How to use the Threshold Sample in Comparative View
To utilize comparative view to its fullest, one must set 3 three properties.
- Method-Limits-Threshold setting – this setting allows the user to set the height of the horizontal threshold bar in data review. There are two settings.
- Threshold – a fixed peak height amount
- % of Threshold the Sample – dynamic threshold according the peak height of the specified Threshold sample, as described below.
- Batch view-samples-groups column – this setting assigns samples to groups that are displayed horizontally in the comparative view peaks panel. A unique alpha numeric symbol is used to assign a sample to a group. Each sample with the same symbol is a member of that group. The samples are shown side by side in the peak review panel and are ordered left to right by descending order in the sample grid above.
- Batch view-threshold samples – the setting allows the user to assign a threshold sample for each group. Any member of the group can be set as the threshold sample. However, only one sample can be utilized at a time in the group. If you want one particular sample to be used as the threshold across the batch make sure it is a member of all the group. For example if you used numbers for the group name and you have 10 groups, the entry for this sample in the groups column would be 1,2,3,4,5,6,7,8,9,10.
The settings in the examples above allow for the display shown below.
The tall red vertical bar marks the expected retention time and the smaller vertical bars are the edges of the retention time window. Both set in the method parameters for each compound. This allows you to see the drift of chromatography within the sample group. The horizontal red line is the threshold as set in the method as a fixed amount or relative percentage of the threshold sample, as set in the method.
A point to note, there were a few instances where everything was setup properly but nothing displayed in the Comparative view. It was found that some older video drivers not comply with technologies Microsoft used to render the images in this complex grid. However, the issue was fixed in all cases by updating to the latest video drivers for the PC.
New TraceFinder 3.0 Data Review Elements
In TraceFinder 3.0, you will find that we have changed the Graphical User Interface quite a bit. Other than changing some of the colors and the navigation style we have also added elements to help review data in a way that can be tailored.
A concept that came across to our team was to help tell the story of the data. This is what TraceFinder was intended to do from its concept. We realized that many scientist that will use this and related products will not be “CLASSICAL” mass spec people. Young new chemist or other scientist not use to mass spec data moving into the lab need to be able to see what they need to know about the data and have a feel on what works best for them. At the end of the day they are telling the story of the data to their customers.
Our concept is to give you the ability to choose what you want to see and how you want to see it.
In forthcoming releases you will have the ability to “Read the Cliff Notes” of the data or the other end of the spectrum of reading “War and Peace,” if you so choose. We don’t want to limit the data or have the data be so overwhelming it can’t make sense.
So in this video we will show you how to navigate in the Compound and Sample Views which are just different ideas on how to look at the data. Also how to arrange the views so it makes sense, or makes it easier to read through the data.
A big plus is the ability to filter out data you don’t care to see or only data you are interested in.
All this and the views are remembered automatically when a User signs out or closes the application.
Although the video only takes place on one screen. Any part of the data review section is a dockable panel so you can have parts on multiple monitors and they will remain synced. I personally use a three monitor setup and have a multipeak panel on one, a detailed view on another and my data review grid on my main display.
Remember we can only make it better if we hear back from you so, please send in your ideas, comments or questions. The video is a little longer than my 2 minute rule but it should explain a lot of the NEW ELEMENTS and their functions.
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.
Sample List???…. Do I need a Sample List??? Yes and here’s how to import one
So the basic element of data navigation and collection is a list of samples.
This list will identify the properties of the data collected and tell the system, what to do to and the names of the files collected or to be collected.
So TF has a couple of different ways to do this.
The first and easiest is to make a template of the defined sample grid you want to use. In TraceFinder, the user can define the columns that are displayed in both the data results and sample definition grids.
In Batch View or in the sample page of the Acquisition Mode/Wizard, right click the mouse in the grid and a menu dialog that opens up.
In that dialog , select “Export to CSV”. This will make a copy of the grid and the header lables is a file that can be opened by any editing grid application. The most common is Excel, but you could open in a text editor also.
Simply, open the file and for daily use just input sample information in the template and save as a daily/batch .csv file.
A LIMS system, can create a .csv file in this same format or even use a bar code reader to fill in certain fields even in Excel.
Once the sample input is done save the file as .csv and close the editor.
If the file is still open in Excel, MS Office will not let it be used by another program so TF can’t import it until it’s closed.
Right click in the grid and select “Import Samples”.
The Dialog below opens, then select the appropriate file.
The information contained in the CSV file will be inserted into the grid either at the end of the current data or where the index indicator is if that is the option selected in the drop down list below the browse section.
There is also a xml format that can be created fromat LIMS system that can be used, or if Xcalibur has previously been in use the .sld files can be utilized also. Any sample type that TF does not recognize will be set to the Unknown Sample type.