Hi Per,
Looking at our code, it looks as though we do not presently pass an ion mode to the DLL supplied to use by Waters for method export:

VerifyESkyline.OperationManager.GenerateMRMMethodFromString(methodTranList.TransitionList,
methodTranList.OutputMethod,
TemplateMethod,
InstrumentType,
RTWindow,
DwellMode,
DwellTime);

The TransitionList argument is a text string in the same format you would get out of File > Export > Transition List which does not include an ion mode specifier.

I am curious whether you might somehow supply Skyline with a template method that implements the ion mode? Are you looking to create a mixed mode method with both positive and negative? Perhaps if you want only negative, you can specify that somehow in the template and the VerifyESkyline.dll would preserve it?

I have begun a discussion with Waters about whether we might be able to support this with the current VerifyESkyline.dll or wether we would need a new DLL to be able to specify ion mode individually for each transition.

Thanks for bringing this up. Sorry it doesn't seem to be working already.

--Brendan

Hi, Big thanks for investigating. The masslynx template i use is the .exp i used originaly to run the lipids. I tried to recreate the method from *.csv to skyline to masslynx. So the exp template have es+ and es-. I could not find any additional column in skyline import more than charge for setting ion mode. I want to run both es+ and es-. This is part of why it is so vital to get the rt windows right so that I can avoid polarity switch in the mrm cycle. Some of my lipids are close so i need to really time this right. I also tested the .exp file supplied in one of your tutorials and mrms created from lipidcreator plugin. Exported methods are always es+ in masslynx. Let me know any suggestions you i can test to assist in troublshooting.

Can you give us an example of a text file transition list that contains the information you want and which is easy for you to load into MassLynx? This would ideally influence how we implement File > Export > Transition List, and what we send to VerifyESkyline.dll to create the .exp file.

I have attached what Nick sent me from a File > Export > Transition List for your targets. This is essentially what we are currently sending to VerifyESkyline.dll (from Waters) to create the .exp file. Yes, it has no polarity information. So, I think a good place to start is to update this format to contain a polarity column. I am just not sure where it should go in this format or what its column header name should be.

Thanks for your feedback.

Hi,
An example import .csv file is uploaded I used the molecule setting for the import as my MRMs are lipids so columns heading are a little different, you can see them in the .csv file I uploaded.
I have setup and experiment where I have optimized the retention time window for each MRM for as efficient acquisition as possible to maximize dwell times. Some MRM windows are a lite bit wider and some are a bit shorter. If there is one MRM in ES+ and the next is ES- i will try to time it so the MRM don't overlap. It is important for me to be able to choose my selected retention time windows in an easy way. This was my issue with waters own Quanpedia software that any automatic update feature of retention time resets my adjusted retention time windows to the same value for all MRMs.

For learning the software, I made a simple list of just a few standards for testing. I used an *.exp file created for the data acquisition in masslynx and write the same parameters into the .csv file in the Skyline format (molecule setting was used not peptide). I can then import .csv file into skyline and it seems to get everything right (MS1/MS2/CV/CE/Charge/RT/RT_window) are all registered. Acquired RAW file seems to work well I get all my MRMs into Skyline as expected with correct RT and RT windows and charge (this I also uploaded). As far as I see import to skyline work fine it shows correct RT and RT_window for imported data and in the preview for the export .

The problem is that values are not exported to the *.exp file. Only MS1/MS2/CE/CV is exhorted not the polarity(charge) or the retention time window. To manually add these for a large nr of MRM is not what I want to do.

From the values in Skyline of charge RT and RT_window the following settings need to be transferred to the waters instrument *.exp file
FunctionIonMode,ES Mode
FunctionPolarity,Positive
(in skyline i charge 1 means it should be positive and -1 it should be negative)
FunctionStartTime(min),0.5
FunctionEndTime(min),3
(from skyline RT and RT_window the start time and end time can be extracted)

I am using a very simple method to test the import and export but for my real methods I need to get this working without manually adjusting polarity and RT windows for all exported methods. Given the tutorials have scheduled methods exported I assume it has worked at some point. Either I am doing it wrong or the function needs to be fixed. Lets see if we can figure it out. Has anyone with a waters xevo tqxs recently been able to export a scheduled MRM method?

It is a bit annoying that the waters .exp file is composed as a text file an not as variable table that would be very easy to import and export to. Given I have not made any error I hope that Skyline and Waters can manage a way to export the required data from skyline to a .exp file that is working with masslynx and Xevo TQXS. I will be happy to help in any way I can but unfortunately I don't know much about programming and have just started to work with skyline. Since there is just a limited nr of parameters needed to be modified to export new MRM exp I am hoping that it can be solved.

Funktion#
*Compound Name
*precursor
*product
*cv
*ce
*RT_start
*RT_end

UPDATE: Using the everify.exp template from skyline tutorial I can export shedulted MRM but only if I use 1 min retention time window.

Regards,
Per