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An Integrated Approach for Microprotein Identification and Sequence Analysis
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Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species.

Adrien Brown1,2, Alexandre Burel1,2, Sarah Cianférani1,2

  • 1Laboratoire de Spectrométrie de Masse Bioorganique (LSMBO), IPHC, UMR7178, Université de Strasbourg, CNS, Strasbourg, France.

Proteomics
|January 6, 2026
PubMed
Summary

A new pipeline, Brownotate, generates protein sequence databases for any species, overcoming a major bottleneck in proteomics research. This user-friendly tool enables researchers to analyze proteomic data from underrepresented species effectively.

Keywords:
genome annotationgenome assemblypipelineprotein databaseproteomics

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Genomics

Background:

  • Proteomics research requires comprehensive protein sequence databases.
  • A lack of databases for many species hinders biological complexity studies.
  • Existing computational tools are often limited or require specialized expertise.

Purpose of the Study:

  • To develop an accessible pipeline for generating protein sequence databases for any species.
  • To enable researchers without bioinformatics expertise to create necessary databases.
  • To address the bottleneck of missing protein sequence data in biological research.

Main Methods:

  • Developed Brownotate, an open-source, user-friendly pipeline for genome assembly and protein annotation.
  • The pipeline extracts existing protein sequences and annotates genome assemblies or DNA datasets.
  • Evaluated pipeline performance across diverse species and phylogenetic groups.

Main Results:

  • Brownotate generates fragmented but good-quality assemblies and annotations.
  • Protein prediction overlap is high, comparable to reference databases.
  • Proteomic data interpretation using Brownotate-generated databases yields results similar to NCBI databases.

Conclusions:

  • Brownotate effectively mitigates the lack of protein sequence databases for understudied species.
  • The pipeline empowers proteomic analysis for species with available sequencing data.
  • Brownotate is a valuable addition to the proteomics research toolbox.