Issue 137: export of scheduled methods to waters xevo

Assigned To:Guest
Opened:2012-01-17 by Alex Jones
Changed:2012-01-18 by Brendan MacLean
Resolved:2012-01-18 by Brendan MacLean
Resolution:By Design
Closed:2012-01-18 by Brendan MacLean
2012-01-17 Alex Jones
Title»export of scheduled methods to waters xevo
Assigned To»Brendan MacLean
Hi Brendan, My methods export Ok to my Xevo except that when I choose 'scheduled' I don't get time windows in the method, just a single time point (see attached screen shot). My chromatography is good, but not that good! I have tried with both the 'use average' and 'from replicate' option with same result. Thanks for your help, Alex

2012-01-17 Brendan MacLean
Hi Alex,
Can you tell me if this also happens when you use File / Export / Transition List instead of File / Export / Method? This will give me a better idea of where to start looking. Thanks.


2012-01-18 Alex Jones
Hi Alex,
Would you mind posting this to the original support thread? It may help someone else, if they run across this error.

Thanks. Glad to hear you solved the problem.

On Wed, Jan 18, 2012 at 4:19 AM, Alex Jones wrote:

Hi Brendan,
Thanks for these tips which have helped me solve the problem! My method did have times in both of the window areas you indicated and I played around not only as you suggested but with various combinations from there. Eventually I decided the error was probably with the Waters method generation code.
I was using a server environment to run these programs and my installation of MassLynx was not very happy – it ran but would frequently throw various Windows related errors. As I have had similar problems with other programs I installed everything on a local PC – and got no more errors from MassLynx – and then the time windows were accepted into my methods generated by Skyline.
Thank you very much for your prompt help that let me work around an installation error at my end.
Best regards, Alex
From: Brendan MacLean
Sent: 17 January 2012 19:40
To: Alex Jones (TSL)
Subject: Re: Issue #137, "export of scheduled methods to waters xevo," has been updated
Hi Alex,
Interesting. I am using MassLynx 4.1 also, but I had not yet noticed the start and end times in that form. Waters did suggest that I write transition lists with only a single retention time, and now that I look at the method export code, it also uses a center point value, and a window width, rather than start end end, like Thermo, and as the UI you highlighted would suggest.
Skyline has two places where that window width might be coming from:
- Settings > Peptide Settings / Prediction tab, check Use measured retention times when present, and check the Time window field
- Settings > Peptide Settings / Prediction tab, Retention time equation, if you have one of these and are not using measured retention times, then the window could be coming from the equation.
Your results would seem to indicate either a bug in the Waters method generation code, or that your window value is in fact zero.
Let me know what you see.
On Tue, Jan 17, 2012 at 8:35 AM, Alex Jones wrote:
Hi Brendan,
Ok, I am wondering if this is a version change (I am using Mass lynx 1.4) and waters made a big recently of ‘now we can schedule’. The current version clearly has a start and stop time for each precursor, I attach a image of the method for just one precursor and the time frames are on the left hand side. Opening the method file in a browser also shows a line start/stop in each precursor (that one I changed by hand). So at the moment to use scheduled files from skyline I go into the window for each precursor and change the start/ stop….functional but tedious. I can’t see a way to set a global window in the Waters method.
At least I know that I am not getting an option wrong in my skyline file. I will ask some colleagues and have a look round more. As you say – if it works for other people then I should be able to get it going.
Thanks for your quick replies 
From: Brendan MacLean
Sent: 17 January 2012 15:12
To: Alex Jones (TSL)
Subject: Re: Issue #137, "export of scheduled methods to waters xevo," has been updated
Hi Alex,
Hmm... True. That is all that the code writes, and all that Waters suggested I write. Also when I look at the code, I find that Waters instruments are included in a method IsSingleWindowInstrumentType(). That leads me to believe that you need to set the window size in your template and that Skyline has no way of setting it otherwise. This is true for both AB SCIEX and Waters instruments, where Agilent and Thermo instruments allow window sized to be set individually for each transition.
Quite a few other people have done this successfully. Have a look. Let me know what you find.
On Tue, Jan 17, 2012 at 7:01 AM, Alex Jones wrote:
Hi Brendan,

I get just a single column for the precursor RT in the attached transition list.

Thanks Alex


2012-01-18 Brendan MacLean
resolve as By Design
Assigned ToBrendan MacLean»Alex Jones
I am not able to fix this issue with Waters software, but I have reported it to my contacts at Waters.

2012-01-18 Brendan MacLean
Assigned ToAlex Jones»Guest