SpliceProt 2.0: A Sequence Repository of Human, Mouse, and Rat Proteoforms

Area of Science:

• Proteogenomics
• Bioinformatics
• Computational Biology

Background:

• The human, mouse, and rat proteomes contain known proteins and potential novel proteoforms.
• Existing databases may not fully capture splice variants, necessitating advanced proteomic validation tools.
• Understanding orthologous proteins is crucial for comparative genomics and functional studies.

Purpose of the Study:

• To introduce SpliceProt 2.0, an enhanced public proteogenomics database.
• To provide a comprehensive repository of computationally translated proteins, including novel proteoforms.
• To facilitate the proteomic validation of splice variants and prediction of orthologous proteins.

Main Methods:

• Utilized ternary matrices for transcript reconstruction using data from Ensembl, UniProt, and APPRIS.
• Integrated transcript reconstruction, sequence annotation, and detection at transcriptome and proteome levels.
• Excluded transcripts predicted to be susceptible to degradation via the NMD pathway.

Main Results:

• SpliceProt 2.0 offers a broader range of computationally translated proteins compared to previous versions.
• Demonstrated the utility of SpliceProt 2.0 in predicting orthologous proteins between humans and murines.
• Successfully identified splice variants absent from the reference UniProtKB/SwissProt database.

Conclusions:

• SpliceProt 2.0 serves as a valuable resource for the proteogenomics community.
• The database aids in the discovery and validation of novel proteoforms and splice variants.
• Its applications extend to predicting orthologous proteins, enhancing comparative proteomic research.