How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource.

Area of Science:

• Genomics
• Proteomics
• Bioinformatics

Background:

• Thousands of small open reading frames (ORFs) are present in genomes but are often missed by standard annotation due to their size or location.
• These alternative ORFs, found in untranslated regions or overlapping known genes, have emerging roles in biological functions.
• Discoveries highlight the need for comprehensive annotation and mining of experimental data for these small ORFs.

Purpose of the Study:

• To introduce OpenProt, the first proteogenomic resource for extensive small ORF annotation.
• To provide a polycistronic annotation model across transcriptomes of 10 species.
• To integrate multi-omics data, including mass spectrometry and ribosome profiling, for ORF validation.

Main Methods:

• Developed OpenProt, a web server and database, utilizing a polycistronic annotation model.
• Re-analyzed 114 mass spectrometry and 87 ribosome profiling datasets to gather experimental evidence.
• Incorporated functional domain prediction and conservation analysis for all identified ORFs.

Main Results:

• OpenProt annotates a vast number of small ORFs across 10 species.
• The resource integrates extensive experimental evidence from re-analyzed omics datasets.
• Functional domains and conservation data are provided for predicted ORFs.

Conclusions:

• OpenProt significantly enhances the annotation of small ORFs, revealing their coding potential.
• The resource serves as a valuable tool for exploring alternative ORFs and their biological significance.
• OpenProt facilitates large-scale mining of proteogenomic data for hidden coding elements.