Proteins Identified from Saliva and Salivary Glands of the Chinese Gall Aphid Schlechtendalia chinensis

Aphid saliva plays an essential role in the interaction between aphids and their host plants. Several aphid salivary proteins have been identified but none from galling aphids. Here the salivary proteins from the Chinese gall aphid are analyzed, Schlechtendalia chinensis, via an LC‐MS/MS analysis. A total of 31 proteins are identified directly from saliva collected via an artificial diet, and 141 proteins are identified from extracts derived from dissected salivary glands. Among these identified proteins, 17 are found in both collected saliva and dissected salivary glands. In comparison with salivary proteins from ten other free‐living Hemipterans, the most striking feature of the salivary protein from S. chinensis is the existence of high proportion of proteins with binding activity, including DNA‐, protein‐, ATP‐, and iron‐binding proteins. These proteins maybe involved in gall formation. These results provide a framework for future research to elucidate the molecular basis for gall induction by galling aphids.     

Characterization of the Proteome of Theobroma cacao Beans by Nano‐UHPLC‐ESI MS/MS

Cocoa seed storage proteins play an important role in flavour development as aroma precursors are formed from their degradation during fermentation. Major proteins in the beans of Theobroma cacao are the storage proteins belonging to the vicilin and albumin classes. Although both these classes of proteins have been extensively characterized, there is still limited information on the expression and abundance of other proteins present in cocoa beans. This work is the first attempt to characterize the whole cocoa bean proteome by nano‐UHPLC‐ESI MS/MS analysis using tryptic digests of cocoa bean protein extracts. The results of this analysis show that >1000 proteins could be identified using a species‐specific Theobroma cacao database. The majority of the identified proteins were involved with metabolism and energy. Additionally, a significant number of the identified proteins were linked to protein synthesis and processing. Several proteins were also involved with plant response to stress conditions and defence. Albumin and vicilin storage proteins showed the highest intensity values among all detected proteins, although only seven entries were identified as storage proteins. A comparison of MS/MS data searches carried out against larger non‐specific databases confirmed that using a species‐specific database can increase the number of identified proteins, and at the same time reduce the number of false positives. The results of this work will be useful in developing tools that can allow the comparison of the proteomic profile of cocoa beans from different genotypes and geographic origins. Data are available via ProteomeXchange with identifier PXD005586.     

Advanced Glycation End Products Increase Salivary Gland Hypofunction in d-Galactose-Induced Aging Rats and Its Prevention by Physical Exercise

A declined salivary gland function is commonly observed in elderly people. Advanced glycation end products (AGEs) are believed to contribute to the pathogenesis of aging. Although physical exercise is shown to increase various organ functions in human and experimental models, it is not known whether it has a similar effect in the salivary glands. In the present study, we evaluated the AGEs burden in the salivary gland in the aging process and the protective effect of physical exercise on age-related salivary hypofunction. To accelerate the aging process, rats were peritoneally injected with D-galactose for 6 weeks. Young control rats and d-galactose-induced aging rats in the old group were not exercised. The rats in the physical exercise group ran on a treadmill (12 m/min, 60 min/day, 3 days/week for 6 weeks). The results showed that the salivary flow rate and total protein levels in the saliva of the d-galactose-induced aging rats were reduced compared to those of the young control rats. Circulating AGEs in serum and secreted AGEs in saliva increased with d-galactose-induced aging. AGEs also accumulated in the salivary glands of these aging rats. The salivary gland of aging rats showed increased reactive oxygen species (ROS) generation, loss of acinar cells, and apoptosis compared to young control mice. However, physical exercise suppressed all of these age-related salivary changes. Overall, physical exercise could provide a beneficial option for age-related salivary hypofunction.     

First identification of tannin-binding proteins in saliva of Papio hamadryas using MS/MS mass spectrometry

