#1 duplicated fragment data

[Jesse Meyer]

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

[guoshou teo]

Hi Jesse Meyer,

Thanks for pointing this out. The latest mapDIA (v2.0.2) can handle rows with common protein/peptide/fragment names.

Thanks.