Kinetics of labelling of organic and amino acids in potato tubers by gas chromatography-mass spectrometry following incubation in (13)C labelled isotopes

Metabolic pathways of primary metabolism of discs isolated from potato tubers were evaluated by the use of a gas chromatography-mass spectrometry (GC-MS) method generated specifically for this purpose. After testing several possible methods including chemical ionization, it was decided for reasons of sensitivity, reproducibility and speed to use electron impact ionization-based GC-MS analysis. The specific labelling and label accumulation of over 30 metabolites including a broad number of sugars, organic and amino acids was analysed following the incubation of tuber discs in [U-(13)C]glucose. The reproducibility of this method was similar to that found for other GC-MS-based analyses and comparison of flux estimates from this method with those obtained from parallel, yet less comprehensive, radiolabel experiments revealed close agreement. Therefore, the novel method allows quantitatively evaluation of a broad range of metabolic pathways without the need for laborious (and potentially inaccurate), chemical fractionation procedures commonly used in the estimation of fluxes following incubation in radiolabelled substrates. As a first experiment the GC-MS method has been applied to compare the metabolism of wild type and well-characterized transgenic potato tubers exhibiting an enhanced sucrose mobilization. The fact that this method is able to rapidly yield further comprehensive information into primary metabolism illustrates its power as a further phenotyping tool for the analysis of plant metabolism.     

Comparison of gas chromatography-mass spectrometry and liquid chromatography-tandem mass spectrometry methods to quantify alpha-tocopherol and alpha-tocopherolquinone levels in human plasma.

Two mass spectrometric methods were established for the quantitative analyses of alpha-tocopherol (TH) and its oxidation product alpha-tocopherolquinone (TQ) in human plasma. Both methods make use of isotopically labeled internal standards of different levels of deuteration (d3-TH and d6-TQ). Plasma (100 microl) was saponified in the presence of a mixture of antioxidants, and then TH and TQ were extracted with hexane. With the GC-MS method, the analytes were first converted into O-trimethylsilyl derivatives before analysis in the selective ion monitoring mode. The derivatization procedure led to the quantitative conversion of TQ into the O-trimethylsilyl derivative of tocopherolhydroquinone, giving rise to a more stable molecule with less fragmentation than for TQ. The increased stability of the molecule resulted in an enhanced contribution of the base peak to the total observed ions and therefore an increased sensitivity of the base peak for quantification. With the liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, TH and TQ were detected by multiple reaction monitoring after positive electrospray ionization. The GC-MS and LC-MS/MS methods showed nearly the same accuracy (>95%) and the same within-day precisions, with less than 5 and 10% for TH and TQ, respectively. The between-day precision and the limit of quantification for TQ in plasma were better by LC-MS/MS (4%; 3 nM) than by GC-MS (21%; 10 nM). Analysis and method validation were carried out with plasma samples obtained from a male volunteer pre- and postexercise. Both techniques showed that the ratio of TQ/TH was elevated by 35% immediately after exercise and had returned to basal levels when measured 24 h later.     

基于气相色谱-质谱联用技术的代谢组学方法在转植酸酶基因玉米代谢物指纹图谱分析中的应用

目的:建立气相色谱-质谱联用技术(GC-MS)的代谢组学方法,初步研究转基因株系与对照株系之间代谢物指纹图谱的差异性,为转基因作物安全的评价提供参考。方法:优化提取条件,考察色谱条件,并采用主成分分析(PCA)数据处理方法对转基因株系及对照进行模式识别。结果:优化了提取条件及色谱条件,建立了GC-MS的代谢组学方法,获得了小分子的代谢产物的表达谱,发现转基因与其对照之间呈现出显著性差异。结论:优化的GC-MS的代谢组学方法可以从代谢水平检测转基因作物,找出差异性,为转基因作物的检测与评价提供技术支持。     

