Purpose: this algorithm calculates peak area for each peptide type (you designate) i.e. all species of H3K9 methylation in a sample then outputs individual replicates peak area. It then averages and provides standard deviation of all replicates in the same sample_group for groups of up to 3 technical/biological replicates for each peptide species i.e. H3K9me1. Furthermore, it is extensible to new modifications if you mark them in the peptide note
Input format: you must export your file to have this format from skyline as a .tsv
Library Peptides #N/A #N/A TKQTAR T[+119]K[+56]QTAR 440.237784 2 ddcc-0-1.raw 14747159552 13504712704 16763347 1242446080 precursor 8498734080 0 K4un
known possible errors:
error1: if you get an Index traceback error there may be space at the end of your outputfile.tsv, remove it... error2: adding samples that aren't present in your dataset causes errors similar to this: File "Automating_MSMS_calculations.py", line 114, in aggreg2