Study on Uncertainty and Scalability in Single-Analysis Salivary Peptidome Studies
10.19756/j.issn.0253-3820.251227
- VernacularTitle:唾液多肽组单次分析结果的不确定性和可拓展性研究
- Author:
Xiu-Feng FANG
1
;
Bing-Jia CUI
;
Jin-Ling XU
;
Yong WANG
Author Information
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
- Keywords:
Peptidomics;
Saliva;
False negative;
Replicates;
High-resolution tandem mass spectrometry
- From:
Chinese Journal of Analytical Chemistry
2025;53(11):1820-1827,中插1-中插3
- CountryChina
- Language:Chinese
-
Abstract:
Nano liquid chromatography-high resolution tandem mass spectrometry(LC-HRMS/MS)is widely used for body fluid peptidome analysis,yet the impact of replicate analyses remains overlooked.Using salivary peptidome,in this work,10 replicate analyses of the same sample were conducted.It was found that although m/z and molecular weight ranges were consistent across replicates,single runs identified only 348-576 unique peptides from 32-39 degraded proteins.Merging all replicates revealed 1237 peptides from 77 proteins,a 2.5 folds increase in peptides and 2 folds increase in proteins.Instrument stability was confirmed via intensity/retention time of 12 peptides.Merged peptides primarily derived from high-abundance proteins(e.g.,Statherin,PRP1/2).Analysis of 20 peptides showed that the some peptides were detected in single analysis but confidence varying(19%-99%),low-confidence peptides(<95%)exceeded 95%after replicate.signal intensity alone didn't determine confidence and peptides spanning the sequence region between the longest and the shortest detected fragments could be identified.The above findings suggested that single-run LC-MS peptidomics analysis carried inherent false negatives and uncertainties.However,by integrating the results of a single analysis with the mechanism of enzymatic hydrolysis for endogenous peptides,it was possible to make reasonable inferences and extrapolations regarding peptides derived from highly abundant degraded proteins.
