Blog Archives

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 Webinar series in Begins in October

please click the link below for more information.

Links to each webinar listed below:


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.

Thermo FreeStyle – Sequence 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 sequence 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.

TF3.0 – Using Estimated/Semi-Quan Amounts

In certain parts of TraceFinder and LabForms, we had exposed the ability to use estimated amounts of substances that did not have their own calibration curve. This feature goes back to the days of the Incos data systems, circa 1980.

In TF 3.0 we have exposed this capability, to be a bit more friendly to use and to be interactive in the user interface, versus just report generated.

In the following video, you will see where to set a compound to use the estimated feature and how it is displayed throughout the applications with visual clues to help you determine that the results you are observing is a semi-quantitative amount.

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

Intelligent Sequencing – Step One – Setting up the method

Intelligent Sequencing is not a new concept. In the late 90’s Thermo had an application called ToxLab which used the concept of flagging data and altering the sequence of the set of samples based on failure criteria.

This allows for insertion of blanks, reinjection of sample or a combination according to criteria that a chemist would normal use to look at his data the next day to determine, which if any samples had to be rerun.

Intel Seq just does this on the fly.

It allows the user to have confidence that the data will be handled in the prescribed manner using the existing on the fly criteria that has existed in TraceFinder for a number of years.

By using this feature the chemist can cut back time on reinjections and sometimes on sample prep since the sample wouldn’t have evaporated. Also it will not have gone beyond the sample stability time threshold before reinjection occurs.

The first part of the operation is setting flagging criteria as you have done previously.

The next is setting of the method criteria for Intel Sequencing.

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

Need to just enter some compound info for the method… Ok here’s a solution

So at times we’ve had the request that chemist just want to enter in some compound data without having a rawfile to extract the spectra from.

And though TF gives you multiple ways of creating methods, some feel they just want to be able to add a compound and input their data by hand.

Though many workflows support doing this in using a CSV file and creating a method from importing that csv file into the CDS, sometimes that just may be too much.

So here is couple of CDS files that you can have on hand just to pull over and fill in place holder information.

One is for XIC/SIM type of experiments and the other is for SRM type of experiments.

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.

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.

  1. Matrix Spike – with compounds spiked into it at a known level
  2. Matrix Spike Duplicate –  with compounds spiked into it at the same level as the Matrix Spike
  3. 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.