, time-of-flight mass spectrometry (MALDI TOF MS) in analyzing the composition of nicotinic acetylcholine receptors (nAChR) from Torpedo californica electric tissue in their membrane-bound, detergent-solubilized, and affinity-purified states. Mass spectra obtained from nAChR-rich membrane fractions gave reasonably good representations of protein compositions indicated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of those same samples. Efficiency of extraction of nAChR from membranes was not markedly different for most detergents, but quality and signal size of mass spectra were clearly influenced by detergent composition and concentration, protein concentration, and MALDI matrix composition. The best spectra, allowing detection and accurate size determinations for samples containing as little as 10 fmol of pure nAChR, were obtained for samples solubilized in Triton X-100 and assayed by use of a sinapinic acid matrix. Although informative spectra could be obtained for nAChR affinity purified on alpha-cobratoxin (Naja naja siamensis) columns and extracted using sinapinic acid, superior spectra with much higher signal:noise were obtained if extraction media contained Triton X-100 or sodium dodecyl sulfate. nAChR subunit masses determined were similar regardless of the membrane-associated, detergent-solubilized, or affinity-purified state of the preparation. These studies illustrate how masses can be determined for nAChR subunits and for other protein components in Torpedo membrane preparations, such as RAPsyn and Na(+)-K(+)-ATPase alpha and beta subunits. They also provide an underpinning for streamlined analysis of the composition of complex transmembrane proteins using MALDI TOF MS.     

Strategies in mass spectrometry for the assignment of Cys-Cys disulfide connectivities in proteins

Elucidating disulfide linkage patterns is a crucial part of protein characterization, for which mass spectrometry (MS) is now an indispensable analytical tool. In many cases, MS-based disulfide connectivity assignment is straightforwardly achieved using one-step protein fragmentation in the unreduced form followed by mass measurement of bridged fragments. By contrast, venom proteins, which are receiving increasing interest as potential therapeutics, are a challenge for MS-based disulfide assignment due to their numerous closely spaced cysteines and knotted disulfide structure, requiring creative strategies to determine their connectivity. Today, these include the use of an array of reagents for enzymatic and/or chemical cleavage, partial reduction, differential cysteine labeling and tandem MS. This review aims to describe the toolkit of techniques available to MS users approaching both straightforward and complex disulfide bridge assignments, with a particular focus on strategies utilizing standard instrumentation found in a well-equipped analytical or proteomics laboratory.     

Proteomics and glycoproteomics of beer and wine

Beer and wine are fermented beverages that contain abundant proteins released from barley or grapes, and secreted from yeast. These proteins are associated with many quality attributes including turbidity, foamability, effervescence, flavour and colour. Many grape proteins and secreted yeast proteins are glycosylated, and barley proteins can be glycated under the high temperatures in the beer making process. The emergence of high-resolution mass spectrometry has allowed proteomic and glycoproteomic analyses of these complex mixtures of proteins towards understanding their role in determining beer and wine attributes. In this review, we summarise recent studies of proteomic and glycoproteomic analyses of beer and wine including their strategies for mass spectrometry (MS)-based identification, quantification and characterisation of the glyco/proteomes of fermented beverages to control product quality.     

Mass spectrometry of nucleotides and oligonucleotides

Recent advances in the use of mass spectrometry for the determination of the molecular weight and sequencing of oligonucleotides are disscussed. Matrix-assisted laser desorption (MALDI) and electrospray ionization (ESI) mass spectrometry have been shown to be especially important techniques for both molecular weight assignment and sequencing of oligonucleotides, and are the focus of this article which covers the literature through early 1996.     

Back-regulation of six oxidative stress proteins with grape seed proanthocyanidin extracts in rat diabetic nephropathy

Diabetic nephropathy (DN) is a major cause of morbidity and mortality in diabetic patients. To prevent the development of this disease and to improve advanced kidney injury, effective therapies directed toward the key molecular target are required. Grape seed proanthocyanidin extracts (GSPE) have been reported to be effective in treating DN, while little is known about the functional protein changes. In this study, we used streptozotocin (STZ) to induce diabetic rats. GSPE (250 mg/kg body weight/day) were administrated to diabetic rats for 24 weeks. Serum glucose, glycated hemoglobin, and advanced glycation end products were determined. Consequently, 2-D difference gel electrophoresis and mass spectrometry were used to investigate kidney protein profiles among the control, untreated and GSPE treated diabetic rats. Twenty-five proteins were found either up-regulated or down-regulated in the kidneys of untreated diabetic rats. Only nine proteins in the kidneys of diabetic rats were found to be back-regulated to normal levels after GSPE therapy. These back-regulated proteins are involved in oxidative stress, glycosylation damage, and amino acids metabolism. Our findings might help to better understanding of the mechanism of DN, and provide novel targets for estimating the effects of GSPE therapy.     

