You can use the Phosphoproteomics module to upload phosphopeptide-level data. This module is designed to bridge site-level quantitative changes with pathway- and network-level mechanisms. It accepts phosphosite-centric quantitative inputs alongside sample metadata. The workflow mirrors the global proteomics module including QC, normalization, and differential analysis – but with an automated step to map phosphosite identifiers to parent proteins.
The workflow includes:
- Data upload with site-level or peptide-level quantification;
- QC and normalization of phosphopeptide intensities;
- Differential phosphorylation analysis;
- Kinase-Substrate Enrichment Analysis (KSEA) to identify active kinases;
- Kinase network visualization showing regulatory relationships;
- Pathway enrichment of differentially phosphorylated sites.