Export method to MassLynx 4.2 version

Export method to MassLynx 4.2 version danielacgranato  2018-11-27


I was wondering if the new version of Skyline (v.4.2) allows to export SRM methods to MassLynx version 4.2. Last year I was unable to do so and I received a response that Waters was working on making it possible. As a solution to the problem I have been exporting the method to a computer not connected to the equipment (Xevo TQ-XS) and to an older version of MassLynx (v.4.1). Do you know if it is possible now to export directly to MassLynx 4.2?

Thank you very much. Best, Daniela

Brendan MacLean responded:  2018-11-29

Hi Daniela,
I just got a similar report from a collaborator inside Waters itself pointing to the error:

System.IO.IOException: ERROR: Method not found: 'Boolean CompoundDatabaseClassLibrary.CompoundDatabase.InsertNewIonDetails(Int32, Int32, TransMode, Int32, Int32, Int32, Int32, Int32, Int32)'.

This turned out to be a compatibility issue between a DLL in MassLynx and the method export DLL Waters gives us to write their methods, which they were able to fix for their case with an updated DLL in MassLynx.

I asked what I should tell you and my contact responded:

"We looked into this earlier today and it appears that it can be case specific. The customer should probably contact her/his local support team to get an updated software version or a copy of the required library but we should probably review this on a case by case basis. I have cc-ed one of our GSS colleagues so that they are aware this as well and can provide assistance."

So, contact your Waters rep and hopefully they can get you a new version of MassLynx or a new DLL quickly.

Thanks for reporting the issue rather than just continuing to work around it. Always helps to get things moving.


hans_vissers responded:  2018-12-07

The following MassLynx 4.2 versions are supported. Please note that these are tandem/triple quadrupole instrument releases. If the instrument type is not listed, please contact the local service support organization for advise.

SCN 977 (Xevo TQ-S micro)
SCN 978 (Xevo TQ-GC)
SCN 982 (Xevo TQ-XS)
SCN 989 (Xevo TQD/SQD/3100)

During installation, also specify the instrument and the TargetLynx application manager. The former is required to create a method template and the latter to populate the newly created method with the SRM/MRM transitions.

neil macdonald responded:  2019-05-16

Please be aware that even with the above MassLynx4.2 SCNs, if MassLynx Security is installed method export from Skyline may fail, all be it with a different error message. Do not install MassLynx Security option if you intend to export methods from Skyline.

danielacgranato responded:  2020-08-27

We have a Xevo-TQXS in the laboratory, and usually we like to export the method in a computer that is not connected to the instrument (just for our convenience).
We have been using two computers for that in which we installed MassLynx older version (v.4.1). We would like to use other computers or even laptops to export the MRM method but we understand it is necessary to install MassLynx software in the same computer in which Skyline is also installed for the method to be exported correctly? Is that true and necessary?Do I always have to install the MassLynx software together with Skyline to export the method? Thank you very much. Best, Daniela

neil macdonald responded:  2020-08-28


The PC being used to export an MRM method must have both a supported version of MassLynx and a copy of the TargetLynx application manager installed, as well as Skyline. Supported MassLynx versions are listed in this article on support.waters.com
Note that only MassLynx 4.2 software change notes (SCNs) support this, not MassLynx 4.1 that you say you're using. Please contact your local Waters service organisation via iRequest for assistance with workarounds that may allow Skyline to export MRM methods using MassLynx 4.1


danielacgranato responded:  2020-09-22

Dear Neil,
Thank you for your reply. We have called our Waters MS specialist to install MassLynx 4.2 (SCN982) for us, and we followed your recommendation regarding installation in the case the computer is not connect to the instrument . Unfortunantly, we are unable to export the method. Now we are getting a different error (attached). Could you help us understand what may be going on. Thank you very much. Best, Daniela

carolina mehaffy responded:  2021-05-27

I wonder if the users reporting the issues here were able to solve the problem. We recently got the latest version of Masslynx and were no longer able to export methods. I was getting the error about the library file not been able to be found. After looking into Skyline support, I was able to find that targetlynx is also needed. Yesterday, masslynx along with targetlynx was reinstalled, but now I am getting the error "ERROR: Method not found: 'Boolean CompoundDatabaseClassLibrary.CompoundDatabase.InsertNewIonDetails(Int32, Int32, TransMode, Int32, Int32, Int32, Int32, Int32, Int32)'."

Any recommendations would be appreciated.

neil macdonald responded:  2021-05-27


The error message you're seeing is a known issue with some MassLynx SCNs. If you click on the link in my reply to Danielacgranato it takes you to a waters support article explaining which SCNs work, and which don't. If your SCN is one of those listed in that article as not working with Skyline please raise an iRequest via the Waters website mentioning the above support article. It may be possible to provide you with a solution to enable other MassLynx 4.2 SCNs to work with Skyline.