两种软件分析唾液多肽组结果的比较

引用本文: 万磊磊, 陈琦, 程思明, 李水明, 王勇. 两种软件分析唾液多肽组结果的比较[J]. 分析化学, 2020, 48(12): 1709-1716. doi: 10.19756/j.issn.0253-3820.201401 shu

Citation: WAN Lei-Lei, CHEN Qi, CHENG Si-Ming, LI Shui-Ming, WANG Yong. Comparison of Two Different Softwares for Analyzing Salivary Peptidome[J]. Chinese Journal of Analytical Chemistry, 2020, 48(12): 1709-1716. doi: 10.19756/j.issn.0253-3820.201401 shu

两种软件分析唾液多肽组结果的比较

1.
深圳大学生命与海洋科学学院, 深圳市海洋生物资源与生态环境重点实验室, 深圳市脑病和大数据研究所, 深圳 518060;
2.
中山大学附属第八医院, 深圳 518026;
3.
深圳湾实验室, 深圳 518055;
4.
深圳-香港脑科学研究院, 深圳 518060

通讯作者: 王勇, wyong@szu.edu.cn

基金项目:
本文系深圳市科技计划项目（No.JCYJ20170818142154551）和深港脑科学创新研究院项目（NO.2019SHIBS0003）资助

摘要: 以10个唾液样本为例，唾液经氧化石墨烯-磷酸镧纳米复合材料（LaGM）方法分离和高分辨串联飞行时间质谱进行多肽鉴定后，使用Peaks studio 8.5（PS）和Protein Pilot Software 4.0（PP）两种软件分别进行搜库分析后对比鉴定结果。研究发现，两种软件鉴定出的阈值以上肽段数量存在差异，PS软件通常能够鉴定出更多阈值以上肽段数目；两种软件鉴定出的阈值以上相同肽段在PS中占30%~60%，在PP中占60%~90%，即某些肽段只能被PS或PP一种软件所鉴定。但是，两种搜库结果在降解蛋白质数目上无明显规律，数目因样本而异。值得注意的是，如果以PP和PS的阳性结果相互参照，发现在一种软件中阈值以下的肽段，在另一种软件中也可能是在阈值以上，而且此概率与肽段的打分呈正相关。研究还发现，两种软件对不同长度肽段的鉴定有一定的偏好性：PS鉴定结果中短肽段较多，而PP软件可以给出更多的长肽段。比较而言，在PP中，短肽段易出现假阴性，在PS中，长肽段易出现假阴性，而信号的相对强度与阈值无明显的相关性。本研究结果表明，只使用一种软件进行分析，结果不能准确地代表多肽组的全部情况，两种软件都能提供另一软件鉴定不到的信息，将两种软件结果综合分析，能够得到更为全面的结果。

关键词:

English

Comparison of Two Different Softwares for Analyzing Salivary Peptidome

1.
College of Life and Ocean Science, Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, Shenzhen University, Shenzhen 518060, China;
2.
The Eighth Hospital Affiliated to Sun Yat-Sen University, Shenzhen 518026, China;
3.
Shenzhen Bay Laboratory, Shenzhen 518055, China;
4.
Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518060, China

Corresponding author: WANG Yong, wyong@szu.edu.cn

Received Date: 10 July 2020
Revised Date: 31 August 2020
Fund Project:
This work was supported by the Shenzhen Science and Technology Innovation Committee (No. JCYJ20170818142154551) and the Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions (No. 2019SHIBS0003).

Abstract: In this study, 10 saliva samples were used as data sets. After the saliva sample was separated by graphene oxide-lanthanum phosphate nanocomposite (LaGM) method and identified by high-resolution tandem time-of-flight mass spectrometry, Peaks studio 8.5 (PS) and Protein Pilot Software 4.0 (PP) were used for searching analysis and the identification results were compared. It was found that the number of peptides identified by the two softwares were different. Under the experimental conditions, not only the PS software could usually identify more peptides, but also the results given by the two softwares did not completely overlap, and the same peptides identified by the two softwares occupied 30%-60% in PS and 60%-90% in PP, which meant that some peptides could be only identified by PS or PP software, but at the level of degraded protein, PS method had no obvious advantages. It was worth noting that if the positive results of PP and PS were cross-referenced, peptides below the threshold in one software may be above the threshold in another software, and this probability was positive related to the score of the peptide. Further research also found that the two softwares had a certain preference for identifying peptides of different lengths. The identified results of PS had more short peptides, while PP software could give more long peptides. In comparison, in PP software, short peptides were prone to false negative result, but long peptides were prone to false negative result in PS software. And the intensity of the signal had no obvious correlation with the threshold. This study showed that it was not advisable to use only one kind of software to analyze or only use the same reference result to represent the entire peptidome. Both softwares could identify the information each other that could not be identified by the other software. Cross-referencing the two analysis softwares each other could improve the accuracy of the results.

Key words:

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1.
沈阳化工大学材料科学与工程学院沈阳 110142

两种软件分析唾液多肽组结果的比较

通讯作者: 王勇, wyong@szu.edu.cn

English

Comparison of Two Different Softwares for Analyzing Salivary Peptidome

Corresponding author: WANG Yong, wyong@szu.edu.cn

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通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

两种软件分析唾液多肽组结果的比较

通讯作者: 王勇, wyong@szu.edu.cn

English

Comparison of Two Different Softwares for Analyzing Salivary Peptidome

Corresponding author: WANG Yong, wyong@szu.edu.cn

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南： 你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

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