Using the Compound Data Store – Variant on a Theme

The CDS once created can be used to create methods in a more simplified way.

Again the CDS is a way to use knowledge you have previously collected about a compound and it analytical conditions.

First in the Method Development section select “Create new method” from the Method view subsection.

Here you can see the select compounds from CDS is enabled.

One thing to note down: only one CDS can be open at one time in TF 2.1, which ever CDs is loaded in memory in the Configuration section is the one used. If you want to use a different CDS, load that one into memory inthe Configuration section.

Next you can select compound from the CDS to be used in a new Master Method.

You have the choice to select all, highlight a few and deselect them or pick and choose. Once you have made your selections click the “Apply”button.

This will create a new Master Method.

Once created you will need to save it witha new name. The data ported over consist of acquistion related feilds in the Acqusition List section, which we will discuss later this week, and compound processing basic data (ie. compound name, retention time, detection window, etc..) At this time you will notice the little red balls next to the row number. If you scroll over this it will tell you that the compound does not have a filter string assigned.

This is important because at Thermo we need a filter string assignment to tease the data about the peak out of the RAWFILE. From the Master Method file menu item select “Associate new raw data file”

By selecting a file, that has data for the compounds you previously selected fromthe CDS, and enabling the “Update scan filters for all peaks” button; TF will use the data in the Acqusition list to automatically update the filter selection box for each peak.

Any conflicts and the red ball will remain, to let you know that you must manually select a filter for that peak. This is where the SRM, XIC and SIM experiment type come into play. It specifies which type of filter to select from as in each method you can have blended experiment types.

Tune in next time for “AUTO-SRM UPDATE”

About humphrjk

Product Manager for Analytical Software for Chemist. Analytical Chemist, Mass Spectrometry Scoutmaster Troop 4277 Skipper Ship 4277 Vice Commodore Texas Sea Scouts

Posted on August 7, 2012, in General Use, Method Development. Bookmark the permalink. Leave a comment.

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