Optimized 25-hydroxyvitamin D analysis using liquid–liquid extraction with 2D separation with LC/MS/MS detection, provides superior precision compared to conventional assays

The analysis of 25-hydroxyvitamin D3 (25(OH)D3) and related metabolites represents a considerable challenge for both clinical and research laboratories worldwide. There is currently debate about the best methodology employed to assess vitamin D status and whether the 3-epi-25-hydroxyvitamin D3 (3-epi-25(OH)D3) should be separated and quantitated when measuring 25(OH)D3. Mass spectrometry techniques are generally regarded as the gold standard due to high specificity for vitamin D metabolites. However, many methods require high sample volumes for analysis. We have developed a new 2 dimensional (2D) ultra performance liquid chromatography (UPLC) separation coupled tandem mass spectrometry (MS/MS) detection to accurately quantitate 25(OH)D3, epi-25(OH)D3, and 25(OH)D2 in adults and children, requiring only 50 μL of human serum. The assay gives excellent separation of epi-25(OH)D3, and 25(OH)D2 from 25(OH)D3, has excellent precision with an intra-assay CV of 0.5 % at 74 nmol/L and can report down to 2 nmol/L for 25(OH)D3. Furthermore, the method shows excellent agreement with the vitamin D external quality assessment scheme (DEQAS) quality control program for vitamin D analysis. We present this approach as a candidate reference method for 25(OH)D3, epi-25(OH)D3, and 25(OH)D2 analysis in humans.     

iTRAQ-coupled 2D LC–MS/MS analysis on differentially expressed proteins in denervated tibialis anterior muscle of Rattus norvegicus

To understand the molecular aspects of denervation-induced atrophy of skeletal muscles, isobaric tags for relative and absolute quantitation (iTRAQ) coupled with two-dimensional liquid chromatography-tandem mass spectrometry were performed to detect a total of 260 proteins that were differentially expressed in the rat tibialis anterior muscle at different times (1, 4, and 8 weeks) after rat sciatic nerve transection. Western blot, gene ontology, and Kyoto Encyclopedia of Genes and Genomes analyses were further conducted for protein validation, functional annotation, and pathway identification, respectively. Among 260 dysregulated proteins, metabolic enzymes represented the largest class of proteins differentially expressed; a down-regulation of β-enolase might be associated with a decreased expression of fast-twitch myosin-4; the 14-3-3 proteins displayed an up-regulation, which might facilitate the inhibition of mTOR signaling; an up-regulation of α-crystallin B chain might be related to the later onset and the slower progress of atrophy; an up-regulation of phosphatidylethanolamine-binding protein-1 perhaps progressively abrogated the cell survival and antiapoptotic properties during muscle atrophy. These results might contribute to the understanding of molecular mechanisms regulating denervation-induced muscle atrophy.     

iTRAQ-Coupled 2D LC–MS/MS Analysis of Secreted Proteome of HBV-Replicating HepG2 Cells: Potential in Biomarkers for Prognosis of HCC

Hepatitis B virus (HBV) infection remains a major health concern with more than 350 million carriers in the world. It is associated with acute and chronic liver diseases including hepatocellular carcinoma (HCC). The early detection of severe liver diseases related to HBV is crucial for the effective treatment. This work aims to investigate the secreted proteins in our recently established cell-based HBV replication system, using isobaric tags for relative and absolute quantitation (iTRAQ)-coupled 2D LC–MS/MS proteomics approach. Such proteins are reflective of early events of HBV infection and thus may have potential as prognostic biomarkers for development of liver diseases.     

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database – Xindice

Background  

Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC) is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database.     

HPLC-DAD和LC/MS/MS测定豆奶中三聚氰胺

目的：建立二极管阵列高效液相色谱仪和三重四级杆液质联用仪对豆奶中三聚氰胺的测定方法。方法：采用三氯乙酸和乙腈为提取剂、蛋白质为沉淀剂,提取液过净化柱纯化。结果：三重四级杆液质联用法对三聚氰胺的检出限为0-001 5 mg/kg,标准曲线在0-01~0-5 μg/mL范围内,R2为0-999 8,线性良好,再回收率为85 %~89 %,适用于检测低浓度的样品;二极管阵列高效液相色谱法检出限为0-024 mg/kg,标准曲线在0-5~100 μg/mL范围内,R2为0-999 9,线性良好,回收率为83 %~91 %,可以快速地对高浓度样品进行筛查。结论以上两种检测方法结合使用,可检测0-01~100 mg/kg的三聚氰胺含量,极大地拓宽了检测范围。     

