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

Comparison of Two Different Softwares for Analyzing Salivary Peptidome

WAN Lei-Lei ^1,3 ,
CHEN Qi ² ,
CHENG Si-Ming ^1,3 ,
LI Shui-Ming ^1,3,4 ,
WANG Yong ^1,3,4,,

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).

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.
- Peptidome,
- Peaks studio,
- Protein Pilot,
- Uncertainty,
- False negative
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