Category Archives: General Use

Excel rules the world or at least it thinks it does…..

So, this week we’ve gotten a few questions on importing a sample list in CSV format.

There is an error that can occur if the csv file you exported and made adjustments to, is still open in Excel when you try to reimport it.

Unfortunately, the error message isn’t as descriptive as maybe it should have been, but it did give us a chance to post another answer to a “Ask A Guru” question

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

What the Heck is ACTIVE VIEW??????(Answer to a “Ask A Guru” question)

Active View is another visualization of the data that is on a Sample Centric Report. These are only availible today on samples that display chromatograms for compounds and contain grouped sample information.

Sucha as the High Density Reports, in the standard reports section of Report View.

When using Report View we generate a temporary view of the report that would be produced by the system. This view is only for the supplied Standard reports delivered with TF and is not available with Custom Reports, today. (Hint be looking to the future.)  😉

But when the report is generated in preview mode, and it has an ActiveView partner, the Active View tab will appear next to it.

In the Active View tab, you will see a grid of data that corresponds with data on the Report and the same Detailed Editing elements in Data Review, with the same functionality.

When data is changed in Active View it is just like editing in Data Review and results are updated.  When this happens and indicator appears to let you know new results are availible for the report. Once clisked the Report is updated. The information is saved. In this manner you can use Report View as your data editor and see exactly what you are giving your clients in real time. You can at this point choose to generate the report, or make all your edits and then generate the reports in a batch process.

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.

https://dl.dropbox.com/u/13860428/Blank%20XIC%20Compound%20CDS.csv

https://dl.dropbox.com/u/13860428/Blank%20SRM%20Compound%20CDS.csv

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.

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.

 

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 ms-utils.org

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.

Quick Path to Data

Below is a short video on how to enter a batch using a template and begin to acquire.

At the beginning of  batch creation from a previously created template, containing the instrument method, processing method and desired reports.

Next you’ll see the ability to import a sample list from variety of file types and then submission of the batch.

Once submitted then user can watch the realtime trace of the collecting data segmented into a customized veiw  components and their order. While also having the capability to see the batch processing on the fly with a growing calibration curve and results.

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