From David Creasy:

We mentioned two features in Distiller that could cause problems for Skyline:

1. The option to save the Fragment ions in MS/MS peak lists as MH+ values will presumably cause problems for Skyline:


[See image 1 attached]


2. The processing option to use the precursor charge as the maximum charge allowed for fragment ions will cause multiple peak lists to be written out for each ms-ms spectrum:

[See image 2 attached]

This can also be caused by clearing the option for a "Single peak list for multiple precursor charges" above. This shouldn't cause a problem for Skyline, but you will see the same (or nearly the same) spectrum appear multiple times. You can detect this because the same TITLE= line will appear multiple time. The difference in the spectra might be for example where a 3+ fragment is excluded from a spectrum where the pre-cursor is 2+

The value:
_MSMS.UsePrecursorAsMaxCharge = 0
appears near the top of the MGF file.

Unfortunately, the formatting options for "Single peak list for multiple precursor charges" and "Output as MH+" don't currently appear in the mgf file. We've raised a bug report and it should be fixed in the next Distiller version. Sorry about that - we'll let you know as soon as it's fixed.

Hasn't come up otherwise in nearly 3 years. Closing until the issue is raised by a user.