HBFP: a new repository for human body fluid proteome

Abstract

Body fluid proteome has been intensively studied as a primary source for disease biomarker discovery. Using advanced proteomics technologies, early research success has resulted in increasingly accumulated proteins detected in different body fluids, among which many are promising biomarkers. However, despite a handful of small-scale and specific data resources, current research is clearly lacking effort compiling published body fluid proteins into a centralized and sustainable repository that can provide users with systematic analytic tools. In this study, we developed a new database of human body fluid proteome (HBFP) that focuses on experimentally validated proteome in 17 types of human body fluids. The current database archives 11 827 unique proteins reported by 164 scientific publications, with a maximal false discovery rate of 0.01 on both the peptide and protein levels since 2001, and enables users to query, analyze and download protein entries with respect to each body fluid. Three unique features of this new system include the following: (i) the protein annotation page includes detailed abundance information based on relative qualitative measures of peptides reported in the original references, (ii) a new score is calculated on each reported protein to indicate the discovery confidence and (iii) HBFP catalogs 7354 proteins with at least two non-nested uniquely mapping peptides of nine amino acids according to the Human Proteome Project Data Interpretation Guidelines, while the remaining 4473 proteins have more than two unique peptides without given sequence information. As an important resource for human protein secretome, we anticipate that this new HBFP database can be a powerful tool that facilitates research in clinical proteomics and biomarker discovery. Database URL: https://bmbl.bmi.osumc.edu/HBFP/

Potential biomarker proteins for aspiration pneumonia detected by shotgun proteomics using buccal mucosa samples: A cross-sectional study

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Artificial intelligence in clinical research of cancers

“…Recently, body fluid proteome has been intensively studied as a primary source for cancer biomarker. For this reason, our research group have developed a new database of human body fluid proteome (HBFP) that archived 11,827 unique proteins reported by 164 scientific publications since 2001 [ 106 ]. By providing a wealth of information, these knowledgebases can be excellent resources and tools for the research community.…”

Chemical Barrier Proteins in Human Body Fluids

“…The interaction network of the chemical barrier proteins in serum is visualized in Figure 1. Currently, more than 1800 proteins have been identified in tears by state-of-the-art proteomics techniques [109]. The major tear proteins, such as lysozyme-C, prolactin-inducible protein, lactotransferrin, and lacritin, have antimicrobial activity; therefore, they are involved in the defense against pathogens [5].…”

“…The protein concentration shows high variability between the individuals depending on the age, sex, sample collection time, and the health status of the oral cavity. Saliva contains more than 2700 proteins [ 109 ] and the most abundant ones are α-amylase, mucins, cystatins, proline-rich peptides, and serum albumin [ 114 ]. Similar to tears, the abundant salivary proteins are part of the immune system due to their antimicrobial activity, antioxidant function, and protective role against microbial proteases [ 115 ].…”

“…Sweat is composed of more than 99% water, making it a very dilute body fluid [ 123 ]. To date, more than 1200 sweat proteins have been identified by proteomic analyses [ 109 ]. Along with the saliva and tear fluid, the abundant sweat proteins are part of the innate immune system.…”