Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus...

Area of Science:

• Proteomics
• Computational Biology
• Mass Spectrometry

Background:

• Label-free quantitative mass spectrometry (MS) using Normalized Spectral Abundance Factor (NSAF) is a key technique for determining relative protein abundance.
• Existing methods may have limitations in dynamic range, data processing, or speed.

Purpose of the Study:

• To introduce Morpheus Spectral Counter (MSpC), the first computational tool designed to directly calculate NSAF values.
• To provide an accessible and efficient software solution for NSAF-based protein quantification.

Main Methods:

• MSpC processes output from the Morpheus peptide-MS/MS matching engine.
• The software calculates both distributed and unique NSAF values.
• It features a user-friendly graphic interface and is compatible with high-resolution accurate-mass spectrometry data.

Main Results:

• MSpC enables direct calculation of NSAF values, offering advantages over other quantification methods like isobaric tags.
• Protein concentration determinations using MSpC showed linearity over several orders of magnitude.
• Validation was performed using high-mass accuracy datasets from PRIDE and spiked cell extracts.

Conclusions:

• MSpC is a novel, open-source computational tool for robust and efficient NSAF-based protein quantification.
• The software facilitates detailed proteomic analyses, including protein families and isoforms/proteoforms.
• MSpC enhances the utility of label-free quantitative MS for biological research.