TopLib: Building and Searching Top-Down Mass Spectral Libraries for Proteoform Identification

Area of Science:

• Proteomics
• Mass Spectrometry
• Bioinformatics

Background:

• Mass spectral library searching is crucial for proteomics.
• Existing tools primarily support bottom-up MS, not top-down MS.
• A gap exists in software for top-down spectral library construction and searching.

Purpose of the Study:

• Introduce TopLib, a novel software package for top-down mass spectral libraries.
• Develop efficient methods for top-down spectral representation, clustering, and searching.
• Address the limitations of current approaches in top-down proteomics.

Main Methods:

• TopLib employs an efficient spectral representation technique.
• Systematic evaluation of spectral representation methods and scoring functions.
• Benchmarking against conventional database search methods for top-down MS.

Main Results:

• TopLib significantly reduces database size and enhances query speed.
• Demonstrated superior performance in proteoform identification reproducibility.
• Outperformed conventional database search methods in top-down MS analysis.

Conclusions:

• TopLib effectively addresses the need for top-down spectral library tools.
• The software offers a faster and more reproducible solution for proteoform identification.
• TopLib advances the capabilities of mass spectrometry-based proteomics.