南美天胡荽及其根际土壤水浸提液化感成分分析

为探讨南美天胡荽对其他植物种子萌发的影响以及筛选影响其他植物的主要化合物,该文采用种子萌发试验、气相色谱-质谱联用以及液相色谱-质谱联用的方法,分析了南美天胡荽不同溶剂浸提液对种子萌发的影响、南美天胡荽植株及其根际土壤浸提液成分。结果表明:(1)南美天胡荽不同溶剂浸提物均具有一定程度的抑制种子萌发作用。(2)气相色谱-质谱分析下,南美天胡荽植株水浸提液中共分离鉴定了35种化合物,其中,邻苯二甲酸二丁酯(15.2%)、10,15-十八烷二元酸(8.58%)、2,4-二叔丁基苯酚(6.81%)相对含量最高; 根际土壤水浸提液中共分离鉴定了17种化合物,其中,油酸酰胺(26.47%)、正二十七烷(9.63%)、十六酸乙酯(4.83%)相对含量最高。(3)液相色谱-质谱分析下,南美天胡荽植株水浸提液共分离鉴定了109种化合物,ESI⁺模式下,L-苯丙氨酸(3 483.99 ng·mg^-1)、木犀草素(2 306.64 ng·mg^-1)含量最多,ESI^-模式下,右旋奎宁酸(21 827.71 ng·mg^-1)、绿原酸(12 589.25 ng·mg^-1)含量最多; 根际土壤水浸提液中共分离鉴定了93种化合物,ESI⁺模式下,丁酸(7 660.53 ng·mg^-1)、棕榈酰胺(3 200.36 ng·mg^-1)含量最多,ESI^-模式下,正二十八酸(18 605.35 ng·mg^-1)、蔗糖(12 183.23 ng·mg^-1)含量最多。(4)南美天胡荽的潜在化感物质主要为脂肪酸类、酰胺类、酯类、芳香酸类化合物,而土壤中直接起化感作用的物质可能为丁酸、正二十八酸、羟基乙酸、油酸酰胺、棕榈酰胺、十六酸乙酯、苯甲酸,其中脂肪酸类化合物输入可能来源于南美天胡荽、土壤微生物和土壤动物,酰胺类、酯类、芳香类化合物则更可能来源于南美天胡荽植株。     

Profiling of central metabolism in human cancer cells by two-dimensional NMR, GC-MS analysis, and isotopomer modeling

Tracking metabolic profiles has the potential to reveal crucial enzymatic steps that could be targeted in the drug discovery process. It is of special importance for various types of cancer known to be associated with substantial rewiring of metabolic networks. Here we introduce an integrated approach for the analysis of metabolome that allows us to simultaneously assess pathway activities (fluxes) and concentrations of a large number of the key components involved in central metabolism of human cells. This is accomplished by in vivo labeling with [U-¹³C]glucose followed by two-dimensional nuclear magnetic resonance (NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS) analysis. A comprehensive isotopomer model was developed, which enabled us to compare fluxes through the key central metabolic pathways including glycolysis, pentose phosphate pathway, tricarboxylic acid cycle, anaplerotic reactions, and biosynthetic pathways of fatty acids and amino acids. The validity and strength of this approach is illustrated by its application to a number of perturbations to breast cancer cells, including exposure to hypoxia, drug treatment, and tumor progression. We observed significant differences in the activities of specific metabolic pathways resulting from these perturbations and providing new mechanistic insights. Based on these findings we conclude that the developed metabolomic approach constitutes a promising analytical tool for revealing specific metabolic phenotypes in a variety of cell types and pathological conditions. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Chen Yang and Adam D. Richardson contributed equally to this work.     

Bile acids: analysis in biological fluids and tissues

The formation of bile acids/bile alcohols is of major importance for the maintenance of cholesterol homeostasis. Besides their functions in lipid absorption, bile acids/bile alcohols are regulatory molecules for a number of metabolic processes. Their effects are structure-dependent, and numerous metabolic conversions result in a complex mixture of biologically active and inactive forms. Advanced methods are required to characterize and quantify individual bile acids in these mixtures. A combination of such analyses with analyses of the proteome will be required for a better understanding of mechanisms of action and nature of endogenous ligands. Mass spectrometry is the basic detection technique for effluents from chromatographic columns. Capillary liquid chromatography-mass spectrometry with electrospray ionization provides the highest sensitivity in metabolome analysis. Classical gas chromatography-mass spectrometry is less sensitive but offers extensive structure-dependent fragmentation increasing the specificity in analyses of isobaric isomers of unconjugated bile acids. Depending on the nature of the bile acid/bile alcohol mixture and the range of concentration of individuals, different sample preparation sequences, from simple extractions to group separations and derivatizations, are applicable. We review the methods currently available for the analysis of bile acids in biological fluids and tissues, with emphasis on the combination of liquid and gas phase chromatography with mass spectrometry.     

