Single Cell Proteomics Pipeline Tutorial

This tutorial outlines a pipeline for differential expression analysis of single-cell proteomics data using:

1. MetaMorpheus for peptide/protein identification
2. FlashLFQ + PIP-ECHO for quantification
3. limpa for differential expression with probabilistic imputation

Navigate using the sidebar or links below:

• MetaMorpheus Setup
• Quantification with FlashLFQ + PIP-ECHO
• DEA with limpa