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