ProteoCombiner

ProteoCombiner integrates shotgun (bottom-up), middle-down, and top-down mass spectrometry data to identify and validate proteoforms and their post-translational modifications.

Key Features:

• Multi-level MS integration: Combines data from shotgun (bottom-up), middle-down, and top-down proteomics to enable comprehensive proteoform assessment.
• Multi-dataset and multi-engine support: Processes multiple experimental datasets and aggregates results from different search engines.
• Proteoform identification and validation: Identifies candidate proteoform sequences and supports their validation across complementary MS approaches.
• Proteolytic fragment characterization: Incorporates characterization of proteolytic fragments alongside intact protein analyses.
• PTM-aware comparison: Compares identified proteoforms including their post-translational modifications.
• Scalability: Applicable to large-scale datasets, with demonstrated reduction of candidate proteoforms derived from multiple search engines on an extensive Escherichia coli dataset.

Scientific Applications:

• Proteoform discovery: Comprehensive identification of intact proteoforms and sequence variants by integrating complementary MS data.
• PTM characterization: Characterization and comparison of post-translational modifications across datasets and proteoforms.
• Proteolytic fragment analysis: Analysis of proteolytic fragments generated by bottom-up and middle-down methods to inform proteoform structure.
• Cross-engine validation: Consolidation and validation of identifications obtained from multiple search engines.
• Large-scale proteomics studies: Application to extensive datasets, exemplified by analyses on Escherichia coli data.

Methodology:

Integrates outputs from shotgun (bottom-up), middle-down, and top-down mass spectrometry experiments and from multiple search engines to identify and validate proteoform sequences, and provides rapid visualization and manual comparison of proteoforms and PTMs.