GC–MS and GC–MS/MS measurement of the cardiovascular risk factor homoarginine in biological samples

l-Homoarginine (hArg) has recently emerged as a novel cardiovascular risk factor and to herald a poor prognosis in heart failure patients. Here, we report on the development and thorough validation of gas chromatography–mass spectrometry (GC–MS) and gas chromatography–tandem mass spectrometry (GC–MS/MS) methods for the quantitative determination of hArg in biological samples, including human plasma, urine and sputum. For plasma and serum samples, ultrafiltrate (10 µL; cutoff, 10 kDa) was used. For urine samples, native urine (10 µL) was used. For sputum, protein precipitation by acetone was performed. hArg is derivatized to its methyl ester tri(N-pentafluoropropionyl) derivative; de novo synthesized trideutero-methyl ester hArg is used as the internal standard (IS). Alternatively, [guanidino-¹⁵N₂]-arginine can be used as an IS. Quantitative analyses were performed after electron-capture negative-ion chemical ionization by selected-ion monitoring in GC–MS and selected-reaction monitoring in GC–MS/MS. We obtained very similar hArg concentrations by GC–MS and GC–MS/MS, suggesting that GC–MS suffices for accurate and precise quantification of hArg in biological samples. In plasma and serum samples of the same subjects very close hArg concentrations were measured. The plasma-to-serum hArg concentration ratio was determined to be 1.12 ± 0.21 (RSD, 19 %), suggesting that blood anticoagulation is not a major preanalytical concern in hArg analysis. In healthy subjects, the creatinine-corrected urinary excretion of hArg varies considerably (0.18 ± 0.22 µmol/mmol, mean ± SD, n = 19) unlike asymmetric dimethylarginine (ADMA, 2.89 ± 0.89 µmol/mmol). In urine, hArg correlated with ADMA (r = 0.475, P = 0.040); in average, subjects excreted in the urine about 17.5 times more ADMA than hArg. In plasma of healthy humans, the concentration of hArg is of the order of 2 µM. hArg may be a low-abundance constituent of human plasma proteins. The GC–MS and GC-MS/MS methods we report in this article are useful to study the physiology and pathology of hArg in experimental and clinical settings.     

BIA–MS–MS: biomolecular interaction analysis for functional proteomics

One of the experimental processes of functional proteomics is the analysis of protein interaction. Here, we review a new analytical platform, BIA–MS, for protein interaction analysis. BIA–MS is an integration of a surface plasmon resonance biosensor for real-time interaction analysis and mass spectrometry for the subsequent identification of interacting molecules.     

iTRAQ结合2D LC-MS/MS技术在草菇不同生长发育时期蛋白质组分析中的应用

【目的】旨在采用iTRAQ标记结合二维液相色谱串联质谱技术对草菇不同生长发育阶段的差异蛋白质组进行研究。【方法】首先将提取的草菇不同生长阶段蛋白样品进行SDS-PAGE分析,其次将经二维液相色谱串联质谱技术获取的串联质谱数据通过MASCOT软件搜库,之后对鉴定蛋白质数据进行了主成分分析(Principal componentanalysis,PCA)、层次聚类(Hierarchy clustering)分析、K-均值(K-means)聚类和GeneOntology(GO)注释分析。【结果】试验结果显示,共计获得2 335个不同肽段,鉴定到1 039个蛋白质,其中1 030个蛋白质具有定量信息。在子实体阶段中显著上调蛋白质64个,下调蛋白质150个。生物信息学分析表明,iTRAQ标记技术结合二维液相色谱串联质谱可对不同生长发育时期的草菇蛋白样品进行有效地分离和鉴定。【结论】这一研究结果为深入研究草菇乃至其他大型担子菌子实体形成和发育的分子机制提供借鉴。     

BIA–MS–MS: biomolecular interaction analysis for functional proteomics

One of the experimental processes of functional proteomics is the analysis of protein interaction. Here, we review a new analytical platform, BIA–MS, for protein interaction analysis. BIA–MS is an integration of a surface plasmon resonance biosensor for real-time interaction analysis and mass spectrometry for the subsequent identification of interacting molecules.     

MS基因缺失的发现

衣阿华大学(Iowa City,IA)和法国的科研人员发现,第17条染色体上缺失adhalin基因可引起严重型儿童常染色体退行性肌营养不良(SCARMD)。该病能引起严重的随意肌功能丧失。 基因的缺失能导致肌蛋白adhalin的缺乏,该蛋白能在肌肉受损害收缩过程中保护肌肉细胞。受此病折磨的患者第17条染色体上缺失2个adhalin基因,它们分别来自患者的双亲。在不久的将来,将通过基     

Using short columns to speed up LC–MS quantification in MS binding assays

The present study describes the use of short columns to speed up LC–MS quantification in MS binding assays. The concept of MS binding assays follows closely the principle of traditional radioligand binding but uses MS for the quantification of bound marker thus eliminating the need for a radiolabelled ligand. The general strategy of increasing the throughput of this type of binding assay by the use of short columns is exemplified for NO 711 binding addressing GAT1, the most prevalent GABA transporter in the CNS. Employing short RP-18 columns with the dimension of 20 mm × 2 mm and 10 mm × 2 mm at flow rates up to 1000 μL/min in an isocratic mode retention times of 8–9 s and chromatographic cycle times of 18 s could be achieved. Based on the internal standard [²H₁₀]NO 711 fast chromatography methods were developed for four different columns that enabled quantification of NO 711 in a range from 50 pM up to 5 nM directly out of reconstituted matrix samples without further sample preparation. A validation of the established methods with respect to linearity, intra- and inter-batch accuracy and precision showed that the requirements according to the FDA guideline for bioanalytical methods are met. Furthermore the established short column methods were applied to the quantification of NO 711 in saturation experiments. The results obtained (i.e., K_d- and B_max-values) were almost identical as compared to those determined employing standard column dimension (55 mm × 2 mm).     

