SCeptre Tutorial

Reanalysis of 8227 data from Schoof et al. 2021

Preparation

Install conda environment.yml (tested on Linux)

Content

Raw data search

• Proteome Discoverer 3.0
• scMS processing & consensus workflow
• TMTpro quantification method (with isotopic impurity correction)
• Export of results:
  • Open in PD, remove “Grouped CV” columns
  • Export as .txt (MSMS, PSMs, Proteins, Input Files)

Data preparation

• Label layout
• Sample layout
• Sort layout
• File sample mapping
• Plate layout mapping
• FACS data

FACS data preparation

• .fcs files
• Flowkit notebook
• Copy facs_data to data

SCeptre & Scanpy analysis

• See notebook