Hamadryas baboons possess salivary proline-rich proteins (PRP), as indicated by the presence of pink-staining protein bands using 1D SDS gel electrophoresis and Coomassie R250 staining. The ability of these protein bands to interact with tannic acid was further examined. In a tannin-binding assay using 5 μg tannic acid mixed with hamadryas whole saliva, we recently found four distinct protein bands of apparently 72, 55, 20, and 15 kDa that were precipitated during the experiments. In this work, we were able to identify these protein bands in a follow-up analysis using MS/MS mass spectrometry after excising such bands out of air-dried gels. Albumin and α-amylase were present in the tannic acid-protein complexes, with albumin already known to nonspecifically interact with a great diversity of chemical compounds. More interesting, we also identified a basic PRP and a cystatin precursor protein. This was the first successful attempt to identify a PRP from precipitated tannin-protein complexes in hamadryas baboons using MS/MS mass spectrometry. On the other hand, the role of cystatins in tannin binding is not yet well understood. However, there are recent reports on cystatin expression in saliva of rats responding to astringent dietary compounds. In conclusion, the follow-up data on tannin-binding proteins present in salivary secretions from hamadryas baboons adds important knowledge to primate physiology and feeding ecology, in order to shed light on the establishment and development of food adaptations in primates. It also demonstrates that tannin binding is characteristic for PRP, but might not be restricted to this particular group of proteins in primate species.     

温和过甲酸氧化辅助酶解结合液质联用技术鉴定大鼠大脑皮层质膜蛋白质

由于膜蛋白质尤其是内在膜蛋白的强疏水性,分析和鉴定质膜蛋白质仍然是以质谱为基础的蛋白质组学的方法中的一个难点.过甲酸氧化是一种应用广泛的打开二硫键的方法,温和的过甲酸试剂能完全的将半胱氨酸转化为半胱磺酸,将甲硫氨酸转化为甲硫氨酸砜,从而使目的蛋白更易溶于水介质.采用蔗糖密度梯度离心法纯化得到大鼠大脑皮层质膜,提取的质膜蛋白质经温和过甲酸氧化处理后经胰酶酶解消化得到肽段,利用LC-MS/MS对所得肽段进行质谱分析,采集的原始数据用Mascot软件进行库搜寻鉴定.此方法是研究质膜蛋白质的新方法,温和过甲酸氧化显示出很好的氧化效果却避免其它不利于鉴定的副反应.从大鼠大脑皮层膜提取物共鉴定出220种蛋白质,其中73种为整合膜蛋白,证明对质膜蛋白质直接进行温和过甲酸氧化然后酶解的方法辅助酶解可以有效的鉴定质膜蛋白质.     

Toward the complete characterization of host cell proteins in biotherapeutics via affinity depletions,LC-MS/MS,and multivariate analysis

Host cell protein (HCP) impurities are generated by the host organism during the production of therapeutic recombinant proteins, and are difficult to remove completely. Though commonly present in small quantities, if levels are not controlled, HCPs can potentially reduce drug efficacy and cause adverse patient reactions. A high resolution approach for thorough HCP characterization of therapeutic monoclonal antibodies is presented herein. In this method, antibody samples are first depleted via affinity enrichment (e.g., Protein A, Protein L) using milligram quantities of material. The HCP-containing flow-through is then enzymatically digested, analyzed using nano-UPLC-MS/MS, and proteins are identified through database searching. Nearly 700 HCPs were identified from samples with very low total HCP levels (< 1 ppm to ∼10 ppm) using this method. Quantitation of individual HCPs was performed using normalized spectral counting as the number of peptide spectrum matches (PSMs) per protein is proportional to protein abundance. Multivariate analysis tools were utilized to assess similarities between HCP profiles by: 1) quantifying overlaps between HCP identities; and 2) comparing correlations between individual protein abundances as calculated by spectral counts. Clustering analysis using these measures of dissimilarity between HCP profiles enabled high resolution differentiation of commercial grade monoclonal antibody samples generated from different cell lines, cell culture, and purification processes.     

Toward the complete characterization of host cell proteins in biotherapeutics via affinity depletions,LC-MS/MS,and multivariate analysis

Host cell protein (HCP) impurities are generated by the host organism during the production of therapeutic recombinant proteins, and are difficult to remove completely. Though commonly present in small quantities, if levels are not controlled, HCPs can potentially reduce drug efficacy and cause adverse patient reactions. A high resolution approach for thorough HCP characterization of therapeutic monoclonal antibodies is presented herein. In this method, antibody samples are first depleted via affinity enrichment (e.g., Protein A, Protein L) using milligram quantities of material. The HCP-containing flow-through is then enzymatically digested, analyzed using nano-UPLC-MS/MS, and proteins are identified through database searching. Nearly 700 HCPs were identified from samples with very low total HCP levels (< 1 ppm to ～10 ppm) using this method. Quantitation of individual HCPs was performed using normalized spectral counting as the number of peptide spectrum matches (PSMs) per protein is proportional to protein abundance. Multivariate analysis tools were utilized to assess similarities between HCP profiles by: 1) quantifying overlaps between HCP identities; and 2) comparing correlations between individual protein abundances as calculated by spectral counts. Clustering analysis using these measures of dissimilarity between HCP profiles enabled high resolution differentiation of commercial grade monoclonal antibody samples generated from different cell lines, cell culture, and purification processes.     

