嵌入
工作流程
计算机科学
软件
维数之咒
降维
相似性(几何)
化学空间
算法
代表(政治)
图形
数据挖掘
理论计算机科学
人工智能
化学
数据库
政治
药物发现
图像(数学)
生物化学
程序设计语言
法学
政治学
作者
Florent Olivon,Nicolas Elie,Gwendal Grelier,Fanny Roussi,Marc Litaudon,David Touboul
出处
期刊:Analytical Chemistry
[American Chemical Society]
日期:2018-10-17
卷期号:90 (23): 13900-13908
被引量:115
标识
DOI:10.1021/acs.analchem.8b03099
摘要
Molecular networking (MN) is becoming a standard bioinformatics tool in the metabolomic community. Its paradigm is based on the observation that compounds with a high degree of chemical similarity share comparable MS2 fragmentation pathways. To afford a clear separation between MS2 spectral clusters, only the most relevant similarity scores are selected using dedicated filtering steps requiring time-consuming parameter optimization. Depending on the filtering values selected, some scores are arbitrarily deleted and a part of the information is ignored. The problem of creating a reliable representation of MS2 spectra data sets can be solved using algorithms developed for dimensionality reduction and pattern recognition purposes, such as t-distributed stochastic neighbor embedding (t-SNE). This multivariate embedding method pays particular attention to local details by using nonlinear outputs to represent the entire data space. To overcome the limitations inherent to the GNPS workflow and the networking architecture, we developed MetGem. Our software allows the parallel investigation of two complementary representations of the raw data set, one based on a classic GNPS-style MN and another based on the t-SNE algorithm. The t-SNE graph preserves the interactions between related groups of spectra, while the MN output allows an unambiguous separation of clusters. Additionally, almost all parameters can be tuned in real time, and new networks can be generated within a few seconds for small data sets. With the development of this unified interface ( https://metgem.github.io ), we fulfilled the need for a dedicated, user-friendly, local software for MS2 comparison and spectral network generation.
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