Identification of fatty acids in submerged cultures of Claviceps species

Abstract Fatty acids were identified in the submerged mycelium of Claviceps purpurea, Claviceps paspali, Claviceps fusiformis and Claviceps sp. SD-58 by gas chromatography-mass spectrometry (GC-MS) and used for a chemotaxonomical study. A close relatedness was found between Claviceps sp. SD-58 and C. fusiformis . The composition of fatty acids in high-production mutants differed substantially from that of the parent strains. Fatty acid analysis is thus probably only applicable in the taxonomy of non-mutated isolates of Claviceps cultured under standard conditions.     

A simple and accurate HPLC method for fecal bile acid profile in healthy and cirrhotic subjects: validation by GC-MS and LC-MS

We have developed a simple and accurate HPLC method for measurement of fecal bile acids using phenacyl derivatives of unconjugated bile acids, and applied it to the measurement of fecal bile acids in cirrhotic patients. The HPLC method has the following steps: 1) lyophilization of the stool sample; 2) reconstitution in buffer and enzymatic deconjugation using cholylglycine hydrolase/sulfatase; 3) incubation with 0.1 N NaOH in 50% isopropanol at 60°C to hydrolyze esterified bile acids; 4) extraction of bile acids from particulate material using 0.1 N NaOH; 5) isolation of deconjugated bile acids by solid phase extraction; 6) formation of phenacyl esters by derivatization using phenacyl bromide; and 7) HPLC separation measuring eluted peaks at 254 nm. The method was validated by showing that results obtained by HPLC agreed with those obtained by LC-MS/MS and GC-MS. We then applied the method to measuring total fecal bile acid (concentration) and bile acid profile in samples from 38 patients with cirrhosis (17 early, 21 advanced) and 10 healthy subjects. Bile acid concentrations were significantly lower in patients with advanced cirrhosis, suggesting impaired bile acid synthesis.     

Chemical Constituents of <i>Pedicularis longiflora</i> var. <i>tubiformis</i> (Orobanchaceae), a Common Hemiparasitic Medicinal Herb from the Qinghai Lake Basin,China

Pedicularis longiflora var. tubiformis (Orobanchaceae) is an abundant parasitic herb mainly found in the Xiaopohu wetland of the Qinghai Lake Basin in Northwestern China. The species has an important local medicinal value, and in this study, we evaluated the chemical profile of its stems, leaves and seeds using mass spectrometry. Dried samples of stems, leaves and seeds were grinded, weighted, and used for a series of extractions with an ultrasonic device at room temperature. The chemical profiles for each tissue were determined using Gas Chromatography-Mass Spectrometry (GC-MS) and Liquid ChromatographyMass Spectrometry (LC-MS). Twenty-seven amino acids and organic acids were identified and quantified from stems, leaves and seeds. The content of amino acids detected in leaves and seeds was higher than the amount found in stems. Six flavonoids were also detected, including isoorientin, orientin, luteolin-7-O-glucoside, luteolin, apigenin and tricin. The concentrations of luteolin-7-O-glucoside, luteolin and tricin were the highest and more concentrated in leaves, while that of orientin was the lowest and mainly found in stems. Soluble monosaccharides and oligosaccharides below tetramer were also examined, and our analyses detected the presence of arabitol, fructose, galacturonic acid, glucose, glucuronic acid, inositol, sucrose, and trehalose. This is the first study to identify and quantify the main components of amino acids, organic acids, flavonoids and soluble sugars from stems, leaves and seeds of P. longiflora var. tubiformis. Eight of the amino acids detected are essential for humans, highlighting the medicinal importance of this species. Results shown here can be used as a reference case to develop future studies on the chemical constituents of Pedicularis herbs and other medicinal plants from the Tibetan region.     

