Chemical informatics combined with Kendrick mass analysis to enhance annotation and identify pathways in soybean metabolomics

Among abiotic stresses to agricultural crops, drought stress is the most prolific and has worldwide detrimental impacts. The soybean (Glycine max) is one of the most important sources of nutrition to both livestock and humans. Different plant introductions (PI) of soybeans have been identified to have different drought tolerance levels. Here, two soybean lines, Pana (drought sensitive) and PI 567731 (drought tolerant) were selected to identify chemical compounds and pathways which could be targets for metabolomic analysis induced by abiotic stress. Extracts from the two lines are analyzed by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The high mass resolution and accuracy of the method allows for identification of ions from hundreds of different compounds in each cultivar. The exact m/z of these species were filtered through SoyCyc and the Human Metabolome Database to identify possible molecular formulas of the ions. Next, the exa..., Direct infusion ESI FT-ICR mass spectrometry was conducted using three replicates from each cultivar; the time-domain data was converted to m/z domain data prior to processing to identify features in the mass spectra.
Direct infusion ESI-FT-ICR data sets were processed as follows using Bruker Daltonics (Bremen, Germany) Data Analysis 4.0 software. Software was instructed to find all peaks with a signal-to-noise ratio > 3 to produce a peak list. Next, the peak list was subjected to the deconvolution process such that isotopic envelopes were determined, and each individual ionic species was then grouped as part of the given isotopic cluster. A threshold of 0.1% peak area relative to the most intense peak (m/z 1073.506 in each cultivar list, corresponding to ion C67H94NaN4O6) was used. The peak list was reduced to the monoisotopic isotope of each isotopic cluster, and this was the m/z value used in compiling lists for each cultivar.
After compilation of the m/z list for each cultivar, i..., , # Chemical informatics combined with Kendrick mass analysis to enhance annotation and identify pathways in soybean metabolomics

[https://doi.org/10.5061/dryad.np5hqc046](https://doi.org/10.5061/dryad.np5hqc046)

## Description of the data and file structure

Leaves from the two cultivars (Pana and PI 567731) were collected from 20 plants/cultivar and flash frozen immediately following tissue collection and transported to the University of Missouri. Afterward, they were placed on dry ice and shipped to the University at Buffalo. There, the specimens were stored in polycarbonate petri-dishes at -20°C until extractions were performed. Flash frozen leaves from multiple plants of each cultivar were pooled. Next, each group was individually macerated manually for five minutes in methanol using mortar and pestle. To remove particulates, vacuum filtration was performed. The samples were subsequently dried in a vacuum oven, and then the dried residue was reconstituted into 2 mL of HPLC grade me...

在农业作物面临的各类非生物胁迫中，干旱胁迫是分布最广泛、危害波及全球的胁迫类型。大豆（Glycine max）是畜禽与人类最重要的营养来源之一。不同大豆引种系（Plant Introduction，PI）已被证实存在不同的耐旱等级。本研究选取两个大豆品系：耐旱敏感型品系Pana与耐旱型品系PI 567731，旨在识别可作为非生物胁迫诱导代谢组学分析靶点的化合物与代谢通路。本研究采用直接注入电喷雾电离傅里叶变换离子回旋共振质谱（direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry，以下简称DI-ESI-FT-ICR-MS）对两个品系的提取物进行分析。该方法具备高质量分辨率与准确度，可实现每个栽培品种中数百种不同化合物对应离子的鉴定。研究人员通过SoyCyc数据库与人类代谢组数据库（Human Metabolome Database，HMDB）对这些离子的精确质荷比（m/z）进行筛选，以确定对应离子的可能分子式。后续，[原文此处截断]

本研究对每个栽培品种的3次生物学重复样本开展直接注入ESI-FT-ICR质谱分析；在识别质谱特征峰的处理步骤前，需将时域数据转换为质荷比域数据。

本研究采用德国不来梅的布鲁克道尔顿（Bruker Daltonics）Data Analysis 4.0软件对DI-ESI-FT-ICR质谱数据集进行如下处理：首先设置软件筛选信噪比大于3的所有峰，生成峰列表。随后对峰列表进行解卷积处理，以确定同位素包络峰，并将每个独立离子物种归类至对应的同位素簇中。本研究设置以每个栽培品种峰列表中强度最高的峰（质荷比为1073.506，对应离子C67H94NaN4O6）的峰面积为基准，设定0.1%的峰面积阈值。将峰列表简化为每个同位素簇的单同位素峰，以此作为每个栽培品种峰列表编制所用的质荷比值。

完成每个栽培品种质荷比列表的编制后，[原文此处截断]

# 结合化学信息学与肯德里克质量分析，优化大豆代谢组学注释并鉴定代谢通路

[https://doi.org/10.5061/dryad.np5hqc046](https://doi.org/10.5061/dryad.np5hqc046)

## 数据与文件结构说明

本研究从两个栽培品种（Pana与PI 567731）的20株植株上采集叶片样本，组织采集后立即进行快速冷冻，并转运至密苏里大学（University of Missouri）。随后将样本置于干冰上，运至布法罗大学（University at Buffalo）。在布法罗大学，样本被保存于聚碳酸酯培养皿中，置于-20℃环境下直至提取操作开展。将每个栽培品种多株植株的快速冷冻叶片进行混合。随后将混合后的样本分别置于研钵与研杵中，以甲醇为溶剂，手动研磨5分钟进行浸提。为去除颗粒物，对浸提液进行真空过滤。随后将样本置于真空烘箱中干燥，再将干燥后的残渣用2毫升高效液相色谱级甲醇（HPLC grade methanol）复溶，[原文此处截断]