基于超高效液相色谱质谱的药物性肝损害患者血清代谢组学研究

目的 应用代谢组学结合多变量统计学方法研究药物性肝损害患者血清当中的小分子代谢物质,寻找可用于药物性肝损害早期诊断的潜在生物标志物.方法 选择药物性肝损害患者26例和正常对照23例,应用非靶向的线性梯度超高效液相色谱质谱系统检测血清中的小分子代谢物质.结果 药物性肝损害组和对照组相比,血清中溶血卵磷脂C16∶0、溶血卵磷脂C18∶0、溶血卵磷脂C18∶3、溶血卵磷脂C18∶2的浓度明显降低,硬脂酰胺、油酰胺、十四酰胺、卵磷脂、甘氨鹅去氧胆酸、甘氨胆酸、胆红素、次黄嘌呤显著升高.结论 药物性肝损害患者代谢发生了显著的变化,根据代谢物质的变化有助于临床诊断,研究表明代谢组学是临床研究的一个强有力工具.     

基于液相色谱-质谱技术的早期胃癌血清多肽组学研究

目的:建立早期胃癌外周血清特征性多肽谱,分析其生物学特征,以探索一种特异且敏感的早期胃癌血清学诊断方法。方法:采集10例早期胃癌和10例正常对照血清,使用蛋白沉淀法去除高丰度血清蛋白质后,通过液相色谱-质谱联用技术重复三次进行多肽分离、离子化、质谱检测,将原始数据应用Label free方法中Max Quant算法对肽段进行相对定量,分析两组差异多肽及差异多肽匹配蛋白。结果:EGC组和N组重复三次所得色谱图总体比较一致,多肽重复检出率分别为87.54%和85.67%。其中EGC组可重复检测到的Unique peptide有65条,匹配对应31个蛋白;在EGC组和N组血清中显著差异的Unique peptide有22条,匹配对应11个蛋白。对血清显著差异多肽所匹配蛋白进行生物学分析,发现这些蛋白质多数位于细胞外,功能类别主要涉及分子水平的序列变换、信号肽、N-糖基化位点等,信号通路主要富集在凝血级联通路和补体级联通路。结论:早期胃癌血清特异性多肽谱图的建立可望成为胃癌早期诊断的血清学标志物,后续试验将进一步针对这些差异多肽进一步分析验证,筛选出早期胃癌标志性多肽,同时应用大样本进行验证,筛选出特异高效的早期胃癌血清标志物。     

一种新的基于STR的染色体三体性疾病诊断策略中遗传标记的评估

背景:在此前发表的文章中,我们提出了一种新的基于短串联重复序列(Short Tandem Repeats,STR)的染色体三体性疾病的诊断策略.当应用这种策略来检测特定染色体拷贝数时,需要从人类基因组众多的STR中选择适宜的染色体特异性STR基因座构建一个诊断系统,根据系统中的STR基因座是否检测到三种不同的等位基因产物来判断个体是否为三体患者.目的:本研究拟进一步提出并验证对单个STR基因座及由多个STR基因座构成的诊断系统的评估方法,旨在帮助选择适宜的STR基因座构建一个高效能的诊断系统.方法:我们提出一个新的参数--三等位基因栓出率,并推导出该参数的计算公式,用于定量评估一个STR基因座在这种诊断策略中的效能.在此基础上,推导出另一个数学公式,计算一个非整倍体诊断系统能够在一个三体性患者?哌 检测到三个不同等位基因的概率,根据这个概率的大小来衡量系统诊断效能的高低.最后,我们将所提出的两个公式用于评估我们在先前研究中构建的一个21三体的诊断系统.结果:这个21三体诊断系统由9个21号染色体特异性STR基因座构成.根据我们所提出的两个公式,这些STR基因座的三等位基因检出率在0.203-0.638之间,该系统在21三体患者能够检测到三个不同等位基因的概率大于0.95.结论:我们所提出并验证的公式可以对单个STR基因座和系统的诊断效能进行定量评估,帮助选择适宜的STR遗传标记,并确定一个高效能诊断系统所需的STR基因座的数量,从而为这种诊断策略的广泛应用提供基础.     