冠突曲霉 veA基因缺失型与野生型的差异代谢物研究

为了鉴定冠突曲霉 veA基因缺失型与野生型的差异代谢物,寻找与 veA 基因产孢相关的代谢物,采用气相色谱-质谱联用（GC-MS）的代谢组学技术,分别收集2个菌株培养48h的菌丝体,经液氮研磨、超声萃取、三甲基氯硅烷衍生化后上机检测,将GC-MS检测的数据进行前处理和代谢物注释,并用统计学相关软件进行差异物筛选和相关性分析。结果显示,共鉴定99种代谢物,其中差异代谢物41种,野生型菌株中表达上调的显著差异代谢物有20种, veA缺失型菌株中表达上调的显著差异代谢物有21种,并预测差异代谢物的相关性,发现与623种代谢物产生相关性,其中313种呈正相关,310种呈负相关。筛选出来的差异代谢物涉及有机酸、氨基酸、碳水化合物、醇类、脂肪酸类等多种代谢物质,其中有机酸和氨基酸类代谢物占主导地位。本研究结果为进一步研究冠突曲霉代谢物与产孢的关联提供了一定的理论基础。     

Identification of very-long-chain polyunsaturated fatty acids from Amphidinium carterae by atmospheric pressure chemical ionization liquid chromatography-mass spectroscopy

A method is described for the enrichment of very-long-chain polyunsaturated fatty acids (VLCPUFAs) from total fatty acids of Amphidinium carterae and their identification as picolinyl esters by means of microbore liquid chromatography-mass spectrometry with atmospheric pressure chemical ionization (LC-MS/APCI). The combination of argentation TLC and LC-MS/APCI was used to identify unusual VLCPUFAs up to hexatriacontaoctaenoic acid. Two acids, 36:7n-6 and 36:8n-3, were also synthesized to unambiguously confirm their structure. The possibilities of VLCPUFAs biosynthesis are proposed.     

Improved detection of polyunsaturated fatty acids as phenacyl esters using liquid chromatography-ion trap mass spectrometry

The fatty acid composition of Shewanella pealeana was determined by the analysis of fatty acid methyl esters via gas chromatography-mass spectrometry (GC-MS) and fatty acid 2-oxo-phenylethyl esters via high-performance liquid chromatography-mass spectrometry (LC-MS) combined with ultra violet (UV) detection. There was good agreement between the percentage composition of components determined by GC-MS and LC-UV analyses. However, LC-MS analysis using Atmospheric Pressure Chemical Ionization (APCI) demonstrated dramatically enhanced detection of unsaturated fatty acid 2-oxo-phenylethyl esters. The degree of enhancement was proportional to the degree of unsaturation. Tests with a pure polyunsaturated fatty acid (PUFA) standard gave an absolute detection limit in full scan mode of 200 pg. In samples, the selectivity of MS over UV gave a significantly lower detection limit due to lack of chemical interferences. In 'Selected Reaction Monitoring' (SRM) mode, the detection limit was 5 pg. This was essentially independent of whether the sample is a standard or complex mixture of fatty acids. Tandem mass spectrometry was used to support structural information and to enhance the ability to target specific fatty acids. Several PUFAs which were not evident from GC-MS analysis were detected and identified by APCI LC-MS, including some rare or novel PUFAs from S. pealeana and a menhaden oil standard. Detailed analysis of bacterial fatty acid composition by either GC-MS or APCI LC-MS is highly preferable to analysis systems based solely on retention time identification.     

8R-Lipoxygenase-catalyzed synthesis of a prominent cis-epoxyalcohol from dihomo-γ-linolenic acid: a distinctive transformation compared with S-lipoxygenases

