Exporting scheduled method for collision energy optimisation

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Exporting scheduled method for collision energy optimisation matthew daly  2022-10-17 08:19
 

Hi,

I am having difficulty exporting a scheduled method for collision energy optimisation.

My colleagues ran a panel of peptides and I have the RT for these peptides, however I don't have the .raw files. I have pasted the results into the iRT calculator.

I am trying to run these same peptides using the same chromatography on a different platform, so I need to optimise the CE and as I am sample limited would like to do it in as few injections as possible. When I try to export a scheduled method optimising CE I get the error "Retention time predictor is unable to autocalculate a regression". Is it possible to export a method for peptides that you've used to train the iRT calculator?

Many thanks
Matt

 
 
Kaipo Tamura responded:  2022-10-17 09:42

Hi Matt,
Would you mind sharing the document here (File > Share...) so I could take a look?

Thanks,
Kaipo

 
matthew daly responded:  2022-10-18 01:31

Hi Kaipo

I've attached the document. The peptides in the target list are those I used to train the iRT, and also the peptides I am trying to generate a CE optimisation method for.

Thanks
Matt

 
Kaipo Tamura responded:  2022-10-18 11:52

Hi Matt,

In this case since you can't import results (since you don't have the raw files), one thing you can do is set explicit retention times. One way to do this is through the document grid (View > Document Grid) and creating a new report (Reports > Manage Reports... > Add...) with the Peptide Sequence column and the Explicit Retention Time column. Then, paste all the retention times into the Explicit Retention Time column (make sure the peptides are in the same order as the retention times being pasted).

Once the peptides have explicit retention times, you can export the scheduled method. Hope that helps - let me know if it solves the problem for you.

Thanks,
Kaipo

 
matthew daly responded:  2022-10-19 03:58

Hi Kaipo

Thanks for the advice.

I can now export a scheduled method, however the time windows in the exported method are 0. I have tried adding the "Explicit Retention Time Window" column to the report also, which hasn't seemed to help.

I am exporting a Waters method, not sure if that has an impact on the method scheduling.

Thanks
Matt

 
Kaipo Tamura responded:  2022-10-19 11:15

Hi Matt,

Setting the Explicit Retention Time Window column as you did should work, or otherwise setting the time window under Peptide Settings > Prediction.
Which specific Waters instrument are you attempting to export a method for (the name listed in the "Instrument type" dropdown on the export method dialog)? Would you mind also re-sharing the updated document with the explicit retention times and windows set?

Thanks,
Kaipo

 
matthew daly responded:  2022-10-19 12:18

Hi Kaipo

I am using the Waters Xevo TQ option for the method export, with a view to run it on a TQ-XS. The template file I specify was generated for a TQ-XS.

I've attached the updated document.

Thanks for your help,
Matt

 
Kaipo Tamura responded:  2022-10-19 14:22

Hi Matt,

Everything looks correct with the document. I will contact Waters about this issue and keep you updated.

Thanks,
Kaipo

 
matthew daly responded:  2022-10-26 02:17

Hi Kaipo

Just wondered if there was any update on this?

Thanks
Matt

 
Kaipo Tamura responded:  2022-10-26 10:53

Hi Matt,
Unfortunately not yet - I've just sent them another email, so hopefully we will get an update soon.

Thanks,
Kaipo

 
Kaipo Tamura responded:  2022-11-01 10:11

Hi Matt,
I just heard back from Waters, they tested and it seems to be working with Skyline-daily and MassLynx 4.2 SCN982. Would you mind checking the SCN you are using?

Thanks,
Kaipo

 
Brendan MacLean responded:  2022-11-01 12:18

Our Waters contact has responded:

"I have tried to reproduce the error, but everything seems to work as expected at my end using Skyline-daily and ML4.2 SCN982."

"Both ‘standard’ (top) and ‘scheduled’ (bottom) were tested."

"Do we know which SCN the customer is using?"

If you can supply the requested information, we can pass it along.

 
matthew daly responded:  2022-11-02 09:25

Hi both

Thanks for the update. I'm using the most recent version of Skyline (not Skyline daily), and my MassLynx version is V4.2 SCN1012.

Thanks
Matt

 
Kaipo Tamura responded:  2022-11-03 11:17

Hi Matt,

It sounds like it should be working with that version of the software. Waters has suggested submitting an iRequest to their support team:

It also with that particular SCN using both Skyline daily and v22.2. I am attaching the relevant created methods in txt format (to be converted back to .exp for MassLynx editing).

There may be something specific to the customer’s setup that we are not capturing so it is suggested that the customer raises an iRequest to ensure that the support request is recorded in our support systems and the customer can be contacted.

Thanks,
Kaipo