FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments.
FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments.
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FiatFlux——一款用于 13C-葡萄糖实验代谢通量分析的软件。
DOI：
10.1186/1471-2105-6-209
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发表时间：
2005-08-25
影响因子：
3
通讯作者：
Sauer U
中科院分区：
文献类型：
--
作者：
Zamboni N;Fischer E;Sauer U
细胞内通量的定量知识是重要的代谢网络及其功能操作的全面表征。与代谢物浓度的直接评估相反，体内代谢物通量必须从13 C实验中的可测量量间接推断。所需的经验，复杂的网络模型，大型和异构的数据集，以及高度控制的实验条件的耗时设置在很大程度上限制了代谢通量分析，以少数专家组。通量分析的概念简化是仅从MS数据分析确定代谢通量比，然后可以在第二步中使用该代谢通量比来估计绝对体内通量。在这里，我们描述了用户友好的软件包FiatFlux，支持非专家用户的通量分析。在第一个模块中，会聚通量的比率自动计算从GC-MS检测的13 C-模式的蛋白质结合的氨基酸。自动识别预定义的裂解模式，并基于MS谱中冗余信息的比较进行适当的统计数据处理。在第二模块中，绝对细胞内通量可以通过13 C约束的通量平衡程序来计算，该程序将实验确定的进出细胞的通量与上述通量比相结合。该软件经过预配置，可从[1- 13 C]和[U-13 C]葡萄糖实验以及各种微生物氨基酸的GC-MS分析中得出通量比和绝对体内通量。FiatFlux是一个直观的工具，用于不熟悉数值方法或同位素示踪实验的用户进行细胞内代谢的定量研究。该开源软件的目的是使非专业人员能够根据其特定的科学兴趣调整软件，包括其他13 C底物，标记混合物和生物体。
Quantitative knowledge of intracellular fluxes is important for a comprehensive characterization of metabolic networks and their functional operation. In contrast to direct assessment of metabolite concentrations, in vivo metabolite fluxes must be inferred indirectly from measurable quantities in 13C experiments. The required experience, the complicated network models, large and heterogeneous data sets, and the time-consuming set-up of highly controlled experimental conditions largely restricted metabolic flux analysis to few expert groups. A conceptual simplification of flux analysis is the analytical determination of metabolic flux ratios exclusively from MS data, which can then be used in a second step to estimate absolute in vivo fluxes. Here we describe the user-friendly software package FiatFlux that supports flux analysis for non-expert users. In the first module, ratios of converging fluxes are automatically calculated from GC-MS-detected 13C-pattern in protein-bound amino acids. Predefined fragmentation patterns are automatically identified and appropriate statistical data treatment is based on the comparison of redundant information in the MS spectra. In the second module, absolute intracellular fluxes may be calculated by a 13C-constrained flux balancing procedure that combines experimentally determined fluxes in and out of the cell and the above flux ratios. The software is preconfigured to derive flux ratios and absolute in vivo fluxes from [1-13C] and [U-13C]glucose experiments and GC-MS analysis of amino acids for a variety of microorganisms. FiatFlux is an intuitive tool for quantitative investigations of intracellular metabolism by users that are not familiar with numerical methods or isotopic tracer experiments. The aim of this open source software is to enable non-specialists to adapt the software to their specific scientific interests, including other 13C-substrates, labeling mixtures, and organisms.
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影响因子：
12.3
作者：
Blank LM;Kuepfer L;Sauer U
通讯作者：
Sauer U
影响因子：
3.2
作者：
Perrenoud, A;Sauer, U
通讯作者：
Sauer, U
DOI：
10.1111/j.1432-1033.1995.tb20829.x
发表时间：
1995-09-01
期刊：
EUROPEAN JOURNAL OF BIOCHEMISTRY
影响因子：
--
作者：
SZYPERSKI, T
通讯作者：
SZYPERSKI, T
影响因子：
4.1
作者：
Marx, A;Hans, S;de Graaf, AA
通讯作者：
de Graaf, AA
影响因子：
3.2
作者：
Hua, Q;Yang, C;Shimizu, K
通讯作者：
Shimizu, K