Blog Archives

Quick Path to Data

Below is a short video on how to enter a batch using a template and begin to acquire.

At the beginning of  batch creation from a previously created template, containing the instrument method, processing method and desired reports.

Next you’ll see the ability to import a sample list from variety of file types and then submission of the batch.

Once submitted then user can watch the realtime trace of the collecting data segmented into a customized veiw  components and their order. While also having the capability to see the batch processing on the fly with a growing calibration curve and results.

If the video is blurry select the cog wheel in the lower right of the video window and adjust the resolution setting.

Wizards and Batches… Removing the Warlock….

In TF there are three main choices to create batches. Each of these come from historical markets that TF is serving.

To start there is a selection of the type of creation you want to see. This is located in the Configuration mode under the Optional features section.

This allows the user to choose between the LabForms style wizard and the TraceFinder Acqustion Mode.

The TraceFinder Mode was made to make a wizard like workflow that naturally fit inside the application, and had a bit more intellegent checking of criteria before submitting a batch for Acqusition. This is the reason, that there are four mode buttons when it is enabled.

The Historical LabForms wizard was left in place to allow for users of that product to transition their existing workflow into the new application of TraceFinder.

Thereby, reducing the cost of the move. This view is more of a popup window and has some unique features. Eirther one allows for templates to be made and utilized in batch creation.

Finally Batches can just be made in a regular, non-templeted fashion by using the Batch View new batch selection.

 

Method General Setting Page – Hmmm.. I missed that setting

One thing that TF has as part of its DNA is to be flexible. Method development is a complex process and we are always looking at ways to reduce the effort, but to give flexibility in our approach.

One page that has alot of power, but is over looked many times is the General Setting Page.

These settings are the general setting for properties in the method.

These settings overide the default settings in the Application and apply to the Method and consiquently all the data that is processed with the method. These settings can be changed in at both the Master and Local Method levels.

Two points to look at.

1) Mass precision – This applies to all the masses used in producing results. It does not apply to the reporting    properties of thethings like RT, or calcualted amounts.

2) Instrument Method Edit/Update – In the master method you have a copy of the selected instrument method, which the ultimate Master instrument method is located in the Xcaliber/Methods directory. When you select edit, you are editing the copy that is located in the Master Method folder. When you select update you are overwriting the changes you made in the Master Method Copy, to the ultimate Instrument Master method in the Xcaliber/Methods directory. When you use these button in the local method you edit the Local Method copy of the instrument method that was copied to the Local Method directory, and the update button copies those changes to the Master Method instrument method. This isolated the Ultimate Master instrument method from batch level changes that you may not want to be inherited by other Master Methods produced in the furture.

Now that I have a CDS, what do I do with it?

Well, the end game of the CDS is to supply information that can be used to create methods and acquire data.

Here we’ll look at the Acquisition List side of the equation.

 

Here in the data we retrieved from a CDS or PMD file is stored.

Note that PMD files do not contain all instrument information but this can be added to a CDS and then adjusted.

From here you can select the export SRM data in the Method View tab and an Xml file containing the instrument specific data will be produced.

 

If you open this file in a text editor such as note pad it will contain the information in the Acquisition List in a format that can be imported into the Instrument Method editor.

 

 

If on the Batch View section or the final page of the Acquisition Mode wizard you select Auto-TSRM update this information is passed to the mass spec at the time of acquisition. This allows the user to collect only the data needed to be processed and allows for manual updates in the batch to be automatically loaded to the mass spec at run time. This does not monitor the RT of peaks and automatically update the mass spec controller, but allows for user input to occur in on place versus having to open the instrument editor for a second adjustment.

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.

 

 

Multiplexing… The old and the new.

TF can be used with Aria MX and AriaOS.

Linked below is a guide on how to work with Aria OS and TraceFinder.

This allows the user to make use of his Aria OS system that has been certified for chemical analysis, but would want to take advantage of the superior TF quantitative properties. This relies on the fact that analysis is performed in a batch processing manner.

Aria OS TraceFinder Walkthrough

Sample List???…. Do I need a Sample List??? Yes and here’s how to import one

So the basic element of data navigation and collection is a list of samples.

This list will identify the properties of the data collected and tell the system, what to do to and the names of the files collected or to be collected.

So TF has a couple of different ways to do this.

The first and easiest is to make a template of the defined sample grid you want to use. In TraceFinder, the user can define the columns that are displayed in both the data results and sample definition grids.

In Batch View or in the sample page of the Acquisition Mode/Wizard, right click the mouse in the grid and a menu dialog that opens up.

In that dialog , select “Export to CSV”. This will make a copy of the grid and the header lables is a file that can be opened by any editing grid application. The most common is Excel, but you could open in a text editor also.

Simply, open the file and for daily use just input  sample information in the template and save as a daily/batch .csv file.

A LIMS system, can create a .csv file in this same format  or even use a bar code reader to fill in certain fields even in Excel.

Once the sample input is done save the file as .csv and close the editor.

If  the file is still open in Excel,  MS Office will not let it be used by another program so TF can’t import it until it’s closed.


Right click in the grid and select “Import Samples”.

The Dialog below opens, then select the appropriate file.

The information contained in the CSV file will be inserted into the grid either at the end of the current data or where the index indicator is if that is the option selected in the drop down list below the browse section.

There is also a xml format that can be created fromat LIMS system that can be used, or if Xcalibur has previously been in use the .sld files can be utilized also. Any sample type that TF does not recognize will be set to the Unknown Sample type.