Blog Archives
Retention Time Reference Compounds Used For Correcting Chromtographic Drift
TraceFinder has an option to allow the user to set a reference compound to assist in corrections of retention time drift.
The feature is the same implementation that has been a part of the Xcalibur feature set for over 20 years and is well characterized. The user simply selects a checkbox in the RT Reference compound column of the Method – Identification tab. This sets the compound for use in linking other compounds to its found RT.
To set a compound to use a RT reference compound, simply select a RT Reference from a dropdown selector in the same definition grid.
The typical use of this feature is to set your Internal Standards as RT Reference Compounds and then link the nearby eluting components to the Reference Compound. Also, the IS retention time peak detection window is set a little larger than the target components to allow for detection if a large RT drift occurs.
When the RT reference is detected the difference, whether + or – in time are adjusted in the connected compounds. This new RT is specific to each compound in each sample. Therefore it is not reflected as a change in the method because the method is set as a batch level setting. The compound using the RT reference must have an original expected retention time to be adjusted, it cannot be left as zero for this feature to work.
TF 3.2 Setting up to Data Review to display Positive results first
In the video below, we have set up the flagging criteria to be able to sort and float Positive results, above the LOR/Cutoff Limit set in the method settings,to the top of the data review grid. We have also setup a flag to allow compounds with detected peaks but fall under the LOR/Cuttoff level in the QAQC section of the master/local method, to appear below the positive results. This should assist in labs wanting to review data by exception and to validate their data review process to incorporate into their SOPs to utilize this criteria.
TraceFinder 3.2 – Method Setup Tweak – Threshold Setting
There have been a few questions on the issue of peaks not being integrated, while performing quantitation, although the signal is strong. A reason could be that when a compound is created in the method, it has a related compound database entry for a threshold setting. This setting is used in targeted screening but is not editable in quantitation mode.
The setting has a default value of 5000 for calculated peak area. This setting does have a global override in the Local and Master method Processing section. The default value is unchecked and blank. This means the default threshold is 5000 for all peaks. If you are having an issue where the peak is not integrated but has a strong signal, then change the setting by checking the box and entering a new value such as 0 or 500. The data will need to be reprocessed as this value is not automatically applied.
Thermo Freestyle – General Navigation Tutorial
In the pending TraceFinder 3.2 release, FreeStyle will be an optional feature that comes with every installation.
FreeStyle is a new qualitative viewing package that is taking on the features of QualBrowser.
TraceFinder 3.2 gives you the ability to utilize both QualBrowser and Freestyle when analyzing data, from links within the application.
Please view the video below as a quick tutorial on the basic navigation of FreeStyle.
Video player has changed. If the picture appears blurry, in the top right hand corner of the player you can enable HD to play back high resolution video.
Note: FreeStyle is a separate application and will require a separate license from TraceFinder.
However, when you apply for a TraceFinder 3.2 license you will receive both a TF license and a FreeStyle license.
You simply apply each to their respective license when using the applications together.
Applying an external/historical curve to a batch of samples after Acquisition – Ask A Guru
The video below shows how to apply a calibration curve from one batch that contains calibration samples to a batch of samples that contain no calibrators.
This workflow is the same as selecting the external curve in the Acquisition workflow, but may be used on any batch of samples after acquisition.
The features allows the user to run a calibration batch in the morning and use that curve for all subsequent batches for the time period their SOP allows.
HMMMMMM… Maybe your day just got alittle easier.
If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.
Associating another batch’s Calibration Curve to the current batch – (Answer to a “Ask A Guru” Question)
I think that the questions below are pretty self explanitory of the feature in the video.
“What would you like to know?: Hi, Jamie,
Example: A Cal curve batch is acquiring.
Case 1: I submit a new batch of just patient samples and forget to extend the cal file to those samples. How do I extend the cal file to those samples w/o pulling them into the Cal Curve batch?
Case 2: I submit a new batch of just patient samples and extend the cal (with the wrong file) to those samples. How do I reprocess with the correct cal file?
Company: TFS
Area Of work: Clinical”
So if you have a batch in flight. You should pause the acquisition while you associate a calibration file. It just makes things cleaner if you have an older system with less RAM.
The video is out of the soon to be released TF 3.0, but if you are using and older version the functionality and menu selections are still the same. Dependant on the resolution setting the last frame may be overlayed with another.
If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.
Matrix Spike and Matrix Spike Duplicate… Understanding the how it works.(Answer to a “Ask a Guru” question)
A question from the Ask a Guru was how to use MS/MSD samples and reports, well read below.
In the Environmental realm there is an experiment for a Matrix Spike and a duplicate, when compared to an unknown sample.
This allows for the chemist to calcualte a recovery of of the compounds contained in the unknown sample.
To set up the experiment the chemist needs three sample types.
- Matrix Spike – with compounds spiked into it at a known level
- Matrix Spike Duplicate – with compounds spiked into it at the same level as the Matrix Spike
- Unknown – a sample with unknown amounts
Under QAQC tab of the Master/Local Method the concetrations of the spikes compounds must be entered in the grid for the MS and MSD tab.
In the Batch View the samples to be grouped together and used to report the Recovery must have the same SAMPLE ID. There must be one of each SAMPLE TYPE, but each one must have the sample SAMPLE ID text in their individual grid cell.
When the batch is processed the data for recovery will be calcuated and a MS/MSD Report can be generated that displays the information about this experiment.
See the picture below of the report in Report View.
Thanks to Gail Harrison for her suggestion on a blog post.
Need To Look At Files With Data Dependant Experiments?
Though TraceFinder is primarily a quantitation application, it does have some provisions for unknown identification.
Mainly used in Single Quad or Ion Trap Analysis, the qualitative processing allows for scanning files along a TIC for peaks of interest and then eliminating the known targets and performing library searches against the unknown peaks. Also, TF gives the ability to look at the peaks that generate data dependant scans(DDS). It will sum the spectra and compare to a NIST style library.
To utilize this feature you must have two things. One a Method template, with the parameters set for Qualitative processing and DDS enabled, and a Sample Type of either and Unknown/TIC or Unknown Qual.
If you are performing Quantitative processing those will be perfromed first and Qualitative will occurs on the sample after Quan results are created.
If you have Qual resuts in data review you will have a green button to select the QualView.
Follow the the Video in setting up a Method Template and then using it in a Batch to review qualitative results.
If the video is blurry select the cog wheel in the lower right of the video window and adjust the resolution setting.
Custom Reports Suddenly Stop Working????? Here’s a reason and a Fix!!!!
If you (suddenly) get an error like the following (which may vary depending on OS) when generating custom reports, it is likely caused by a recent security update for MS Office.
Good news is that Microsoft realized this problem and provided a “fix it” tool at http://support.microsoft.com/kb/2703186.
This is what happens based on my investigation if you care:
There is an EXD file created for some VB 6.0 runtime files when you use the controls provided by the runtime files in the Visual Basic designer. Those files are located in %APPDATA%\Microsoft\Forms\ folder (which may vary depending on OS). The problem is that, when security update installs new versions of certain runtime files, the EXD files become invalid and hence this error occurs.
To fix the error, you need to delete the EXD files and they will be re-created as needed. To delete those files, you can either use Microsoft provided “fix it” tool from the link above, or go to the folder directly and delete them.
This link http://technet.microsoft.com/en-us/security/bulletin/ms12-027 gives you some details why the security update is necessary and which software are affected.
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.
TraceFinder: Direct Knowledge 