Comprehensive tracking of host cell proteins during monoclonal antibody purifications using mass spectrometry

An advanced two-dimensional liquid chromatography/mass spectrometry platform was used to quantify individual host cell proteins (HCPs) present at various purification steps for several therapeutic monoclonal antibodies (mAbs) produced in Chinese hamster ovary cells. The methodology produced reproducible identifications and quantifications among replicate analyses consistent with a previously documented individual limit of quantification of ~13 ppm. We were able to track individual HCPs from cell culture fluid to protein A eluate pool to subsequent viral inactivation pool and, in some cases, further downstream. Approximately 500 HCPs were confidently identified in cell culture fluid and this number declined progressively through the purification scheme until no HCPs could be confidently identified in polishing step cation-exchange eluate pools. The protein A eluate pool of nine different mAbs contained widely differing numbers, and total levels, of HCPs, yet the bulk of the total HCP content in each case consisted of a small subset of normally intracellular HCPs highly abundant in cell culture fluid. These observations hint that minimizing cell lysis during cell culture/harvest may be useful in minimizing downstream HCP content. Clusterin and actin are abundant in the protein A eluate pools of most mAbs studied. HCP profiling by this methodology can provide useful information to process developers and lead to the refinement of existing purification platforms.     

Comprehensive tracking of host cell proteins during monoclonal antibody purifications using mass spectrometry

An advanced two-dimensional liquid chromatography/mass spectrometry platform was used to quantify individual host cell proteins (HCPs) present at various purification steps for several therapeutic monoclonal antibodies (mAbs) produced in Chinese hamster ovary cells. The methodology produced reproducible identifications and quantifications among replicate analyses consistent with a previously documented individual limit of quantification of ~13 ppm. We were able to track individual HCPs from cell culture fluid to protein A eluate pool to subsequent viral inactivation pool and, in some cases, further downstream. Approximately 500 HCPs were confidently identified in cell culture fluid and this number declined progressively through the purification scheme until no HCPs could be confidently identified in polishing step cation-exchange eluate pools. The protein A eluate pool of nine different mAbs contained widely differing numbers, and total levels, of HCPs, yet the bulk of the total HCP content in each case consisted of a small subset of normally intracellular HCPs highly abundant in cell culture fluid. These observations hint that minimizing cell lysis during cell culture/harvest may be useful in minimizing downstream HCP content. Clusterin and actin are abundant in the protein A eluate pools of most mAbs studied. HCP profiling by this methodology can provide useful information to process developers and lead to the refinement of existing purification platforms.     

An in-gel digestion procedure that facilitates the identification of highly hydrophobic proteins by electrospray ionization-mass spectrometry analysis

A procedure is described for in-gel tryptic digestion of proteins that allows the direct analysis of eluted peptides in electrospray ionization (ESI) mass spectrometers without the need of a postdigestion desalting step. It is based on the following principles: (a) a thorough desalting of the protein in-gel before digestion that takes advantage of the excellent properties of acrylamide polymers for size exclusion separations, (b) exploiting the activity of trypsin in water, in the absence of inorganic buffers, and (c) a procedure for peptide extraction using solvents of proven efficacy with highly hydrophobic peptides. Quality of spectra and sequence coverage are equivalent to those obtained after digestion in ammonium bicarbonate for hydrophilic proteins detected with Coomassie blue, mass spectrometry-compatible silver or imidazole-zinc but are significantly superior for highly hydrophobic proteins, such as membrane proteins with several transmembrane domains. ATPase subunit 9 (GRAVY 1.446) is a membrane protein channel, lipid-binding protein for which both the conventional in-gel digestion protocol and in solution digestion failed. It was identified with very high sequence coverage. Sample handling after digestion is notably simplified as peptides are directly loaded into the ESI source without postdigestion processing, increasing the chances for the identification of hydrophobic peptides.     

Mass spectrometry methods in metabolomics

The review deals with metabolomics, a new and rapidly growing area directed to the comprehensive analysis of metabolites of biological objects. Metabolites are characterized by various physical and chemical properties, traditionally studied by methods of analytical chemistry focused on certain groups of chemical substances. However, current progress in mass spectrometry has led to formation of rather unified methods, such as metabolic fingerprinting and metabolomic profiling, which allow defining thousands of metabolites in one biological sample and therefore draw “a modern portrait of metabolomics.” This review describes basic characteristics of these methods, ways of metabolite separation, and analysis of metabolites by mass spectrometry. The examples shown in this review, allow to estimate these methods and to compare their advantages and disadvantages. Besides that, we consider the methods, which are of the most frequent use in metabolomics; these include the methods for data processing and the required resources, such as software for mass spectra processing and metabolite search database. In the conclusion, general suggestions for successful metabolomic experiments are given.     

基于温度-伤害度关系分析酿酒葡萄根系及芽抗寒性

采用差热分析系统(DTA)对8个主栽酿酒葡萄品种的芽和根系进行低温放热分析(LTE),建立各品种芽、根系韧皮部及木质部的温度-伤害度(LT-I)回归方程,评估不同品种的根系及芽抗寒性.结果表明： 8个品种的根系韧皮部伤害度50%的温度从高到低为马瑟兰>品丽珠>赤霞珠>小芒森>霞多丽>蛇龙珠>贵人香>熊岳白;不同品种木质部伤害度50%的温度从高到低为马瑟兰>霞多丽>赤霞珠>小芒森>品丽珠>蛇龙珠>贵人香>熊岳白;芽伤害度50%的温度从高到低为赤霞珠>小芒森>蛇龙珠>品丽珠>霞多丽>贵人香>马瑟兰>熊岳白.利用模糊隶属函数值法综合评价根系及芽的抗寒性,马瑟兰根系的抗寒性最差,熊岳白根系的抗寒性最好;赤霞珠、品丽珠、小芒森和蛇龙珠芽的抗寒性最差,贵人香和熊岳白芽的抗寒性最好.