SpliceProt: a protein sequence repository of predicted human splice variants

Area of Science:

• Proteomics and Bioinformatics
• Molecular Biology
• Genomics

Background:

• Alternative splicing of the transcriptome increases proteome diversity in eukaryotes.
• Current protein sequence repositories are limited in detecting protein isoforms from mRNA splice variants.
• Accurate annotation of mass spectrometry (MS) experiments requires comprehensive protein sequence data.

Purpose of the Study:

• Introduce SpliceProt, a novel protein sequence repository.
• Facilitate the investigation of putative splice variants in human proteomes.
• Improve the detection and annotation of protein isoforms derived from alternative splicing.

Main Methods:

• Developed SpliceProt using transcriptome experimental data.
• Compiled 159,719 non-redundant putative polypeptide sequences.
• Assessed SpliceProt's capability using publicly available proteomics data.

Main Results:

• Detected 173 peptides hypothetically derived from splice variants.
• Identified 54 novel peptides not present in the UniProtKB/TrEMBL repository.
• SpliceProt identified more splice variants compared to other repositories.

Conclusions:

• SpliceProt offers a valuable resource for identifying protein isoforms from alternative splicing.
• The repository enhances the annotation of proteomics experiments, particularly for splice variants.
• SpliceProt provides a greater number of unique peptides and detects more splice variants than existing databases.