Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and...

Area of Science:

• Proteomics
• Genomics
• Bioinformatics

Background:

• High-throughput mass spectrometry is crucial for genome annotation.
• Peptide identification validates gene models and coding sequences (CDSs).

Purpose of the Study:

• To analyze mass spectrometry data for human genome annotation.
• To identify and characterize alternatively spliced protein isoforms.

Main Methods:

• Comprehensive analysis of experimental spectra from public mass spectrometry databases.
• Peptide identification to validate gene models and detect protein isoforms.

Main Results:

• Peptides covered 35% of GENCODE human genome annotations.
• Confirmed protein translation for novel, putative, pseudogene, and nonsense-mediated decay transcripts.
• Identified 150 genes with multiple alternative protein isoforms, the largest set yet.
• Overrepresentation of alternative isoforms in heterogeneous nuclear ribonucleoproteins, interchangeable homologous exons, and short indels.
• 25% of detected alternative isoforms showed subtle differences from constitutive ones.
• Many alternative splicing events are conserved in mouse, without disrupting protein structure or function.

Conclusions:

• Mass spectrometry is a powerful tool for genome annotation and alternative splicing discovery.
• A significant proportion of alternative splicing events result in subtle, conserved protein variations.
• These findings suggest selective constraints on the translation of alternative transcripts.