jlacava10th January 2020 at 11:13am
- uses MaxQuant (MQ) peptides.txt file
- 0, 1, 2 missed cleavages
- will want to see most have 0 missed cleaveges, with some 1 missed cleavages and few to no 2 missed cleavages etc. This will depend on how many missed cleavages the MQ search was permitted to explore. See MQ for suggested default settings. This is a basic QualityControl on the tryptic digest.
- We discussed test: peptide must end in K/R and have N+1 K/Rs where N is the number of missed cleavages. I.e. 0 missed has 1 K/R at the C-termus, 1 missed has 1 K/R at the C-termus and 1 K/R elsewhere.
- which peptides are K cleavages (K C-term, can have K/R missed cleavage)
- which peptides are R cleavages (R C-term, can have K/R missed cleavage)
- this feeds into %H incorporation assessment