Conversion of fatty acid hydroperoxides to epoxyalcohols is a well known secondary reaction of lipoxygenases, described for S-specific lipoxygenases forming epoxyalcohols with a trans-epoxide configuration. Here we report on R-specific lipoxygenase synthesis of a cis-epoxyalcohol. Although arachidonic and dihomo-γ-linolenic acids are metabolized by extracts of the Caribbean coral Plexaura homomalla via 8R-lipoxygenase and allene oxide synthase activities, 20:3ω6 forms an additional prominent product, identified using UV, GC-MS, and NMR in comparison to synthetic standards as 8R,9S-cis-epoxy-10S-erythro-hydroxy-eicosa-11Z,14Z-dienoic acid. Both oxygens of (18)O-labeled 8R-hydroperoxide are retained in the product, indicating a hydroperoxide isomerase activity. Recombinant allene oxide synthase formed only allene epoxide from 8R-hydroperoxy-20:3ω6, whereas two different 8R-lipoxygenases selectively produced the epoxyalcohol.A biosynthetic scheme is proposed in which a partial rotation of the reacting intermediate is required to give the observed erythro epoxyalcohol product. This characteristic and the synthesis of cis-epoxy epoxyalcohol may be a feature of R-specific lipoxygenases.     

Metabolic flux analysis in Escherichia coli by integrating isotopic dynamic and isotopic stationary 13C labeling data

The novel concept of isotopic dynamic 13C metabolic flux analysis (ID-13C MFA) enables integrated analysis of isotopomer data from isotopic transient and/or isotopic stationary phase of a 13C labeling experiment, short-time experiments, and an extended range of applications of 13C MFA. In the presented work, an experimental and computational framework consisting of short-time 13C labeling, an integrated rapid sampling procedure, a LC-MS analytical method, numerical integration of the system of isotopomer differential equations, and estimation of metabolic fluxes was developed and applied to determine intracellular fluxes in glycolysis, pentose phosphate pathway (PPP), and citric acid cycle (TCA) in Escherichia coli grown in aerobic, glucose-limited chemostat culture at a dilution rate of D = 0.10 h(-1). Intracellular steady state concentrations were quantified for 12 metabolic intermediates. A total of 90 LC-MS mass isotopomers were quantified at sampling times t = 0, 91, 226, 346, 589 s and at isotopic stationary conditions. Isotopic stationarity was reached within 10 min in glycolytic and PPP metabolites. Consistent flux solutions were obtained by ID-13C MFA using isotopic dynamic and isotopic stationary 13C labeling data and by isotopic stationary 13C MFA (IS-13C MFA) using solely isotopic stationary data. It is demonstrated that integration of dynamic 13C labeling data increases the sensitivity of flux estimation, particularly at the glucose-6-phosphate branch point. The identified split ratio between glycolysis and PPP was 55%:44%. These results were confirmed by IS-13C MFA additionally using labeling data in proteinogenic amino acids (GC-MS) obtained after 5 h from sampled biomass.     

Proteomic analysis on acetate metabolism in Citrobacter sp. BL-4

Mass production of glucosamine (GlcN) using microbial cells is a worthy approach to increase added values and keep safety problems in GlcN production process. Prior to set up a microbial cellular platform, this study was to assess acetate metabolism in Citrobacter sp. BL-4 (BL-4) which has produced a polyglucosamine PGB-2. The LC-MS analysis was conducted after protein separation on the 1D-PAGE to accomplish the purpose of this study. 280 proteins were totally identified and 188 proteins were separated as acetate-related proteins in BL-4. Acetate was converted to acetyl-CoA by acetyl-CoA synthetase up-regulated in the acetate medium. The glyoxylate bypass in the acetate medium was up-regulated with over-expression of isocitrate lyases and 2D-PAGE confirmed this differential expression. Using (1)H-NMR analysis, the product of isocitrate lyases, succinate, increased about 15 times in the acetate medium. During acetate metabolism proteins involved in the lipid metabolism and hexosamine biosynthesis were over-expressed in the acetate medium, while proteins involved in TCA cycle, pentose phosphate cycle and purine metabolism were down-regulated. Taken together, the results from the proteomic analysis can be applied to improve GlcN production and to develop metabolic engineering in BL-4.     

Metabolic dynamics of Desulfovibrio vulgaris biofilm grown on a steel surface

In this study, a comparative metabolomics approach combining gas chromatography–mass spectrometry (GC-MS) and liquid chromatography–mass spectrometry (LC-MS) was applied first between planktonic cells and biofilms and then between pure cultures and biofilms of Desulfovibrio vulgaris. The results revealed that the overall metabolic level of the biofilm cells was down-regulated, especially for metabolites related to the central carbon metabolism, compared to the planktonic cells and the pure culture of D. vulgaris. In addition, pathway enrichment analysis of the 58 metabolites identified by GC-MS showed that fatty acid biosynthesis in the biofilm cells was up-regulated, suggesting that fatty acids may be important for the formation, maintenance and function of D. vulgaris biofilm. This study offers a valuable perspective on the metabolic dynamics of the D. vulgaris biofilm.     

