msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease

Area of Science:

• Proteomics
• Mass Spectrometry
• Bioinformatics

Background:

• Phosphorylation site identification and quantification are crucial for phosphoproteomics experiments.
• Current data independent acquisition mass spectrometry (DIA-MS) phosphoproteomics software struggles with site-level reporting due to complex peptide-site relationships and protein isoforms.
• Existing commercial solutions offer limited functionality and basic quantification methods.

Purpose of the Study:

• To develop a robust software tool for reporting phosphosites and phosphopeptides from DIA-MS experiments.
• To enable accurate site-level quantification using the MaxLFQ method.
• To facilitate downstream data analysis and benchmarking of DIA-MS processing software.

Main Methods:

• Implementation of the "sitereport" tool within the extendable Python package "msproteomics".
• Utilizing the MaxLFQ algorithm for quantitative analysis of phosphosites.
• Command-line interface for user accessibility.

Main Results:

• Successfully developed "sitereport" for comprehensive phosphosite reporting in DIA-MS.
• Demonstrated the tool's capability for site-level data analysis and quantification.
• Enabled effective benchmarking of different DIA-MS data processing software.

Conclusions:

• "sitereport" addresses key challenges in DIA-MS phosphoproteomics data analysis.
• The tool enhances the biological interpretation of phosphoproteomics experiments by providing accurate site-level quantification.
• "sitereport" facilitates the comparison and validation of various DIA-MS processing pipelines.