A large-scale spectral counting data analysis using PAW pipeline, edgeR, R, and Jupyter notebooks.

The data is from a recent study where human retinal and choroidal endothelial cells were compared. The study was 5 donor eyes where retinal and choroidal cells were collected and cultured in a paired design. The cell lysates from each of the 10 cell cultures were profiled using large-scale separations with a fast-scanning linear ion trap. There were about half a million MS2 scans per sample for a dataset size of a little over 5 million. The data are available at the PRIDE archive (PXD005972).

There is a direct link to the rendered notebook HTML file.

A few relevant files from the archive are present in the repository:

• analysis_overview.pptx - summary of the data analysis steps
• quant_protein_summary_8.txt - a grouped protein summary file
• edgeR_input.txt - data extracted from results file for edgeR analysis
• edgeR_results.txt - statistical testing results
• HCEC_HREC_quant_protein_summary_sprot.xlsx - final summary sheet
  • proteomics data from quant_protein_summary_8.txt
  • statistical results from edgeR
  • extra protein annotations