Category Archives: Instrument Methods

TraceFinder 3.2 – New Instrument Method Managed Location

In previous versions of TraceFinder, the Instrument Method utilized for data collection was required to belong in the c:/Xcalibur/Methods directory folder.

In TraceFinder 3.2, the new location for the Instrument Methods is located under the C:/TraceFinderData/Instrument Methods directory folder.

Since TF has is a “managed systems”, meaning that we provide the unique capability of synced updates and other functions the Instrument Method, we have a need to know where the method is at all times.

Therefore, the use of the managed directory is a requirement. By moving the Instrument Method for TraceFinder into it’s unique folder, it allows you the freedom to use any folder for method development purposes.

When you have the final version for use in data collection simply save the “.meth” file into the C:\TraceFinderData\Instrument Methods directory folder, so that it will be used as a template for all the sample sets going forward.

Instrument Methods Folder

Method Development Unleashed – TF 3.1 and Multiple Instrument Methods

In an effort to help make TF a more friendly method development platform, we have introduced the ability to have an option to use multiple instrument methods in a batch of samples.

This ability is enabled simply by exposing the instrument method column in the sample definition grid.

When enabled the master method’s instrument selection is overridden, and the selected instrument method is used in its place.

This allows the user to have the same processing conditions but monitor the effects of chromatography differences on the peaks of interest.

Once an instrument method is optimized and chosen, simply turn off the column, update the Master Method and save.

All future batches of samples will use that instrument method.

See the video below.

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

The Master Method – A trinity of information

We will start a short series on the Master Method. So here we go.

Think of the Master Method as the supply truck that comes everytime you want to run an assay. It contains what you need to get things done. It’s alittle bulky and can be somewhat intimidating the first time you see it. Since it controls alot of the available power TF gives you, it has lots that can be,but doenst have to be configured and used.

For example, if a value is set to zero in the QAQC section it isnt turned on for use by the flagging system.

But lets start off with the basics.

The Master Method is a repository for the three things needed to gather and process a data file.

  1. The instrument method
  2. The peak processing parameters
  3. The selected reports to be produced.

With these three things we can submit a batch of samples and acquire, process and produce reports on the fly, after every sample. (but you need a sample list too)

The instrument method is a copy of a stored instrument method somewhere on your hard disk. It is associated with the processing method and can be changed according your your needs. But you always have the ability to go back to your orginal instrument method and copy over any changes. It’s a safety net.

It also insures that you only have to pick the Master Method when making a batch of samples. This keeps a batch consistant, run after run and technician to technician.

The processing parameters are set up for each peak and compound grouping. Once set up again it keeps things consistant.

Thirdly, is the report section. This seems to be a bit of confusion at times. By selecting which reports and what format you want them produced in, ahead of time. The data is always produced in the same way without missing a page. It’s also nessary for the reporting on the fly feature.

If you want to create reports after each injection, simply check the box on batch submission that says “Create Reports”. Then however you selected the report to be produced and one or multiple formats, it make them once the sample has been acquired and automatically processed. Except for Batch level reports, which are produced at the end of the batch sequence.

Follow the video below to see the process.

The video is from the soon to be release TF 3.0 but the workflow is the same.

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

Make it easy on yourself… Update in one place

In the Master Method you can review settings for your Triple Quad mass specs, such as Retention time, window of detection, collision energy…..

You can also make adjustments in the Master or Local Method to your Retention Time. Either by manual entry or by using several ways of performing automatic adjustments.

The issue comes in that when you make these adjustments in processing part of the method, the instrument method doesn’t know about them. So if you are using TSRM  you have to update in two places.

The Acquisition List is updated with the changes to windows and Retention times and can produce a file that can linked or exported out for adoption by the instrument method.

This allows you to edit in one place and by using the Auto TSRM update check box on the Acquisition section, You’ve just now reduced the typing and file coordination, that has to be done.

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

Edit Instrument Methods in Master Method

In the Master Method, a user assigned an instrument method that resides in the c:/Xcalibur/Methods folder. This method is then copied into the Master Method folder when the Master Method is created. Thsi allows the Xcalibur copy to remain as a safe back up.

Two things can be done, you can open the Xcalibur method up and make changes and do method development in xcalibur, and once satified, update the Master method from the altered Xcalibur Method. Alternatively, you can edit the Master Method copy of the instrument method and once satified update the c:/Xcalibur/Methods folder copy of the instrument method so that new Master Methods created with that instrument method will inherit the changes you made.

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

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.