Targeted label‐free quantification of interleukin‐8 in PMA‐activated U937 cell secretome by nanoLC‐ESI‐MS/MS‐sSRM

Monocytes are a part of the innate immune system. Their differentiation into macrophages changes their cellular proteome and secretome. Particularly secretome components such as cytokines are crucial for immune response and inflammation in many diseases. Differentiation of human lymphoma cell line U937 can be triggered by phorbol 12‐myristate 13‐acetate (PMA). Screening of the cytokine release in U937 upon PMA stimulation by cytometric bead array almost exclusively showed interleukin‐8 (IL‐8). Next, a label‐free nanoLC‐ESI‐MS/MS‐sSRM method for quantification of IL‐8 in the cell secretome was established and applied to monitor the time kinetics of PMA treatment in different concentrations. Targeted secretome analysis was achieved by scheduled SRM‐MS using one proteotypic peptide as precursor ion and four mass transitions. Label‐free quantification was performed by external calibration using IL‐8 standard. Validation results indicated that the method was suited for the quantification of IL‐8 in the secretome. The maximal IL‐8 release of 62.4 ng/mL was observed after incubating cells treated by 50 ng/mL PMA for 48 h. The method can now be used for quantification of IL‐8 release from different cells under various conditions. Furthermore, it can be easily expanded to other secreted proteins detected by untargeted screening methods.     

蛋白质组学方法分析多T迷宫训练后的小鼠空间记忆蛋白

应用双向凝胶电泳结合质谱鉴定和数据库检索,分析比较C57BL/6J小鼠在多T迷宫(MTM)训练和记忆测试组与未训练组海马蛋白表达的差异,探讨与MTM空间记忆相关的蛋白质.C57BL/6J小鼠经MTM训练后,可对相应的空间线索保持记忆能力,其海马蛋白质表达存在明显差异,14个蛋白质与MTM空间记忆形成显著相关.其中,6个蛋白点表达显著上调,8个蛋白点表达水平显著降低.这些蛋白按功能可分为6类: 细胞骨架相关蛋白,物质运输相关蛋白,蛋白合成相关蛋白,能量和物质代谢相关蛋白,信号转导相关蛋白,通道蛋白. 这些空间记忆形成相关蛋白的研究深化了对空间记忆机制的认识,为研究和治疗认知相关疾病提供了新靶标.     

Absolute quantification of DcR3 and GDF15 from human serum by LC‐ESI MS

Biomarkers are widely used in clinical diagnosis, prognosis and therapy monitoring. Here, we developed a protocol for the efficient and selective enrichment of small and low concentrated biomarkers from human serum, involving a 95% effective depletion of high‐abundant serum proteins by partial denaturation and enrichment of low‐abundant biomarkers by size exclusion chromatography. The recovery of low‐abundance biomarkers was above 97%. Using this protocol, we quantified the tumour markers DcR3 and growth/differentiation factor (GDF)15 from 100 μl human serum by isotope dilution mass spectrometry, using ¹⁵N metabolically labelled and concatamerized fingerprint peptides for the both proteins. Analysis of three different fingerprint peptides for each protein by liquid chromatography electrospray ionization mass spectrometry resulted in comparable concentrations in three healthy human serum samples (DcR3: 27.23 ± 2.49 fmol/ml; GDF15: 98.11 ± 0.49 fmol/ml). In contrast, serum levels were significantly elevated in tumour patients for DcR3 (116.94 ± 57.37 fmol/ml) and GDF15 (164.44 ± 79.31 fmol/ml). Obtained data were in good agreement with ELISA and qPCR measurements, as well as with literature data. In summary, our protocol allows the reliable quantification of biomarkers, shows a higher resolution at low biomarker concentrations than antibody‐based strategies, and offers the possibility of multiplexing. Our proof‐of‐principle studies in patient sera encourage the future analysis of the prognostic value of DcR3 and GDF15 for colon cancer patients in larger patient cohorts.     

