Comments need to be deleted

Comments need to be deleted mattkarasu  2020-09-11

When exporting an MS Method for our Waters Xevo TQ from Skyline it seems to be creating an .exp file with comments added to every line of the MRM table. Oddly, there seem to be two different comments though? One mentioning Quanpedia and the other mentioning VerifyESkylinLibrary.

It is also worth pointing out that the output .exp file has these comments present even when opened as a raw text file, so I know it is not something our MS File Editor is adding or misinterpreting.

Brian Pratt responded:  2020-09-14

Are these perhaps contained in the template file you're providing to Skyline?

Thanks for using the Skyline support board,

Brian Pratt

Brendan MacLean responded:  2020-09-14

I doubt our code has any control over this. We are using a DLL (VerifyESkyline.dll) supplied by Waters to write the exported method. I have notified our contacts at Waters. Hopefully, we will hear back soon.

Brendan MacLean responded:  2020-09-15

So, it is the Waters VerifyESkyline.dll which does this, but our Waters contacts point out that it has always been like this with those exact comments being used since 2013. It was apparently implemented like this to get around a limitation in the Waters Qanpedia software.

Unless this is causing some sort of blocking issue, I doubt we can get Waters to change it now.


mattkarasu responded:  2020-09-15

Our issue with the comments is that it only allows the first five transitions to run. So if we want to do method development of 32 transitions per peptide and running them across 20 methods, it can take two hours to go through all comments and delete them. Deleting them allows all transitions to be scanned for. The first five comments in the editing page refer to quanpedia. The rest are appended by VerifyESkyline preventing them from being run.

Christopher Johnstone responded:  2020-09-16

Please raise an iRequest via and ask your local Waters service organisation to pass details of the problem to Global Service Support, including the MassLynx SCN number installed, whether this has always been an issue or whether it’s only started to occur recently.