Limits of detection for the determination of mono- and dicarboxylic acids using gas and liquid chromatographic methods coupled with mass spectrometry

The chromatographic separation and instrumental limits of detection (LODs) were obtained for a broad range of C(1)-C(18) monocarboxylic (MCAs) and C(2)-C(14) dicarboxylic acids (DCAs) employing either chemical derivatization followed by gas chromatography-mass spectrometry and flame ionization detection (GC-MS/FID) or direct analysis with liquid chromatography high resolution MS and tandem MS (LC-MS). Suitability, efficiency and stability of reaction products for several derivatization agents used for esterification (BF(3)/butanol), and trimethysilylation, including trimethylsilyl-N-N-dimethylcarbamate (TMSDMC) and N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) were evaluated. The lowest limits of detection for the majority of compounds below 10 pg (with the exception of acetic acid) were obtained for derivatization with BF(3)/butanol followed by GC-MS in the total ion current (TIC) mode. Further improvements were achieved when applying either selected ion monitoring (SIM), which decreased the LODs to 1-4 pg or a combination of SIM and TIC (SITI) (2-5 pg). GC-FID provided LODs comparable to those obtained by GC-MS TIC. Both trimethylsilylation (followed by GC-MS) and direct LC-MS/MS analysis yielded LODs of 5-40 pg for most of the acids. For volatile acids the LODs were higher, e.g., 25 and 590 ng for TMSDMC and BSTFA derivatized formic acid, respectively, whereas the LC-MS methods did not allow for the analysis of formic acid at all.     

Odd-numbered very-long-chain polyunsaturated fatty acids from the dinoflagellate Amphidinium carterae identified by atmospheric pressure chemical ionization liquid chromatography-mass spectrometry

A method is described for the enrichment of odd very-long-chain polyunsaturated fatty acids (VLCPUFAs) by means of RP-HPLC and argentation TLC from total fatty acids of the dinoflagellate A. carterae and their identification as picolinyl esters by means of microbore liquid chromatography-mass spectrometry with atmospheric pressure chemical ionization (LC-MS/APCI). The combination of argentation TLC and LC-MS/APCI was used to identify rare and unusual odd VLCPUFAs up to nonacosahexaenoic acid. Two acids, (allZ)-nonacosa-11,14,17,20,23-pentaenoic acid (29:5n-6) and (allZ)-nonacosa-11,14,17,20,23,26-hexaenoic acid (29:6n-3), were synthesized for the first time to unambiguously confirm their structure. Possible biosynthetic pathways for odd VLCPUFAs are also proposed.     

LC-MS and GC-MS metabolite profiling of nickel(II) complexes in the latex of the nickel-hyperaccumulating tree Sebertia acuminata and identification of methylated aldaric acid as a new nickel(II) ligand

Targeted liquid chromatography-mass spectrometry (LC-MS) technology using size exclusion chromatography and metabolite profiling based on gas chromatography-mass spectrometry (GC-MS) were used to study the nickel-rich latex of the hyperaccumulating tree Sebertia acuminata. More than 120 compounds were detected, 57 of these were subsequently identified. A methylated aldaric acid (2,4,5-trihydroxy-3-methoxy-1,6-hexan-dioic acid) was identified for the first time in biological extracts and its structure was confirmed by 1D and 2D nuclear magnetic resonance (NMR) spectroscopy. After citric acid, it appears to be one of the most abundant small organic molecules present in the latex studied. Nickel(II) complexes of stoichiometry NiII:acid=1:2 were detected for these two acids as well as for malic, itaconic, erythronic, galacturonic, tartaric, aconitic and saccharic acids. These results provide further evidence that organic acids may play an important role in the transport and possibly in the storage of metal ions in hyperaccumulating plants.