Study of rat hypothalamic proteome by HPLC/ESI ion trap and HPLC/ESI‐Q‐TOF MS

The proteomic profile of hypothalamus, a key organ of CNS, is explored here by employing two widely used MS techniques, i.e. HPLC/ESI‐ion trap and HPLC/ESI‐quadrupole‐TOF MS. Strong cation exchange is used for the fractionation of peptides and protein search engine MASCOT is employed for data query. One hundred and thirty six proteins with 10 973 peptides were identified by HPLC/ESI‐ion trap MS, while 140 proteins with 32 183 peptides were characterized by HPLC/ESI‐quadrupole‐TOF MS. Among the total 198 proteins identified in both experiments, 78 proteins were common in both sets of conditions. The rest of the 120 proteins were identified distinctly in both MS strategies, i.e. 58 unique proteins were found using the quadrupole‐TOF while 62 were found with the HPLC/ESI‐ion trap. Moreover, these proteins were classified into groups based on their functions performed in the body. Results presented here identified some important signal and cellular defense proteins inevitable for survival in stressed conditions. Additionally, it is also shown that any single MS strategy is not reliable for good results due to loss of data depending on sensitivity of the instrument used.     

A novel LC‐MS/MS method to quantify eumelanin and pheomelanin and their relation to UVR sensitivity – A study on human skin biopsies

Melanin in the skin can be divided into eumelanin and pheomelanin subtypes. Simultaneous quantification of these subtypes could clarify their relation to skin type and skin cancer development. We describe a novel, sensitive liquid chromatography–tandem mass spectrometry method to quantify two eumelanin markers, pyrrole‐2,3,5‐tricarboxylic acid (PTCA) and pyrrole‐2,3‐dicarboxylic acid (PDCA), and two pheomelanin markers, thiazole‐4,5‐dicarboxylic acid (TDCA) and thiazole‐2,4,5 tricarboxylic acid (TTCA), performed in a single run using the same biopsy. Volunteers with either Fitzpatrick skin type (FST) I/II or III/IV (n = 30) each provided a 4‐mm punch biopsy from the buttock. Upon analysis, the FST I + II group had significantly less of all four melanin biomarkers (PTCA, 0.75 ng/mm²; PDCA, 0.08 ng/mm²; TTCA, 0.24 ng/mm²; and TDCA, 0.10 ng/mm²) versus the FST III + IV group (PTCA, 4.89 ng/mm²; PDCA, 0.22 ng/mm²; TTCA, 2.61 ng/mm²; and TDCA, 0.72 ng/mm²), p ≤ 0.003. We find that this new LC‐MS/MS method is sensitive enough to quantify eumelanin and pheomelanin markers even in the lightest skin types.     

Large-scale identification of proteins in human salivary proteome by liquid chromatography/mass spectrometry and two-dimensional gel electrophoresis-mass spectrometry

Human saliva contains a large number of proteins and peptides (salivary proteome) that help maintain homeostasis in the oral cavity. Global analysis of human salivary proteome is important for understanding oral health and disease pathogenesis. In this study, large-scale identification of salivary proteins was demonstrated by using shotgun proteomics and two-dimensinal gel electrophoresis-mass spectrometry (2-DE-MS). For the shotgun approach, whole saliva proteins were prefractionated according to molecular weight. The smallest fraction, presumably containing salivary peptides, was directly separated by capillary liquid chromatography (LC). However, the large protein fractions were digested into peptides for subsequent LC separation. Separated peptides were analyzed by on-line electrospray tandem mass spectrometry (MS/MS) using a quadrupole-time of flight mass spectrometer, and the obtained spectra were automatically processed to search human protein sequence database for protein identification. Additionally, 2-DE was used to map out the proteins in whole saliva. Protein spots 105 in number were excised and in-gel digested; and the resulting peptide fragments were measured by matrix-assisted laser desorption/ionization-mass spectrometry and sequenced by LC-MS/MS for protein identification. In total, we cataloged 309 proteins from human whole saliva by using these two proteomic approaches.     

