Monthly Archives: September 2012

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.

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.

A Useful Website for Widgets

So as a mass spectrometrist I’m always looking for a way to look at data in different ways.

Even though I’m the product manager for TraceFinder and I have a group of developers that I work with, it’s always a good thing to look outside the box.

So a few years ago I found this really good site that has alot of utilities that are open source and do the little things that I need.

You can even request someone to help out in times of need.

Everyone needs some special at times so here’s a good place to look.

So take a look at

Add A Confirming Ion From A Compound With A Separate Mass Filter

At times compounds must be confirmed from another compound using ion ratio.

Here’s how to set it up with SRM and SIM type of experiments.

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Second Patch From Microsoft For A Security Update That Breaks Custom Reporting

A security update sent out on Aug 14 apparently breaks portions of MS Office.
Microsoft has released this update:
That fixes this issues. We had several reports of custom reporting failure and after applying this fix the issues were resolved.

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.

Changes to My Method… Alot of them… Really?

So as a chemist sometimes it’s hard to believe that I didn’t make the perfect method.  Well, not really. Things change, cloumns go bad, my boss changed the SOP.

So considering the Master Method is my template used for creating batches with the same compounds and parameters, and it can hold up to 3000 compounds, which can have up to 66 components each, I don’t want to have to manually adjust each component.

In each section of the Compound detection tab there is a right click option that allows for copying of those settings to each component in the particular compound or across the entire method.

We hope this saves you time and lets you hit the weekend sooner so your not rerunning samples on a friday night.

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.