A poorly organized repository for mass spectrometry analysis for Physical Underpinnings of Biological Systems (PUBS) 2015 at UCSF, group E. Poss — PyND. Authors: Douglas Myers-Turnbull, Yuliya Birman, Nick Rettko, and Paul Thomas.
This code and analysis was hacky, poorly organized, and ultimately not used.
See https://github.com/tlnagy/seq-analysis for sequencing data analysis, which was used.
The code (.py and .ipynb files) is licensed under the Apache License, Version 2.0.
All files:
- Parse (read in tab-separated columns, split some columns by "i" and "|")
- Normalize (filter out non-ubiquitin proteins/peptides)
- When filtering out, might want to use 'REV' peptides and 'contaminant' fields and 'Posterior Error Probability'
First data file:
- Take note of abundance of kinases; also: make sure ALK1 isn't there for knockout
- Identify which peptides are phosphorylated (directly in file)
- Isolate the serine-threonine ALK1 (not the ALK1 that phosphorylates tyrosine)
- Try to find ALK1 binding motif?
- Analyze peptide/protein abundance
- Make list of sites that we know are not phosphorylated (or, at least, there is a high probability that they're not phosphorylated). Also, somehow account for sites that COULD be phosphorylated
Going through the table:
(Mostly use Evidence table. For Summary, just use "peaks" data. For Experiment, look at PEP . Don't need to do much with Peptides. For Modifications)