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Bug in export with Explicit RT to waters .exp

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Bug in export with Explicit RT to waters .exp per larsson  2025-12-12 05:04
 

FIXED workaround see my reply

Hello,
I have had great use of the possibility to export methods as .exp files to Masslynx. I have used the Skyline variables to adjust the acquisition times in masslynx:

Explicit_Retention_Time
Explicit_Retention_Time_Window

Usually this has worked but I have found that sometimes I don't get the expected values in the exported file. I have therefore investigated what triggers the problem. I could se that for the same parameters in my two skyline templates with same compounds one way of formatting resulted in wrong times in exported file.
I have created two simple compound tables of same analytes just different names and would appreciate of you could take a look at this and see if it can be fixed.

  1. "MRM template to skyline CE.xlsx" the excel file that I use to insert transitions from one sheet with working format and one with the format that does not work
  2. "CE working.sky" "CE not working.sky" the skyline dokuments I used for export
  3. Masslynx EXP files has the export template and the export with correct times and the one with wrong times

Overall this has worked Fabolous so if this bug could be fixed it would be amazing!
I have tested the problem on two different computers with latest Skyline Daily installed (Skyline-daily (64-bit) 25.1.1.271 (67f3e15e7))

Regards
Per
 
 
per larsson responded:  2025-12-12 05:32

I cant edit so I will respond to myself and hopefully this can help others.

By trial and error I could narrow down the problem to the variable "MoleculeGroup". When this variable had the string SE 27:1
the export did not work, probably due to the ":" if I replaced this with CE then it works! In LipidCreator the CEs are written as SE 27:1 so I would just need to relabel this group, HURRAY!

Per
 
Nick Shulman responded:  2025-12-12 10:27

It sounds like the mass spectrometer is choking on the colon character somewhere.

In the file "CE wrong RT.exp" that you sent us, there are only 3 lines with "SE 27:1" on it:

CompoundName_1,SE_27 SE 27:1/16:0.[M+NH4]
CompoundFormula_1,SE 27:1/16:0.[M+NH4],642.618357
CompoundComment_1,SE_27:1 - Generated by Quanpedia

Usually, the way to investigate something like this would be create several different files where a different one of those colons has been replaced with a different character.
Can you figure out which of those lines should not have a colon in the molecule name?

You can edit a .exp file with any text editor including Notepad.exe.

I guess the other thing to figure out is which other characters besides a colon would also cause problems.

I am not the expert on method export, so it could be a better answer exists. But, usually, with things like this we figure out which fields cannot handle special characters and then change Skyline so that when it is outputting the method it replaces dangerous characters with safe ones such as underscore.
-- Nick
 
per larsson responded:  2025-12-15 00:15

I have identified the problem to the character ":" in the MoleculeGroup variable. So its a really simple workaround to just avoid this by replacing with_
So replace SE 27:1 with SE 27_1 and it works.

Since the LipidCreator format is probably used for many users it just good to know that for export to waters TQ with scheduled RTs then one needs to avoid certain characters.