Work

ProteomeScout v4: An open-source, harmonized, ecosystem for post-translational modifications

Year: 2026

Type: preprint

Abstract: Motivation There are many databases of post-translational modifications, but each has different protein and PTM coverage, making the current state of post-translational modifications difficult to obtain, assess, or harmonize. ProteomeScout has been a relational database that harmonized a myriad of resources to address this challenge. In this update, we wished to create a lightweight, sustainable open source resource for the community that retained the power of harmonization, protein visualization, and Python tools for interacting with the database. Results ProteomeScout-v4 presents an ecosystem of open-source tools for aggregating and updating proteins and post-translational modifications and presenting the web-based and code-based access tools for interacting with the data. ProteomeScout has moved from using a complex relational database to a flat-text file format. The database file update is version controlled on FigShare and all features have processes for continuous updating, including migrating PTMs to updated protein records, when external databases are updated. The open-source nature and flexibility allow for user-based control and community-based feature integration. Fast and easy analysis is possible with the API, with example analyses provided here. Availability and implementation ProteomeScout-v4 web interface is available at https://proteomescout.research.virginia.edu/ ; the web interface package is available at: https://github.com/NaegleLab/proteomescout-v4 ; the API is available at https://github.com/NaegleLab/ProteomeScoutAPI ; database update code is available at https://github.com/NaegleLab/ProteomeScout-v4_Update ; and current database files are maintained at: https://doi.org/10.6084/m9.figshare.31129045 .

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.64898/2026.10.01.756115

Authors: Sam Crowl, Saqib Rizvi, Logan Campbell, Alekhya Kandoor, Kristen M. Naegle

Institution: University of Virginia

Language: English

Topic: Advanced Proteomics Techniques and Applications

Subfield: Spectroscopy

Field: Chemistry

Domain: Physical Sciences

Open Access status: green

Funders: National Institutes of Health, National Cancer Institute, National Institute of General Medical Sciences

Awards: Systematic approaches to reveal novel regulatory functions of tyrosine phosphorylation, Inferring Kinase Activity from Tumor Phosphoproteomic Data