SPACEPro: A Software Tool for Analysis of Protein Sample Cleavage for Tandem Mass Spectrometry

The efficiency of shotgun proteomic analysis is dependent on the reproducibility of the peptide cleavage process during sample preparation. To generate rapid and useful metrics for peptide cleavage efficiency, as in enzymatic or chemical cleavage, SPACEPro was developed to evaluate efficiency and reproducibility of protein cleavage in peptide samples following data-dependent analysis by mass spectrometry. SPACEPro analyzes samples at the peptide-spectrum match (PSM), peptide, and protein levels to provide a comprehensive representation of the overall sample processing to peptides. All output is provided in human-readable text and JSON files that can be further processed to assess the cleavage efficiency on proteins within the sample. SPACEPro provides a snapshot of the protein cleavage efficiency through very minimal effort so that the user is informed of the quality of the sample processing efficiency and can accordingly develop protocols to improve the initial sample preparation for subsequent analyses.

Automated summary

SPACEPro is a tool developed to evaluate the efficiency and reproducibility of protein cleavage in peptide samples, providing comprehensive information on sample processing to peptides at the PSM, peptide, and protein levels. It helps users understand the quality of sample processing efficiency and develop protocols for improvement with minimal effort.