Thanks for waiting for these changes. I added 'Methyl@E' to psm_reader.yaml to test that fragment m/z calculations are correct for c-term mods. It can be deleted, but I am wondering why only a handful of PTMs are added, rather than putting all the entries in modification.tsv into it?
Tested using pepxml files generated from msfragger search of data from PXD014879, including c-terminal methyl as a variable mod. Ran code below from Python terminal in PyCharm IDE to ensure it works:
from alphabase.psm_reader import *from alphabase.peptide import *
Thanks for waiting for these changes. I added 'Methyl@E' to psm_reader.yaml to test that fragment m/z calculations are correct for c-term mods. It can be deleted, but I am wondering why only a handful of PTMs are added, rather than putting all the entries in modification.tsv into it?
Tested using pepxml files generated from msfragger search of data from PXD014879, including c-terminal methyl as a variable mod. Ran code below from Python terminal in PyCharm IDE to ensure it works:
from alphabase.psm_reader import *from alphabase.peptide import *psm_reader = psm_reader_provider.get_reader("msfragger_pepxml")msf_df = psm_reader.import_file("20190131_QExHFX3_Ogris_MFPL_gel_PP2A_EV_90p.pepXML")methyl_df = msf_df[msf_df['mods'].str.contains('Methyl')].copy()fragment.create_fragment_mz_dataframe_by_sort_precursor(methyl_df, ['b_z1', 'y_z1', 'b_z2', 'y_z2', 'b_modloss_z1', 'y_modloss_z1', 'b_modloss_z2', 'y_modloss_z2'])