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bioRxiv · 10.1101/2025.07.31.667843

ProteoParc: A tool to generate protein reference databases for ancient and non-model organisms

Carrillo-Martin, G.·Krueger, J.·Marques-Bonet, T.·Lizano, E.
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Abstract

Over the last few years, the increasing interest in analysing the proteome of extinct and non-model organisms has generated a new field of research expanding the scope of proteomics. The lack of curated databases and/or molecular data from these organisms forces researchers to manually search in different public repositories for related protein sequences, either for MS/MS peptide identification or ZooMS marker annotation. This can lead to format incongruences and hinder reproducibility between studies. To address this issue, we introduce ProteoParc, a user-friendly software that generates reference databases by systematically downloading and processing protein sequences from the most widely used public repositories. The pipelines output is a non-redundant protein database, formatted to be interpreted by typical peptide identification software. Moreover, the user can adjust the database dimension and composition by applying different criteria to include only a certain number of genes or species. Thus, ProteoParc is an easy and fast, custom-made bioinformatic tool useful for future paleoproteomics analysis in ancient samples related to understudied organisms.

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Carrillo-Martin, G., Krueger, J., Marques-Bonet, T., Lizano, E.. 2025-08-02. ProteoParc: A tool to generate protein reference databases for ancient and non-model organisms. https://doi.org/10.1101/2025.07.31.667843

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