Hi,

I did TPP tandem search with the following parameters,

modification mass 57.021...@c
potential modification mass 15.994...@m
potential modification mass 15.994...@m,0.9...@n,0.9...@q

However, many warnings popped up when i convert the .tandem file
to .pep.xml file.
i.e.
Tandem2XML.exe ./$x.tandem ./$x.tandem.pep.xml
WARNING: Multiple variable modifications on Q for scan 11685.
WARNING: Multiple variable modifications on Q for scan 11257.
WARNING: Multiple variable modifications on Q for scan 11086.
WARNING: Multiple variable modifications on Q for scan 11062.
....
....
etc.

There are 100+ such WARNINGS.

I am very grateful if any expert can point it out to me what is the
problem?

-Thanks in advance

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