Monthly Archives: August 2012

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”

Compound Data Store or Compound Database – Kinda the same thing….

TF has the concept of bring in a data you know about compounds and storing it for later use.

This we call the Compound Data Store (CDS), but what’s in a name… Its a an XML file that contains information about the compound.

The picture above shows this data in excel. It contains information like the compound name, experiment type, collicion energy, retention time, fragments relationships.

Attached here is a copy of the csv template TEMPLATE.

This information can be edited in excel and uploaded into TF to add to a database or to alter the data base. The changes will be reflected in the TF CDS module.

Once the data is in the CDS, a method developer can utilize it to create processing methods which in turn can be used in syncing acquistion methods in the Master Method.

A blog post to come later this week will highlight the use of the information in the Auto-SRM feature.

A quick note is that the CDS is not automatically turned on at installation.

The user will have to configure the option and restart TF to take advantage of this feature.



“Got Data?” – New Version on the way – TF 2.1

We are glad to announce that TraceFinder 2.1 is being cut to disks this week and will be on the shelves shortly.

The version has many “bug” fixes and performance improvements, but the BIGGEST feature is the ability to be run  on any detector Thermo supports. So if yo have a QExactive or a FID standalone GC, its supported. As well as, blended configurations.

So “Got Data?” we have a tool for you.

Plus soon to be published iBook for getting started with TF. “The Guru Guide”, written by the product manager for TraceFinder.

Remember if you have a question please fill out the form on the “Ask A Guru” tab. That message goes directly to the product manager or one of the support staff.