mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data.
mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data.
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DOI：
10.1093/bioinformatics/bts674
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发表时间：
2013-01-15
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影响因子：
--
通讯作者：
Breitling R
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文献类型：
--
作者：
Chokkathukalam A;Jankevics A;Creek DJ;Achcar F;Barrett MP;Breitling R
动机：稳定同位素标记实验最近在代谢组学研究中越来越受欢迎，它提供了对代谢通量动力学的独特见解，超出了常规质谱法收集的稳态信息。然而，大多数液相色谱-质谱数据分析软件缺乏能够自动注释和相对定量标记代谢物峰的功能。在这里，我们描述了代谢组学分析管道mzMatch.R的新扩展mzMatch-ISO。结果：通过四种类型的诊断图，使用mzMatch-ISO进行靶向和非靶向同位素分析，可以方便地直观地总结每种代谢物的标记质量和数量，这些诊断图显示(i)每个样品组中每种化合物的同位素峰的色谱图；（ii）单同位素峰与标记峰的比值，表示标记的比例；（iii）每组样品中单同位素和标记峰的平均峰面积；（iv）在预定的同位素体中标记的相对数量的趋势。为了帮助进一步的统计分析，还提供了用于生成这些图的值作为一个以制表符分隔的文件。通过分析来自锥虫寄生虫的13c标记代谢组数据集，我们展示了mzMatch-ISO的功能和多功能性。可用性:mzMatch。R和mzMatch-ISO可从http://mzmatch.sourceforge.net免费获取，Linux和Windows平台均可使用最新版本的R。联系邮箱：rainer.breitling@manchester.ac.uk。补充信息：补充数据可在生物信息学在线获取
Motivation: Stable isotope-labelling experiments have recently gained increasing popularity in metabolomics studies, providing unique insights into the dynamics of metabolic fluxes, beyond the steady-state information gathered by routine mass spectrometry. However, most liquid chromatography–mass spectrometry data analysis software lacks features that enable automated annotation and relative quantification of labelled metabolite peaks. Here, we describe mzMatch–ISO, a new extension to the metabolomics analysis pipeline mzMatch.R. Results: Targeted and untargeted isotope profiling using mzMatch–ISO provides a convenient visual summary of the quality and quantity of labelling for every metabolite through four types of diagnostic plots that show (i) the chromatograms of the isotope peaks of each compound in each sample group; (ii) the ratio of mono-isotopic and labelled peaks indicating the fraction of labelling; (iii) the average peak area of mono-isotopic and labelled peaks in each sample group; and (iv) the trend in the relative amount of labelling in a predetermined isotopomer. To aid further statistical analyses, the values used for generating these plots are also provided as a tab-delimited file. We demonstrate the power and versatility of mzMatch–ISO by analysing a 13C-labelled metabolome dataset from trypanosomal parasites. Availability: mzMatch.R and mzMatch–ISO are available free of charge from http://mzmatch.sourceforge.net and can be used on Linux and Windows platforms running the latest version of R. Contact: rainer.breitling@manchester.ac.uk . Supplementary information: Supplementary data are available at Bioinformatics online
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影响因子：
14.9
作者：
Wishart DS;Knox C;Guo AC;Eisner R;Young N;Gautam B;Hau DD;Psychogios N;Dong E;Bouatra S;Mandal R;Sinelnikov I;Xia J;Jia L;Cruz JA;Lim E;Sobsey CA;Shrivastava S;Huang P;Liu P;Fang L;Peng J;Fradette R;Cheng D;Tzur D;Clements M;Lewis A;De Souza A;Zuniga A;Dawe M;Xiong Y;Clive D;Greiner R;Nazyrova A;Shaykhutdinov R;Li L;Vogel HJ;Forsythe I
通讯作者：
Forsythe I
影响因子：
14.9
作者：
Kanehisa M;Goto S;Sato Y;Furumichi M;Tanabe M
通讯作者：
Tanabe M
影响因子：
7.4
作者：
Melamud E;Vastag L;Rabinowitz JD
通讯作者：
Rabinowitz JD
影响因子：
5.8
作者：
Rogers, Simon;Scheltema, Richard A.;Breitling, Rainer
通讯作者：
Breitling, Rainer
影响因子：
29
作者：
Le A;Lane AN;Hamaker M;Bose S;Gouw A;Barbi J;Tsukamoto T;Rojas CJ;Slusher BS;Zhang H;Zimmerman LJ;Liebler DC;Slebos RJ;Lorkiewicz PK;Higashi RM;Fan TW;Dang CV
通讯作者：
Dang CV