ABSTRACT Background Saliva has emerged as a promising diagnostic resource due to its accessibility, noninvasiveness, and repeatability, enabling early disease detection and timely intervention. However, current studies often overlook the distinction between whole saliva (WS) and cell‐free saliva (CFS). Objective This study aims to compare the proteomic profiles of WS and CFS. Method and result The saliva was detected with and without low‐abundance protein enrichment using nanoparticles, employing DIA‐MS technology. Our findings reveal a substantial enhancement in the detectability of low‐abundance proteins in saliva with utilization of nanoparticles, enabling identification of 12%–15% low‐abundance proteins previously undetectable in WS or CFS. In total, 3817 saliva proteins were identified, with 3413 found in WS and 2340 in CFS. More interestingly, we found that it was not the similarity of the samples that did the clustering, but rather it depended more on the different detection methods and sample types. And the predominant functions of the identified proteins in WS were related to oxidative phosphorylation and neurodegenerations, whereas those in CFS were primarily associated with nitrogen and glycosaminoglycan metabolism. And both exhibited functions in immune response and proteasome. Conclusion This study represents the first comparison of WS and CFS, providing valuable experimental evidence for guiding the selection of research subjects in future saliva omics studies.

Ling‐ling Jiao

Hui‐lin Dong

Yan‐hua Qin

Jun Zhu

Peng‐lin Wu

Jing Liu

Yi Cao

Chang‐jian Wu

Yuan Zhang

Fan Cao

Feng Li

Huai‐yuan Zhu

PROTEOMICS - CLINICAL APPLICATIONS

蛋白质组学 - 临床应用已发展成为将蛋白质组学应用于人类疾病研究和临床转化领域的重要信息来源。该杂志每年出版 12 期，将在所有相关领域发表论文，包括：-旨在进一步了解人类疾病功能障碍的分子机制的基础蛋白质组学研究-致力于发现和验证诊断和预后疾病的蛋白质组学研究结果生物标志物——蛋白质组学用于发现新的药物靶点——蛋白质组学在药物开发过程中的应用——蛋白质组学作为临床试验的组成部分的应用。

Proteomics - Clinical Applications has become an important source of information for applying proteomics to human disease research and clinical translation. The journal publishes 12 issues annually, covering all relevant fields of research, including: - Basic proteomics studies aimed at further understanding the molecular mechanisms of human disease; - Proteomics research dedicated to discovering and validating biomarkers for diagnostic and prognostic diseases; - The application of proteomics in discovering new drug targets; - The role of proteomics in the drug development process; - The application of proteomics as part of clinical trials.

《Proteomics - Clinical Applications》已发展成为将蛋白质组学应用于人类疾病研究和临床转化领域的重要信息来源。该杂志每年出版12期，涵盖所有相关领域的研究，包括：- 基础蛋白质组学研究，旨在深入了解人类疾病的分子机制；- 发现和验证用于诊断和预后疾病的生物标志物的蛋白质组学研究；- 蛋白质组学在新药靶点发现中的应用；- 蛋白质组学在药物开发过程中的作用；- 蛋白质组学作为临床试验组成部分的应用。

Proteomics - Clinical Applications

Comparisons of Whole Saliva and Cell Free Saliva by DIA‐Based Proteome Profiling

基于DIA蛋白质组学分析的全唾液与无细胞唾液比较

Category	Quartile
生物学	4
生物学, 生化研究方法	4

Comparisons of Whole Saliva and Cell Free Saliva by DIA‐Based Proteome Profiling

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Journal Info

Category	Quartile
BIOCHEMICAL RESEARCH METHODS	3