ALLocator: an interactive web platform for the analysis of metabolomic LC-ESI-MS datasets, enabling semi-automated, user-revised compound annotation and mass isotopomer ratio analysis.
ALLocator: an interactive web platform for the analysis of metabolomic LC-ESI-MS datasets, enabling semi-automated, user-revised compound annotation and mass isotopomer ratio analysis.
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DOI：
10.1371/journal.pone.0113909
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Nattkemper TW
中科院分区：
文献类型：
--
作者：
Kessler N;Walter F;Persicke M;Albaum SP;Kalinowski J;Goesmann A;Niehaus K;Nattkemper TW
加合物形成、裂解事件和基质效应对LC-ESI-MS数据集中代谢物的识别和定量提出了特殊的挑战。化合物识别的一个重要步骤是对海量信号进行去卷积。在该处理步骤中，代表同一分析物的加合物、碎片和同位素的峰被分配到不同的组，以便将峰与洗脱化合物分开。从这些峰群中提取中性质量和伪光谱，并通过质量分解和数据库匹配用于代谢物鉴定。在LC-ESI-MS测量中，代谢物的定量受到基质效应和非线性响应的阻碍。校正这些影响的一种常见方法是添加U-13C标记的内标并计算每个代谢物的质量同位异构体比率。在这里，我们提出了一个新的网络平台来分析LC-ESI-MS实验。分配器涵盖了从原始数据处理到代谢物识别和质量同分异构体比率分析的工作流程。用于光谱去卷积的集成处理流水线“ALLocatorSD”生成伪光谱，并自动识别从U-13C标记的内标中出现的峰。来自后者的信息改进了对中性点损耗的质量分解和注释。Allocator提供了一个交互和动态的界面，以深入探索和增强结果。已识别代谢物的伪光谱可以存储在用户和方法特定的参考列表中，这些参考列表可以应用于后续的数据集。通过比较谷氨酸菌类型菌株ATCC 13032和L精氨酸产生菌ATCC 21831合成L精氨酸的代谢产物丰度倍数变化的实验，说明了该软件的潜力。此外，通过在同一菌株中鉴定(γ-)谷氨酰二肽，显示了对罕见的大的中性损失的检测和注释的能力。分配器可在以下网址在线获得：https://allocator.cebitec.uni-bielefeld.de.需要登录，但可以免费使用。
Adduct formation, fragmentation events and matrix effects impose special challenges to the identification and quantitation of metabolites in LC-ESI-MS datasets. An important step in compound identification is the deconvolution of mass signals. During this processing step, peaks representing adducts, fragments, and isotopologues of the same analyte are allocated to a distinct group, in order to separate peaks from coeluting compounds. From these peak groups, neutral masses and pseudo spectra are derived and used for metabolite identification via mass decomposition and database matching. Quantitation of metabolites is hampered by matrix effects and nonlinear responses in LC-ESI-MS measurements. A common approach to correct for these effects is the addition of a U-13C-labeled internal standard and the calculation of mass isotopomer ratios for each metabolite. Here we present a new web-platform for the analysis of LC-ESI-MS experiments. ALLocator covers the workflow from raw data processing to metabolite identification and mass isotopomer ratio analysis. The integrated processing pipeline for spectra deconvolution “ALLocatorSD” generates pseudo spectra and automatically identifies peaks emerging from the U-13C-labeled internal standard. Information from the latter improves mass decomposition and annotation of neutral losses. ALLocator provides an interactive and dynamic interface to explore and enhance the results in depth. Pseudo spectra of identified metabolites can be stored in user- and method-specific reference lists that can be applied on succeeding datasets. The potential of the software is exemplified in an experiment, in which abundance fold-changes of metabolites of the l-arginine biosynthesis in C. glutamicum type strain ATCC 13032 and l-arginine producing strain ATCC 21831 are compared. Furthermore, the capability for detection and annotation of uncommon large neutral losses is shown by the identification of (γ-)glutamyl dipeptides in the same strains. ALLocator is available online at: https://allocator.cebitec.uni-bielefeld.de. A login is required, but freely available.
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影响因子：
4.4
作者：
Petri K;Walter F;Persicke M;Rückert C;Kalinowski J
通讯作者：
Kalinowski J
DOI：
10.1093/bioinformatics/btt414
发表时间：
2013-10-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Kessler N;Neuweger H;Bonte A;Langenkämper G;Niehaus K;Nattkemper TW;Goesmann A
通讯作者：
Goesmann A
影响因子：
4.3
作者：
Bueschl, C.;Krska, R.;Kluger, B.;Schuhmacher, R.
通讯作者：
Schuhmacher, R.
影响因子：
2.3
作者：
Harrison, AG
通讯作者：
Harrison, AG
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y