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other·ophthalmology, proteomics, bioinformatics, cataract surgery, glaucoma·PMC10878049

AHP DB: a reference database of proteins in the human aqueous humor

Database: The Journal of Biological Databases and Curation · 14 authors, 18 centres

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TL;DR

This paper presents the Aqueous Humor Proteomics Database (AHP DB), a publicly accessible web resource containing proteomic data from 307 human aqueous humor samples analyzed by LC-MS/MS, identifying 1683 proteins. The database integrates clinical and demographic information, enabling researchers to explore protein expression patterns in ocular health and disease. This resource addresses the lack of a reference proteomic database for aqueous humor, facilitating further studies on ocular physiology and pathology.

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**Background:** The aqueous humor (AH) is a low-viscosity biofluid that circulates from the posterior to the anterior chamber of the eye, playing essential roles in nutrient supply, waste removal, and intraocular pressure regulation. The proteomic composition of AH is crucial for cellular processes such as cell-to-cell communication, signal transduction, immunological modulation, and cell proliferation. Previous studies have linked specific AH proteins to ocular diseases including cataracts, glaucoma, age-related macular degeneration, uveitis, retinoblastoma, and diabetic retinopathy. However, reproducibility in AH proteomic profiling has been limited due to the small volume and low protein concentration of AH, as well as the absence of a reference database. To address these challenges, the authors developed the Aqueous Humor Proteomics Database (AHP DB), a web-based resource containing proteomic data from 307 human AH samples analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS).

**Methods:** Participants were recruited from patients undergoing cataract or glaucoma surgery at Augusta University Medical Center. Written informed consent was obtained, and the study was approved by the Institutional Review Board of Augusta University. AH samples (50–200 µL) were collected via paracentesis and stored at −80°C. Samples were lyophilized, reconstituted in urea buffer, reduced and alkylated, and digested with trypsin. LC-MS/MS analysis was performed using an Ultimate 3000 nano-UPLC system and Orbitrap Fusion Tribrid mass spectrometer. Protein identification and quantification were carried out using Proteome Discoverer (version 2.2) with the SequestHT algorithm against the UniProt-SwissProt database. Peptide-spectrum match (PSM) counts were used as a semi-quantitative measure. The database was developed on a Microsoft platform using Asp.net, JavaScript, and Microsoft SQL Server, hosted on an Internet Information Services web server.

**Key Results:** The current version of AHP DB contains 1683 proteins detected in >5% of AH samples from 307 subjects. The database provides comprehensive information including UniProt ID, gene symbol, protein name, PSM counts, and detection levels. The top 50 most abundant proteins are listed, with albumin (mean PSM 4271.56, detected in 100% of samples), serotransferrin (mean PSM 847.75, 100%), and alpha-1-antitrypsin (mean PSM 254.65, 100%) being the most abundant. Other notable proteins include complement C3, hemopexin, immunoglobulins, and pigment epithelium-derived factor. The database also includes clinical data such as ocular pathology (cataract or glaucoma), demographic information (sex, age, race, ethnicity), ocular characteristics (IOP, cup area, disc area), comorbidities, and medications. Users can filter and sort data by various columns and download datasets for offline analysis.

**Clinical Implications:** AHP DB provides a valuable reference for the vision research community, enabling in-depth investigations into the role of AH proteins in ocular physiology and pathology. The database can help identify protein signatures associated with different ocular diseases and demographic variables, potentially leading to novel biomarkers and therapeutic targets. Previous analyses using subsets of this data have revealed differences in AH proteomic content between African American and Caucasian subjects, as well as sex- and race-specific differences in apolipoprotein levels in primary open-angle glaucoma. The database is freely accessible at https://ahp.augusta.edu/ and will be updated regularly as additional samples are analyzed.

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other

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ophthalmology

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ORIGINAL PAPER

PMC10878049

AHP DB: a reference database of proteins in the human aqueous humor

Database: The Journal of Biological Databases and Curation

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ABSTRACT

Abstract The aqueous humor (AH) is a low-viscosity biofluid that continuously circulates from the posterior chamber to the anterior chamber of the eye. Recent advances in high-resolution mass-spectrometry workflows have facilitated the study of proteomic content in small-volume biofluids like AH, highlighting the potential clinical implications of the AH proteome. Nevertheless, in-depth investigations into the role of AH proteins in ocular diseases have encountered challenges due to limited accessibility to these workflows, difficulties in large-scale AH sample collection and the absence of a reference AH proteomic database. In response to these obstacles, and to promote further research on the involvement of AH proteins in ocular physiology and pathology, we have developed the web-based Aqueous Humor Proteomics Database (AHP DB). The current version of AHP DB contains proteomic data from 307 human AH samples, which were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The database offers comprehensive information on 1683 proteins identified in the AH samples. Furthermore, relevant clinical data are provided for each analyzed sample. Researchers also have the option to download these datasets individually for offline use, rendering it a valuable resource for the scientific community. Database URL : https://ahp.augusta.edu/

CITATION EXPORT

Tae Jin Lee, Arnav Goyal, Garrett Jones et al.. AHP DB: a reference database of proteins in the human aqueous humor. Database: The Journal of Biological Databases and Curation. (2024). https://doi.org/10.1093/database/baae001

AUTHORS

14 · 18 CENTRES

Tae Jin Lee, Arnav Goyal, Garrett Jones, Joshua Glass, Vishal Doshi, Kathryn Bollinger, Lane Ulrich, Saleh Ahmed, Sai Karthik Kodeboyina, Amy Estes, Marc Töteberg-Harms, Wenbo Zhi, Shruti Sharma, Ashok Sharma

1 Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
2 Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
3 Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
4 Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
5 Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
6 Department of Ophthalmology, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
7 Department of Ophthalmology, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
8 Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
9 Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
10 Mass General Brigham, 399 Revolution Drive, Somerville, MA 02145, USA
11 Department of Ophthalmology, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
12 Department of Ophthalmology, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
13 Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
14 Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
15 Department of Ophthalmology, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
16 Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
17 Department of Ophthalmology, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
18 Department of Population Health Sciences, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA