MSpC

MSpC computes Normalized Spectral Abundance Factor (NSAF) values from Morpheus peptide–MS/MS search outputs to determine relative protein abundances in quantitative proteomics.

Key Features:

• Direct NSAF calculation: Computes Normalized Spectral Abundance Factor (NSAF) values from Morpheus peptide–MS/MS outputs, including both distributed and unique NSAF metrics.
• Compatibility with high-resolution accurate-mass data: Operates on Morpheus outputs generated from high-resolution accurate-mass instruments.
• Increased dynamic range: NSAF-based quantification provides greater dynamic range compared to isobaric tag–based methods.
• MS1-independent quantification: Relies on MS/MS spectral counts and NSAF, obviating the need to align and re-extract MS1 peaks.
• Computational speed: NSAF computation from Morpheus outputs enables faster analysis compared to workflows requiring MS1 re-extraction.
• Quantitative linearity and validation: Demonstrated linear determination of protein concentrations over several orders of magnitude using high-mass accuracy datasets from PRIDE and datasets spiked with Arabidopsis 20S proteasomes.

Scientific Applications:

• Comparative proteomics: Relative quantification of proteins across samples using NSAF-based spectral counting.
• Biomarker discovery: Identification of proteins with differential abundance supported by NSAF estimates.
• Functional genomics: Estimation of protein abundance to correlate proteomic data with gene function and expression studies.

Methodology:

Calculates NSAF values (both distributed and unique) directly from Morpheus peptide–MS/MS matching outputs.