Issue 363: Handle Mascot Distiller settings which are problematic for Skyline

Assigned To:Guest
Opened:2014-11-09 by Brendan MacLean
Changed:2017-06-08 by Brendan MacLean
Resolved:2017-06-08 by Brendan MacLean
Resolution:Won't Fix
Closed:2017-06-08 by Brendan MacLean
2014-11-09 Brendan MacLean
Title»Handle Mascot Distiller settings which are problematic for Skyline
Assigned To»
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.
 distiller settings1.png
 distiller settings2.png

2017-06-08 Brendan MacLean
resolve as Won't Fix
Assigned»Brendan MacLean
Hasn't come up otherwise in nearly 3 years. Closing until the issue is raised by a user.

2017-06-08 Brendan MacLean
Assigned ToBrendan MacLean»Guest