Proteome profile of bovine ruminal epithelial tissue based on GeLC–MS/MS

The proteome of rumen epithelial tissue was analysed by SDS-PAGE coupled with LC–MS/MS. 813 non-redundant proteins were identified of which 7.4 % featured membrane-spanning domains and 15.4 % harboured a signal peptide. According to the gene ontology annotation, the most abundant proteins exhibited binding activities related to their molecular functions, were proteins of cellular components or belonged to various metabolic processes. A predominant group of canonical pathways in the rumen epithelial tissue was identified using the IPA software. The GeLC–MS/MS approach was used to characterise the entire protein expression repertoire in rumen tissue, providing a more detailed understanding of the important biological processes in the rumen.     

MS4000U生物信号定量记录分析系统（MS4000U）简介

我公司1995年推出了MS302生物信号记录分析系统,在国内拥有众多用户,受到用户的好评。经过近年的努力,MS4000U终于以崭新的面貌问世了!MS4000U的设计站在了一个全新的高度,其基本设计思想是硬件集成度高、图形质量好、分析结果准确、软件功能齐全而且操作简单。为科研提供高性能产品是MS4000U的定位,突出做好信号的定量分析是MS4000U不同其他产品的重要标志!     

MS4000U生物信号定量记录分析系统（MS4000U）简介

我公司1995年推出了MS302生物信号记录分析系统,在国内拥有众多用户,受到用户的好评。经过近年的努力,MS4000U终于以崭新的面貌问世了！MS4000U的设计站在了一个全新的高度,其基本设计思想是硬件集成度高、图形质量好、分析结果准确、软件功能齐全而且操作简单。为科研提供高性能产品是MS4000U的定位,突出做好信号的定量分析是MS4000U不同其他产品的重要标志！     

Sub-proteomic fractionation,iTRAQ, and OFFGEL-LC–MS/MS approaches to cardiac proteomics

Using an in solution based approach with a sub-proteomic fraction enriched in cardiac sarcomeric proteins; we identified protein abundance in ischemic and non-ischemic regions of rat hearts stressed by acute myocardial ischemia by ligating the left-anterior descending coronary artery in vivo for 1 h without reperfusion. Sub-cellular fractionation permitted more in depth analysis of the proteome by reducing the sample complexity. A series of differential centrifugations produced nuclear, mitochondrial, cytoplasmic, microsomal, and sarcomeric enriched fractions of ischemic and non-ischemic tissues. The sarcomeric enriched fractions were labeled with isobaric tags for relative quantitation (iTRAQ), and then fractionated with an Agilent 3100 OFFGEL fractionator. The OFFGEL fractions were run on a Dionex U-3000 nano LC coupled to a ThermoFinnigan LTQ running in PQD (pulsed Q dissociation) mode. The peptides were analyzed using two search engines MASCOT (MatrixScience), and MassMatrix with false discovery rate of < 5%. Compared to no fractionation prior to LC–MS/MS, fractionation with OFFGEL improved the identification of proteins approximately four-fold. We found that approximately 22 unique proteins in the sarcomeric enriched fraction had changed at least 20%. Our workflow provides an approach for discovery of unique biomarkers or changes in the protein profile of tissue in disorders of the heart.     

Multidimensional protein fractionation of blood proteins coupled to data-independent nanoLC–MS/MS analysis

In order to exploit human blood as a source of protein disease biomarkers, robust analytical methods are needed to overcome the inherent molecular complexity of this bio-fluid. We present the coupling of label-free SAX chromatography and IMAC to a data-independent nanoLC–MS/MS (nanoLC–MS^E) platform for analysis of blood plasma and serum proteins. The methods were evaluated using protein standards added at different concentrations to two groups of samples. The results demonstrate that both techniques enable accurate protein quantitation using low sample volumes and a minimal number of fractions. Combining both methods, 883 unique proteins were identified, of which 423 proteins showed high reproducibility. The two approaches resulted in identification of unique molecular signatures with an overlap of approximately 30%, thus providing complimentary information on sub-proteomes. These methods are potentially useful for systems biology, biomarker discovery, and investigation of phosphoproteins in blood.     

Evaluation of oxysterol levels of patients with silicosis by LC–MS/MS method

Molecular and Cellular Biochemistry - Aberrant structural formations of Cu/Zn superoxide dismutase enzyme (SOD1) are the probable mechanism by which circumscribed mutations in the SOD1 gene cause...