Enantioselective Separation and Simultaneous Determination of Tolperisone and Eperisone in Rat Plasma by LC‐MS/MS

Tolperisone and eperisone used as muscle relaxants possess one chiral center each and exist as two optical isomers for each drug. Therefore, enantioselective assays to measure each enantiomer in biological matrices are of great importance. In the present study a simple and complete reverse‐phase liquid chromatography tandem mass spectrometric method for separation and enantioselective determination of tolperisone and eperisone in rat plasma was developed. The analytes were extracted from rat plasma by a simple protein precipitation method with acetonitrile as the extraction solvent. The enantioselective separation of analytes was achieved on a Cellulose Tris (4‐chloro‐3‐methylphenylcarbamate) chiral column with a mobile phase of acetonitrile: 10 mM ammonium acetate in an isocratic mode of elution and mass spectrometric detection. The calibration curve for each enantiomer was found to be linear over 0.2 to 20 ng/mL for each enantiomer. The proposed method exhibited good intra‐ and interday precision (% CV) ranged between 0.95–6.05% and 1.11–8.21%, respectively. The intra‐ and interday accuracy for the proposed assay method ranged between 94.0–100.5% and 92.7–102.1%, respectively. The proposed method was validated as per regulatory guidelines. Chirality 25:622–627, 2013. © 2013 Wiley Periodicals, Inc.     

Performance of five different electrospray ionisation sources in conjunction with rapid monolithic column liquid chromatography and fast MS/MS scanning

The performances of five different ESI sources coupled to a polystyrene–divinylbenzene monolithic column were compared in a series of LC‐ESI‐MS/MS analyses of Escherichia coli outer membrane proteins. The sources selected for comparison included two different modifications of the standard electrospray source, a commercial low‐flow sprayer, a stainless steel nanospray needle and a coated glass Picotip. Respective performances were judged on sensitivity and the number and reproducibility of significant protein identifications obtained through the analysis of multiple identical samples. Data quality varied between that of a ground silica capillary, with 160 total protein identifications, the lowest number of high quality peptide hits obtained (3012), and generally peaks of lower intensity; and a stainless steel nanospray needle, which resulted in increased precursor ion abundance, the highest‐quality peptide fragmentation spectra (5414) and greatest number of total protein identifications (259) exhibiting the highest MASCOT scores (average increase in score of 27.5% per identified protein). The data presented show that, despite increased variability in comparative ion intensity, the stainless steel nanospray needle provides the highest overall sensitivity. However, the resulting data were less reproducible in terms of proteins identified in complex mixtures – arguably due to an increased number of high intensity precursor ion candidates.     

家蚕雌性附腺及其Ng突变体的蛋白质组差异研究(英)

家蚕雌蛾性附腺在化蛾前2到3天开始大量分泌胶状粘性蛋白,其贮存部迅速地膨大,而其Ng突变体的雌蛾性附腺不能正常分泌胶状粘性物质.分别对家蚕（Bombyx mori）的正常及Ng突变体雌蛾性附腺分泌部组织的蛋白质进行提取,并采用双向凝胶电泳和计算机辅助分析方法,对提取的蛋白质混合物进行分离和比较分析,并对主要差异表达的蛋白质用质谱鉴定.实验结果表明,用银染法,平均每张电泳图谱可以分离约700个蛋白质点,其中大部分的蛋白质点分布在pH 4～8 范围内,其分子质量主要集中在30～70 ku区域.比较分析发现一些差异表达蛋白,其中No2, 3蛋白质点经质谱鉴定为肌动蛋白A3,该蛋白质只在化蛹后期正常雌性附腺组织中特异表达,而Ng突变体中肌动蛋白A3的缺失,暗示了肌动蛋白A3可能与家蚕雌性附腺的胶状粘性物质的胞外分泌有关.     

Identification of common and differential mechanisms of glomerulus and tubule senescence in 24‐month‐old rats by quantitative LC–MS/MS

Kidney aging together with related renal disease had become a major clinical problem. Understanding the mechanisms of aging was important for suspending senescence and decreasing the incidence of aging‐related diseases. In the present work, 24‐month‐old F344 rats were used as aging rats and 3‐month‐old rats were used as young controls. Senescence‐associated‐β‐galactosidase staining results showed that the degree of senescence in renal tubules was more severe than that in glomeruli. We performed quantitative LC–MS to assess the differential protein expression profiles of senescent glomeruli and tubules. Bioinformatics analysis showed that aging, response to oxidative stress, nucleotide metabolism, amine acid metabolism, and inflammatory response were common mechanisms of glomerulus and tubule senescence. Differentially expressed proteins network mediated Golgi vesicle transport, actin filament based process, and regulation of cell death were associated with tubule senescence. More importantly, we found that the changes of four and a half LIM protein 2 (FHL2) were opposite in senescent glomeruli and tubules, and FHL2 could regulate p16 by suppressing T‐box 3, which was involved in regulation of senescence in glomeruli and tubules. In conclusion, we assessed the mechanisms of senescence in aging glomeruli and tubules, and the results yielded new insight into kidney senescence.