Hello,
I'm having some issues getting a "duplicated fragment data" error when trying to run fragment-level analysis on PTM peptides. In some cases where I have multiple precursor charge states for a peptide, I do measure the same m/z fragment for that peptide from different precursors. mapDIA doesn't like this so I tried to trick it by appending the integer precursor charge state to that fragment m/z value, and while this works for one file, I'm stuck on another file where I can't find the duplicated fragment mass. It doesn't seem like the actual value in frag m/z matters to mapDIA, so I might just replace that column with a series of real numbers. Would that be OK until you can fix this?
Thanks,
Jesse
Hi Jesse Meyer,
Thanks for pointing this out. The latest mapDIA (v2.0.2) can handle rows with common protein/peptide/fragment names.
Thanks.