Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms

Area of Science:

• Proteomics
• Molecular Biology
• Genomics

Background:

• Proteoforms, the diverse protein products from a single gene, are significantly shaped by alternative splicing (AS).
• AS affects at least 90% of human genes, altering protein structure and function, with implications for phenotype and disease.
• Understanding splicing-derived protein isoforms is vital for comprehending human biology and disease mechanisms.

Purpose of the Study:

• To review recent innovations in mass spectrometry (MS) and bioinformatics for analyzing protein isoforms generated by alternative splicing.
• To highlight advancements enabling deeper exploration of the alternative proteome.
• To discuss the impact of splicing on proteoform diversity and its relevance to human health.

Main Methods:

• Review of recent advancements in mass spectrometry instrumentation and acquisition strategies.
• Analysis of updated sample preparation protocols for proteomic studies.
• Integration of bioinformatics pipelines for comprehensive proteoform analysis.

Main Results:

• Mass spectrometry technology and acquisition strategies have significantly improved protein isoform detection.
• Integrative bioinformatics pipelines enhance the depth of alternative proteome sampling.
• Both bottom-up and top-down MS approaches, with discovery and targeted methods, offer distinct advantages for isoform coverage.

Conclusions:

• Innovations in MS and bioinformatics are crucial for characterizing splicing-generated protein isoforms.
• Deeper proteome sampling is now achievable, advancing the understanding of proteoform diversity.
• Splicing's role in proteoform variation continues to be a key area of research in proteomics.