Defining and Detecting Complex Peak Relationships in Mass Spectral Data: The Mz.unity Algorithm.
Defining and Detecting Complex Peak Relationships in Mass Spectral Data: The Mz.unity Algorithm.
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DOI：
10.1021/acs.analchem.6b01702
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发表时间：
2016-09-20
影响因子：
7.4
通讯作者：
Patti GJ
中科院分区：
文献类型：
--
作者：
Mahieu NG;Spalding JL;Gelman SJ;Patti GJ
通过质谱法分析单个分析物可导致检测到超过100个简并峰。这些简并峰使光谱解释复杂化，并且注释具有挑战性。在基于质谱的代谢组学中，这种简并性导致虚假发现率膨胀，数据集包含比分析物多一个数量级的特征，以及数据分析期间资源的低效使用。虽然软件已经被引入到注释光谱简并，目前的方法是无法代表几个重要类的峰的关系。这些包括异二聚体和更高的复杂加合物，远端片段，不同极性的峰之间的关系，以及特征和背景峰之间的复杂加合物。在这里，我们概述了质谱中峰简并的来源，这些来源没有被当前的方法注释，并介绍了一个名为mz.unity的软件包来检测这些关系，在准确的质量数据。使用mz.unity，我们发现数据集包含的关系比我们预期的要复杂得多。示例包括谷氨酸和烟酰胺腺嘌呤二核苷酸（NAD）的加合物、以相同或相反极性检测到的NAD片段以及谷氨酸和背景峰的加合物。此外，我们确定的复杂关系表明，在解释质谱简并性时通常作出的几个假设一般不成立。这些贡献提供了新的工具和见解，以帮助在复杂的光谱关系的注释，并提供了一个基础，改进数据集识别。Mz.unity是一个R软件包，可在https://github.com/nathaniel-mahieu/mz.unity以及我们的实验室网站http://pattilab.wustl.edu/software/上免费获得。
Analysis of a single analyte by mass spectrometry can result in the detection of more than 100 degenerate peaks. These degenerate peaks complicate spectral interpretation and are challenging to annotate. In mass spectrometry-based metabolomics, this degeneracy leads to inflated false discovery rates, data sets containing an order of magnitude more features than analytes, and an inefficient use of resources during data analysis. Although software has been introduced to annotate spectral degeneracy, current approaches are unable to represent several important classes of peak relationships. These include heterodimers and higher complex adducts, distal fragments, relationships between peaks in different polarities, and complex adducts between features and background peaks. Here we outline sources of peak degeneracy in mass spectra that are not annotated by current approaches and introduce a software package called mz.unity to detect these relationships in accurate mass data. Using mz.unity, we find that data sets contain many more complex relationships than we anticipated. Examples include the adduct of glutamate and nicotinamide adenine dinucleotide (NAD), fragments of NAD detected in the same or opposite polarities, and the adduct of glutamate and a background peak. Further, the complex relationships we identify show that several assumptions commonly made when interpreting mass spectral degeneracy do not hold in general. These contributions provide new tools and insight to aid in the annotation of complex spectral relationships and provide a foundation for improved data set identification. Mz.unity is an R package and is freely available at https://github.com/nathaniel-mahieu/mz.unity as well as our laboratory Web site http://pattilab.wustl.edu/software/.
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影响因子：
50.3
作者：
Xu W;Yang H;Liu Y;Yang Y;Wang P;Kim SH;Ito S;Yang C;Wang P;Xiao MT;Liu LX;Jiang WQ;Liu J;Zhang JY;Wang B;Frye S;Zhang Y;Xu YH;Lei QY;Guan KL;Zhao SM;Xiong Y
通讯作者：
Xiong Y
影响因子：
50.3
作者：
Ward PS;Patel J;Wise DR;Abdel-Wahab O;Bennett BD;Coller HA;Cross JR;Fantin VR;Hedvat CV;Perl AE;Rabinowitz JD;Carroll M;Su SM;Sharp KA;Levine RL;Thompson CB
通讯作者：
Thompson CB
DOI：
10.1093/bioinformatics/btu370
发表时间：
2014-10
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Daly R;Rogers S;Wandy J;Jankevics A;Burgess KE;Breitling R
通讯作者：
Breitling R
影响因子：
7.4
作者：
Ipsen, Andreas;Want, Elizabeth J.;Lindon, John C.;Ebbels, Timothy M. D.
通讯作者：
Ebbels, Timothy M. D.
影响因子：
3
作者：
Wolf S;Schmidt S;Müller-Hannemann M;Neumann S
通讯作者：
Neumann S