What does the column GlyFrag mean?
Opened this issue · 5 comments
I am checking the assignment of pGlyco for my glycopeptide. I am a bit confused by the GlyFrag column in the results file. What exactly do the values mean? I see for example the 3 3 0 0 0 in the list, but I cannot find any signal in my raw data (also not in gLabel data) that would match a B (oxonium) or Y ion matching that composition. Can you please explain?
@abondt Dear sir, the glycans in the GlyFrag column are the theoretical Y fragment ions, not the matched ones. If you need to access the matched fragments, use gLabel.
@abondt You are really a very important user of pGlyco. We will release a new version of pGlyco in a few days with some bug fixed, would you please tell me you email, or you can email me. And I will email you back once the new version is ready.
@abondt Dear sir, the glycans in the GlyFrag column are the theoretical Y fragment ions, not the matched ones. If you need to access the matched fragments, use gLabel.
Dear Jalew,
It would be really great if pGlyco could output the values of the actually used fragments in the result files. It should be in the data somewhere, since gLabel can figure out which fragments to annotate. To have the actually used fragment ions (either their m/z value or their composition) in the output file would really give it another advantage over Byonic and other software. I am actually not sure what the purpose of the current output column is...
Ideally there would be two columns then: one with the oxonium ions and one with the Y ions (pep+composition).
@abondt If you need the information of matched fragmens, use gLabel, the batch mode. It will output a matched file in your chosen folder. Because gLabel will do the online match for pGlyco result files.
Configure the glabel.gconf in the bin folder:
glycan_type = N
result_has_fragments = 1
plot_decoy_peptide = 0
plot_max_glycan_FDR = 1.0
plot_max_peptide_FDR = 1.0
plot_max_total_FDR = 1.0
plot_min_glycan_score = 0
plot_min_peptide_score = 0
plot_min_total_score = 0.0
is_batch_plot = 1
glyco_as_text = 0
Set “is_batch_plot = 0” if you do not need the plotted image.