Issue 51: CE Optimization mass shifts limited to m/z match tolerance

Assigned To:Guest
Opened:2011-07-07 by Brendan MacLean
Changed:2017-08-31 by Brendan MacLean
Resolved:2017-08-31 by Brendan MacLean
Closed:2017-08-31 by Brendan MacLean
2011-07-07 Brendan MacLean
Title»CE Optimization mass shifts limited to m/z match tolerance
Assigned To»Brendan MacLean
Hi Brendan,
First of all, let me thank you and your team for a great job!

I tried CE optimization for 4000 QTRAP which worked well using default settings (Step size = 1, Step count = 5). However, when I changed the settings to Step size = 1.5, Step count = 8 something wrong happened… after uploading the results, the Peak Area Graph showed just 14 columns instead of 17 and the chromatogram also displayed only 14 transitions. The data in Analyst were displayed correctly - see the attached file.

Juraj Lenco
 CE Optimization.docx

2010-06-04    Brendan
Hi Juraj,
Interesting! Thanks for posting, and sending me the sample data. I will think about how to handle this better in v0.7. For now, there is a work-around to this issue for anyone using the current public v0.6 release.

The CE optimization functionality relies on making 0.01 shifts in the product m/z values for each CE "step" value as outlined in this publication:

This means that the product m/z values for the most extreme CE values will be step-count*0.01 from the true product m/z value for your product ions. Unfortunately, the current code relies on these altered product m/z values falling within the m/z tolerance set in the Transition Settings form. We did all our testing with 5 steps, and by chance the default m/z match tolerance is 0.055. So, we never noticed this limitation.

The work-around for your data is to expand the m/z match tolerance to 0.08. You don't even have to re-import the data, just do the following in your current document:
- On the Settings menu, click Transition Settings.
- Click on the Instrument tab.
- Enter '0.08' in the M/Z match tolerance field.
- Click the OK button.

That should be it. On my machine, after I do this, I can see all the data, similar to the Analyst screenshots you sent.

Thanks again for the report. Let me know if this doesn't solve your problem for now.

Since you sent a WIFF file, I should note that most people doing a lot of CE optimization with scheduled runs have been encountering an issue with the WIFF file reader library Skyline uses to import WIFF files. ABScies assures us they are working on it, but until we get a fix, the work-around for that is to convert scheduled WIFF files to mzXML before importing. This thread explains and provides the converter, which depends on Analyst:


2015-10-16 Brendan MacLean
Issue 435 marked as duplicate of this issue.
2017-08-31 Brendan MacLean
resolve as Fixed
This has been fixed.

2017-08-31 Brendan MacLean
Assigned ToBrendan MacLean»Guest