Proteomic analysis of the tetraspanin web using LC-ESI-MS/MS and MALDI-FTICR-MS

Tetraspanins are integral membrane proteins involved in a variety of physiological and pathological processes. In cancer, clinical and experimental studies have reported a link between tetraspanin expression levels and metastasis. Tetraspanins play a role as organizers of a molecular network of interactions, the "tetraspanin web". Here, we have performed a proteomic characterization of the tetraspanin web using a model of human colon cancer consisting of two cell lines derived from primary tumor and metastasis from the same patient. The tetraspanin complexes were isolated after immunoaffinity purification and the proteins were identified by MS using LC-ESI-MS/MS and MALDI-FTICR. The high resolution and mass accuracy of FTICR MS allowed reliable identification using mass finger printing with only two peptides. Thus, it could be used to resolve the composition of complex peptide mixtures from membrane proteins. Different types of membrane proteins were identified, including adhesion molecules (integrins, Lu/B-CAM, GA733 proteins), receptors and signaling molecules (BAI2, PKC, G proteins), proteases (ADAM10, TADG15), and membrane fusion proteins (syntaxins) as well as poorly characterized proteins (CDCP1, HEM-1, CTL1, and CTL2). Some components were differentially detected in the tetraspanin web of the two cell lines. These differences may be relevant for tumor progression and metastasis.     

LC-ESI-MS/MS Chemical Characterization,Antioxidant and Antidiabetic Properties of Propolis Extracted with Organic Solvents from Eastern Anatolia Region

Geographic conditions (altitude, climate, and local flora) lead to significant differences in the chemical composition of propolis. Therefore, more research is needed for propolis in different geographical regions. So, the aim of this study was to evaluate the phenolic profile, total phenolic content, antioxidant, and antidiabetic properties of Pülümür propolis from Turkey. Methanol (MeOH), chloroform (CHCl₃), and hexane extracts of propolis were analyzed. LC-ESI-MS/MS analysis of the extracts showed that the most abundant phenolic compound is caffeic acid in the MeOH extract (2943.12±11.12 μg phenolics/g extract), while on the other hand, CHCl₃ extract had the highest total phenolic content (125.75±1.02 mg GAE/g extract). Antioxidant activity was measured using ABTS and DPPH assays, whereas CHCl₃ extract (IC₅₀=6.35±0.11 and 28.84±0.10 μg/mL, respectively) and MeOH extracts (IC₅₀=5.04±0.07 and 28.80±0.09 μg/mL, respectively) showed relatively high antioxidant activity. The MeOH extract showed better antidiabetic activity than the standard compound, acarbose (IC₅₀=0.544 and 0.805 mg/mL, respectively).     

Screening and identification of the levoglucosan kinase gene (lgk) from Aspergillus niger by LC-ESI-MS/MS and RT-PCR

A protein of 75,000 Daltons with levoglucosan kinase activity was purified from Aspergillus niger. After in-gel digestion by trypsin, a 14-mer peptide was sequenced and analyzed by LC-ESI-MS/MS. Using a primer derived from the 14-mer peptide in combination with Oligo-(dT)18, a cDNA fragment was obtained by RT-PCR. A search of the GenBank database indicated that the protein had not been identified before. A similar protein named hypothetical protein FG07802.1 (EAA77996.1) was found to exist in Gibberella zeae by Blastx search. Using a primer derived from the protein, a cDNA fragment of second RT-PCR was cloned into plasmid pAJ401, which was transformed to Saccharomyces cerevisiae H158 and expressed. Two positive levoglucosan assimilating recombinants were selected. The lgk gene was screened and identified.     

Identification of lignans and related compounds in Anthriscus sylvestris by LC-ESI-MS/MS and LC-SPE-NMR

The aryltetralin lignan deoxypodophyllotoxin is much more widespread in the plant kingdom than podophyllotoxin. The latter serves as a starting compound for the production of cytostatic drugs like etoposide. A better insight into the occurrence of deoxypodophyllotoxin combined with detailed knowledge of its biosynthestic pathway(s) may help to develop alternative sources for podophyllotoxin. Using HPLC combined with electrospray tandem mass spectrometry and NMR spectroscopy techniques, we found nine lignans and five related structures in roots of Anthriscus sylvestris (L.) Hoffm. (Apiaceae), a common wild plant in temperate regions of the world. Podophyllotoxone, deoxypodophyllotoxin, yatein, anhydropodorhizol, 1-(3′-methoxy-4′,5′-methylenedioxyphenyl)1-ξ-methoxy-2-propene, and 2-butenoic acid, 2-methyl-4-[[(2Z)-2-methyl-1-oxo-2-buten-1-yl]oxy]-, (2E)-3-(7-methoxy-1,3-benzodioxol-5-yl)-2-propen-1-yl ester, (2Z)- were the major compounds. α-Peltatin, podophyllotoxin, β-peltatin, isopicropodophyllone, β-peltatin-a-methylether, (Z)-2-angeloyloxymethyl-2-butenoic acid, anthriscinol methylether, and anthriscrusin were present in lower concentrations. α-Peltatin, β-peltatin, isopicropodophyllone, podophyllotoxone, and β-peltatin-a-methylether have not been previously reported to be present in A. sylvestris. Based on our findings we propose a hypothetical biosynthetic pathway of aryltetralin lignans in A. sylvestris.     

