CsoDIAq Software for Direct Infusion Shotgun Proteome Analysis.

Area of Science:

• Proteomics
• Mass Spectrometry
• Bioinformatics

Background:

• Direct infusion shotgun proteome analysis (DISPA) offers rapid mass spectrometry-based proteomics.
• The original DISPA data analysis workflow was complex and time-consuming.
• Efficient software is needed to fully leverage DISPA's potential.

Purpose of the Study:

• To introduce CsoDIAq, a user-friendly software package for DISPA data analysis.
• To establish a complete and automated workflow for peptide and protein identification and quantification.
• To improve the speed and sensitivity of peptide identification in DISPA.

Main Methods:

• Developed CsoDIAq with a graphical user interface for automated analysis.
• Implemented algorithmic improvements for spectrum-spectrum matching, including spectra pooling.
• Introduced a novel 'match count and cosine' scoring system for improved target discrimination.
• Incorporated fragment mass tolerance correction.

Main Results:

• CsoDIAq provides a user-friendly, automated workflow for DISPA data.
• Algorithmic enhancements significantly improved peptide identification speed and sensitivity.
• The 'match count and cosine' score enhanced discrimination in target-decoy analysis.
• Fragment mass tolerance correction increased the number of identified peptides.
• CsoDIAq demonstrated superior performance compared to other spectrum-spectrum matching software when adapted for LC-MS DIA.

Conclusions:

• CsoDIAq effectively addresses the challenges of DISPA data analysis.
• The software enhances the efficiency and accuracy of proteomics studies.
• CsoDIAq shows promise for broader application in mass spectrometry-based proteomics, including LC-MS DIA.