MS1 filtering from hybrid MS1 (Thermo) raw files

MS1 filtering from hybrid MS1 (Thermo) raw files heusel  2015-06-25
Dear Skyline team,

I want to use Skyline MS1 filtering to do QC by quantitation of standard peptides that we inject inbetween sample runs on an LTQ Orbitrap XL.
The acquisition method cycles between FTMS1, FTMS2, ITMS1 and ITMS2 in order to also spot issues at various levels.

Now, if I do MS1 filtering with FT mass accuracies, something funny happens:
All MS1 scans (FTMS and ITMS) are considered for extraction (settings for FTMS's accuracy).
While the FTMS1 signal is stable (high mass accuracy), the ITMS1 scans yield unstable intensities (low mass accuracy, saved in centroided mode). Thus, the extracted MS1 trace looks shaky (left pane, _23), sometimes nearly normal (middle pane, _034) or partially spiky (right pane, _045). The areas are obviously distorted.

My question: Is there a trick to select a subset of MS1 scans (i.e. only the FTMS scans) for extraction to overcome this?

Thanks and best regards,
Brendan MacLean responded:  2015-06-28
Hi Moritz,
Good one. There is no simple fix for this right now, but I have added an issue to the issues list:

Hopefully we will be able to fix this in the near future.

Thanks for the clear report of the problem.