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

The authors developed AHP DB, a freely accessible web-based reference database containing proteomic data from 307 human aqueous humor samples analyzed by LC-MS/MS, comprising 1683 identified proteins and corresponding clinical metadata to support future ocular proteomics research.

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AHP DB is a publicly accessible web-based database designed to address the absence of a reference human aqueous humor proteomic resource. Proteomic data were generated using shotgun (bottom-up) liquid chromatography-tandem mass spectrometry on 307 human AH samples, yielding identification of 1683 proteins detected in more than 5% of samples. Each sample entry includes corresponding clinical metadata. The database allows users to load, filter, and download data according to clinical or proteomic profiles. Subsets of the compiled data have been previously analyzed to reveal inter-population differences in AH proteomic content, including sex- and race-specific differences in apolipoprotein levels among subjects with primary open-angle glaucoma. The authors note inherent limitations of shotgun proteomics, including relative rather than absolute quantification, potential confounding of protein identification when multiple proteins share common peptides, and reduced reliability for detecting lower abundance proteins.

STUDY TYPE

other

SPECIALTY

ophthalmology

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AI pipeline

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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