Category Archives: System Properties
Tip for Optimizing the Speed of Processing Data for TraceFinder 4.0 and later
TraceFinder 4.0 introduced the ability to perform target analysis on peptide sequences. Given that these chemical analysis methods can be very long (i.e. 3hours for a single sample) and have drastically shifting retention times between samples, TF 4.0 introduced the Extraction Time Window as a peak detection setting.
This new setting allows the user to set a window around where the peak might elute. The default setting is 3 minutes, which means +/- 1.5 minutes from the expected retention time.
This setting may be a bit wide for stable chromatography. A typical setting for the Extraction Time Window is 1 minute or +/- 30 seconds from the expected retention time. This setting can be changed in the Master Method Template or the Local Method. This new setting can then be pushed to all the compounds with two mouse clicks or can be optimized for each target peak, clicking the Three Lined Button in the right coner of the settings page and selecting “Apply current extraction window settings to all peaks in the method”
Since the amount of data being extracted for the targeted peak is reduced, the amount of time per peak analysis is reduced. This setting is separate from the Peak Detection and View Width Window under the Retention Times Tab.
Peak Extraction Window
TraceFinder 3.2 – Intelligent Sequencing as a Standard Feature
TraceFinder 3.2 will include Intelligent Sequencing as part of the standard features set.
Previously, this was an additional add-on to the TF applications, with a separate license.
Now Intelligent Sequencing will be able to be configured in the Application Configuration section of TF, as shown below.
If you are not familiar with Intelligent Sequencing, it is the capability to perform actions on the sequence list of samples from real-time analysis of the flagging system.
The uses of this feature are numerous, the main benefit is that you have a safeguard for your samples.
– If you have a QC sample that is out of tolerance, you can stop the acquisition of following samples.
– If you have carryover in your blank, the system can automatically introduce additional blanks until it is clear or stop the sequence after so many blanks have been injected.
Troubleshooting – Windows 7 Themes Performance Issues
Change the theme to improve performance
If your computer is working slowly, you might see a message saying that the theme is using most of its allowed memory. If this happens, you can change to the Windows 7 Basic theme or a high-contrast theme to improve performance.
If you change the theme to Windows 7 Basic, you will no longer get the full Aero experience. Aero is the premium visual experience in this version of Windows. It features a transparent glass design, window animations, Aero Flip 3D, and live window previews.
To change the theme
- Open Personalization by clicking the Start button
, and then clicking Control Panel. In the search box, type personalization, and then click Personalization. - Under Basic and High Contrast Themes, click Windows 7 Basic or one of the High Contrast themes.
My Filter String Is Missing After I Updated My Methods Associated Rawfile.. HMMMMMM
So in both the local and master methods, a user can update the associated rawfile to see the peaks they are looking for.
This dialog has an option to update the filter strings. Which makes it easy to do especially if you have hundereds of compounds.
When you do this, the logic looks to the compound database info that is in the Acquisition list and to help it determine the filter with the right precusor and then the extracted ion setting to see which filter contains its value within the range of product ions in the brakets of the mass filter. If everything matches from the newly selected rawfile it sets the filter accordingly. If it doesn’t then the compound will have a little red dot next to its name and a missing filter error lights up.
This typically occurs when the new file has a slightly different filter string and the method’s extracted mass falls outside of the product mass range of the filter.
The following video shows you how to manually fix this issue.
If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.
TF 3.0 – What is Intelligent Sequencing? ” A new/old feature to increase reliability”
Intelligent Sequencing Control
The figure on the below illustrates the wide range of operator-defined
settings that may be utilized to allow TraceFinder 3.0 intelligent sequencing
to make real-time decisions that prevent manual review and re-analysis
of suspect samples. Data review is done immediately following
acquisition, and any defined actions can take place automatically
without user intervention.
Each of the key sample types – calibrators, quality controls,
specimens, etc. have their own review settings that can be unique
to a particular sample type.
For example, if a quality control does
not meet required QA/QC limits, the calibration can be completely
resubmitted and re-analyzed, effectively restarting the entire batch,
while a specimen not meeting that same QA/QC limit may only be
targeted for re-injection.
In each sample type, data review steps and defined actions can
be specified for acceptance criteria on data quality as outlined in the
laborotory’s SOP. The settings for these checks are shown in
the figure on the above.
Intelligent sequencing options can also be set
for quantitative values, such as limits of detection, blank cleaniness,
and carry over. Actions may be defined as well for review
steps based on ion ratio acceptance.
The benefit of utilizing this feature is that batches of samples can be run in realtime
with on the spot rejections or cleaning steps. This eliminates the need to return the
next morning and rerun samples. If samples have a short shelf life then they are kept from
having to be remade or running out of sample. Therefor, increasing the efficiency of the
lab and reducing waste of time and material.
Need to Share Data – Here’s a Freebie from Microsoft
So we’ve had a couple of people want to send data across to help them look at methods and such, but they were limited by the amount of storage on dropbox or the security concerns of an outside source.
Here is a link to signup for Microsoft’s SkyDrive
This gets you 7 Gigs of storage right off the bat. No money required. The beauty of this is that it can sync with all your MS Office applications, which you can share or keep to yourself.
It also works as a location on your desktop so you don’t have to ftp large files, simply drag and drop.
The really cool part about this is, if I have a iPad or other mobile device and use the SkyDrive app, I can edit my stored documents real time in the cloud. I have access to them from anywhere at anytime, and anyone I have shared the document with can collaborate in real time.
For all those of you with large data sets this is a great spot to shared the files, and it works with your intergrated Windows security just as if it was a mapped drive.
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.
Sneak Peek – Targeted Screening
As Always the TF team is looking forward and addressing market driven issues.
One thing that has become highly vocal in the applied markets is the ability to screen for target molecules, and then quantitatate on the positive hits.
So in a forth coming release, TF has incorporated the ExactFinder Screening workflow into its core set of capabilities.
We’ve expanded on this, to include nominal mass instruments, as well as, the high resolution accurate mass systems. This will allow for us to screen utilize screening from the single quandrupoles all the way to up to the QExactive.
So below is a shot of the new screening data review, and you can get an idea of the new UI style adopted by Thermo Scientific.
We still will have the same quan workflow, but have added acquistion and realtime reporting to ExactFinder screening workflow.
Licensing….. How many licenses do I really need?
A question came across the Blog that asked about Licensing and Multiplexing?
The answer to the question is two.
One License for the version of the application(ie. TraceFinder EFS, TraceFinder Clinical, ect..) and One for the Additional Module such as Multiplexing support for the Aria OS.
IF you go to the upper left section of the application in the menu bar and select Help, at the bottom of the dropdown will be an item called License Activation.
Here you can open the licensing window and request or enter license data.
If your trial period is over then only a license screen will appear when you open the application from the file menu or from the desktop icon.
This is true for both the Application and the Additional Feature of Multiplexing.
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.
TraceFinder: Direct Knowledge 