Blog Archives

Making changes in to the multiple peaks in a compound (Answer to a “Ask A Guru” question)

There are times that a chemist may make a method from a PMD file or from CDS, and things need to be changed.

An istance would be swapping an existing quan peak with its confirming peak, or removing a confirming peak.

These changes while seemingly trivial can be a hassel if you have to do many of them. So the TF team has given these options as right click contect menus to make it easier to perfrom these functions.

Watch the video below to get an idea of how to use these tools.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

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.

 

 

The Sum of All Peaks

One of the key features of TF is the use of a compound being composed of multiple components.

So the gist, of it is that a specified compound can consist of up to 6 quantitative peaks, each of those can have up to 10 confirming ion ratio peaks.

So A compound can consist of up to 66 chromatographic peaks when using mass spectral data.

This means that you can visualize under the compound name quantitative peaks and their associated ion ratio confirming ions.

 

The compound is composed of these multiple peaks, which have summed areas. But they can be visualized separately. The total response of adding all the, lets say peak areas, is the total response of the compound. And by using the multiple quan peak feature, these chromatographic peaks don’t have to be at the same retention time. So if you were doing a chiral separation but wanted the total response, you would just make them individual quan peaks under the compound.

 

Now if you have coeluting peaks and want one big peak to represent your compound, then you can use the signal pane’s mass grid to accomplich this type of mass intergration.

All the responses are summed, but no individual visualizations.