Identification of Leishmania-specific protein phosphorylation sites by LC-ESI-MS/MS and comparative genomics analyses

Human pathogenic protozoa of the genus Leishmania undergo various developmental transitions during the infectious cycle that are triggered by changes in the host environment. How these parasites sense, transduce, and respond to these signals is only poorly understood. Here we used phosphoproteomic approaches to monitor signaling events in L. donovani axenic amastigotes, which may be important for intracellular parasite survival. LC-ESI-MS/MS analysis of IMAC-enriched phosphoprotein extracts identified 445 putative phosphoproteins in two independent biological experiments. Functional enrichment analysis allowed us to gain insight into parasite pathways that are regulated by protein phosphorylation and revealed significant enrichment in our data set of proteins whose biological functions are associated with protein turn-over, stress response, and signal transduction. LC-ESI-MS/MS analysis of TiO(2)-enriched phosphopeptides confirmed these results and identified 157 unique phosphopeptides covering 181 unique phosphorylation sites in 126 distinct proteins. Investigation of phosphorylation site conservation across related trypanosomatids and higher eukaryotes by multiple sequence alignment and cluster analysis revealed L. donovani-specific phosphoresidues in highly conserved proteins that share significant sequence homology to orthologs of the human host. These unique phosphorylation sites reveal important differences between host and parasite biology and post-translational protein regulation, which may be exploited for the design of novel anti-parasitic interventions.     

Use of a Label-Free Quantitative Platform Based on MS/MS Average TIC to Calculate Dynamics of Protein Complexes in Insulin Signaling

A label-free quantification strategy including the development of in-house software (NakedQuant) to calculate the average TIC across all spectral counts in tandem affinity purification (TAP)-tagging liquid chromatography-mass spectrometry MS/MS (LC/MS/MS) experiments was applied to a large-scale study of protein complexes in the MAPK portion of the insulin signaling pathway from Drosophila cells. Dynamics were calculated under basal and stimulating conditions as fold changes. These experiments were performed in the context of a core service model with the user performing the TAP immunoprecipitation and the MS core performing the MS and informatics stops. The MS strategy showed excellent coverage of known components in addition to potentially novel interactions.     

Simultaneous quantitative LC-ESI-MS/MS analyses of salicylic acid and jasmonic acid in crude extracts of Cucumis sativus under biotic stress

Salicylic acid (SA) and jasmonic acid (JA) are plant hormones involved in basal resistance against plant pathogens and also in induced resistance. The aim of this study is to develop a fast and sensitive method to determine simultaneously the levels of both these hormones. The present paper proposes a method that includes hormone extraction with MeOH-H(2)O-HOAc (90:9:1, v/v), evaporation of the extracts, and injection into the liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) system in multiple reaction monitoring (MRM). Endogenous SA and JA levels in noninfested control cucumber cotyledons were 30.96 and 0.73ngg(-1) fresh weight, respectively. In roots, the levels were 8.31 and 15.82ngg(-1) FW, respectively. In plants treated with the biological control agent Trichoderma asperellum strain T-34, the levels of SA and JA did not differ from control plants. Rhizoctonia solani-diseased cucumber plants showed higher levels of SA and JA compared to noninfested controls (up to 2 and 13-fold higher, respectively). Detection limits for SA and JA were 0.45 and 0.47ngg(-1) fresh weight, respectively. The results of our research include the development of a method that is both fast and highly sensitive in the simultaneous quantitation of SA and JA from crude cucumber plant extracts, avoiding any purification and derivatization steps.     

Quantitative Detection of 15 Serum Bile Acid Metabolic Products by LC/MS/MS in the Diagnosis of Primary Biliary Cholangitis

To determine 15 bile acid metabolic products in human serum by liquid chromatography-tandem mass spectrometry (LC/MS/MS) and value their diagnostic outcome in primary biliary cholangitis (PBC). Serum from 20 healthy controls and 26 patients with PBC were collected and went LC/MS/MS analysis of 15 bile acid metabolic products. The test results were analyzed by bile acid metabolomics, and the potential biomarkers were screened and their diagnostic performance was judged by statistical methods such as principal component and partial least squares discriminant analysis and area under curve (AUC). 8 differential metabolites can be screened out: Deoxycholic acid (DCA), Glycine deoxycholic acid (GDCA), Lithocholic acid (LCA), Glycine ursodeoxycholic acid (GUDCA), Taurolithocholic acid (TLCA), Tauroursodeoxycholic acid (TUDCA), Taurodeoxycholic acid (TDCA), Glycine chenodeoxycholic acid (GCDCA). The performance of the biomarkers was evaluated by the AUC, specificity and sensitivity. In conclusion, DCA, GDCA, LCA, GUDCA, TLCA, TUDCA, TDCA and GCDCA were identified as eight potential biomarkers to distinguish between healthy people and PBC patients by multivariate statistical analysis, which provided reliable experimental basis for clinical practice.