Skyline command runner fails to write the exp file.

Skyline command runner fails to write the exp file. shridevi patil  2021-06-17

Hello ,

We are working on tool which automates the manual process of creating MRM method using skyline and MassLynx.
we are using Water's Xevo TQ S instrument.
test was to find the min dwell supported to create write MRM methods.
Attaching the file where command passed to Skyline is shown and output of command runner also been provided.
Does Command runner splits the method into multiple experiment files?
Kindly suggest if anything is wrong with using command runner.

Thank you

Brendan MacLean responded:  2021-06-17

I would agree that the error messages and proposed solutions you are seeing are a bit of jumble.

Error: The file C:\Users\conspai\AppData\Local\Temp\biw5zqm5\OptimizeCe_105Trans.exp could not be saved. Check that the specified file directory exists and is writeable.
Failed to schedule the following peptides with the current settings:

R.HLHFTLVK.D [34, 41] - 42 transitions
R.DYYFALAHTVR.D [50, 60] - 42 transitions
K.ARPEFTLPVHFYGR.V [192, 205] - 42 transitions
R.VLYPNDNFFEGK.E [278, 289] - 42 transitions
R.HLQIIYEINQR.F [399, 409] - 42 transitions
K.DFYELEPHK.F [470, 478] - 42 transitions
K.VFADYEEYVK.C [773, 782] - 42 transitions

Check max concurrent transitions count and optimization step count.

But, I think this final message is the one to focus on, since your command-line contains the argument "--exp-max-trans=40". That means that you are not allowing for enough transitions, since these peptides need 42. Try increasing this number to 42 or more to see if that removes these error messages.