Match MS problem

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Teun-de.Joode
Posts: 8
Joined: December 7th, 2018, 5:30 am

Match MS problem

Post by Teun-de.Joode » December 18th, 2018, 5:52 am

Hi,
When I make a template from an analysis, I used "create qualifier CLIC constraints When adding blobs to template". I flagged the "Match MS" checkbox and set the limits to min 600 and max 999. Then included identified target peaks from the blob table to the template table and saved the template. So far, so good, the target components are in the template. When I then match an other analysis against the template, a lot of targets are not found, although they are there for sure. When I select 'template mode' and right click on the blobs, I see that the Qualifier CLIC MS-Match is not between 600-999, but set to > 903 for instance (varying per blob). This has the consequence that a lot of targets are missed (nearest blob's CLIC constraint test failed). When I manually correct this value to > 600, then the targets are found. But then I have to correct all my target components in the template manually. Where is the initial CLIC MS-match (903-value from the example) coming from? It's not the library-fit score. Is there a smarter way to do this? I would like to set a general MS-matching against the template of say > 600 for all targets in one go.

qtao
Posts: 148
Joined: October 7th, 2011, 10:16 am

Re: Match MS problem

Post by qtao » December 18th, 2018, 9:54 am

Auto CLIC determines the matching threshold automatically by comparing the spectrum of a blob with its neighbors. The Min and Max settings are used to limit the range of the generated threshold. More details are here:
https://www.gcimage.com/gcxgc/usersguid ... pyTemplate

If you only want to use a constant threshold, for example, 600, you can set both Min and Max to 600.

If the template peaks are already added, you can select all of them > right click > Change Qualifier CLIC to

Code: Select all

Match("<ms>") >= 600

Teun-de.Joode
Posts: 8
Joined: December 7th, 2018, 5:30 am

Re: Match MS problem

Post by Teun-de.Joode » December 19th, 2018, 11:46 am

The first option works well: setting the upper and lower MS-match both at 600 in the 'configure' - 'template' setting.
The second option causes the retention time constrains (which were also in the qCLIC specification) being deleted.
So, the first option is the best method.

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