Category Archives: Reporting
Internal Standard Retention Time and Peak Width Diagnostic Chart
This a useful and simple report that is best viewed in Excel.
Click here to download the zip file:
Internal Standard Retention Time and Peak Width At Half Height
Place in the folder: C:\TraceFinderData\4.0\Templates\ReportTemplates
The chart shows the Retention Time and the Chromatographic Peak Width at Half Height, in a line chart over the entire batch. It should show you the performance of the internal standard and the reliability of the chromatographic conditions. A moving retention time and/or a widening of the chromatographic peak may indicate issues with the columns or mobile phase. This is useful in determining the health of the system and variability of the assay over time.
The Chromatographic Peak Width can be attained by setting the conditions in the detection portion of the method as shown below. You can change the width measurement to be any desired value. Default is 50% of peak height, though 25% may better gauge peak fronting or tailing.
The report is currently set up to show 59 samples from the data table. If your data set is typically large or smaller you can adjust the ending row in the series section of the chart dialog. Simply open the editor for this report, double click on the chart and the dialog will open as shown below. Expand the section for the Data Source/Series and enter your typical ending row. Any empty cells will not be charted.
Residuals Chart Report Template
In many instances, individuals wish to see the residual values of their calibration curves. This plotted chart may give a better visualization of how the curve is actually performing versus the singular R-squared value.
Click here to download the report templates for data that contains either internal or external standard curve types: Residual Chart Reports
Extract the files to the file location: C:\TraceFinderData\4.0\Templates\ReportTemplates
For use with TraceFinder 4.0 and later versions.
Presented are charts in both natural and logrithmic scales. If you only require one type of chart, the delete the one not desired and resize to meet your needs.
The chart will automatically adjust for a normal amount of calibration standards or a large validation set.
Internal Standard Charting Report – TF 4.1
This a useful and simple report that is best viewed in Excel.
Click here to download the zip file: Internal Standard Response Chart
Place in the folder: C:\TraceFinderData\3.3\Templates\ReportTemplates
The chart shows the response in a line chart over the entire batch. It should show you the performance of the internal standard and if you have carry-over in samples such as a Solvent or Double-Blank sample. This is useful in determining the health of the system and variability of the assay over time.
The report is currently set up to show 59 samples from the data table. If your data set is typically large or smaller you can adjust the ending row in the series section of the chart dialog. Simply open the editor for this report, double click on the chart and the dialog will open as shown below. Expand the section for the Data Source/Series and enter your typical ending row. Any empty cells will not be charted.
TF3.3 Example of a Sample Report Using Compound Groups
This a series of reports based on one set of common elements. The only difference is the activation of elements in the grid. This shows how one report can simply be utilized to create multiple reports. Utilizes basic Excel functions.
This particular report makes use of two fields in the method that contain free text entries on a compound basis and are repurposed. The fields are used to add a comment for labeling a compound and to calculate a flag based on library score.
Click here to download the templates. Sample Quantitation-Sorted by Compound Group then Comment With Library01
Simply unzip into the folder C:\TraceFinderData\3.3\Templates\ReportTemplates
The data table utilizes many custom functions to create this functionality. These functions are typical Excel function statements. All the examples I used to construct this report were found by searching for them on the net.
The data table utilizes a sort function by utilizing the Compound Group as the first sort. By checking the Repeat Header Per Group element and unchecking the Grid Entry allows for the element not to shown in the grid but raises it to the row above the set of rows that represent the Compound Group. This give a natural division between the groups. The second sort can be by compound name, or by comment. In these reports we utilized the comment to label the compounds as a parent or metabolite. By using the secondary sort in Descending order you can ensure the parent is listed first in the group and metabolites next in alphabetical order.
The data table is constructed as listed below.
- Compound Name – peakresult.compoundName
- RT(Custom Column)– if(peakresult.peakfound = false, “N/F”, Text(peakresult.rt, “0.00”))
- This function declares a N/F for not found compounds, but sets the RT to a limit of 2 decimal places
- RT Drift – peakresult.rtDrift
- Quan Peak – peakresult.detectedMass
- MZ Delta PPM (Custom Column)– IF(peakresult.peakfound = false, “N/F”,(quanresults.mass-quanresults.detectedMass)/quanresults.mass*1000000)
- This function sets the cell to show N/F in case of a peak not being found. If a peak is found it calculates the PPM mass difference and sets the value to be positive.
- Response – quanresults.totalresponse
- Calculated Concentration (Custom Column)– if(peakresult.peakfound = false, “N/F”, if(sample.issolventsample,””,quanresults.reportedinsampleconcentrationprefix & Text(quanresults.reportedinsampleconcentrationdouble, “0.000”)))
- This function sets the cell to show N/F in case of a peak not being found. It sets the value of the calculated amount to be converted to TEXT and limited to 3 decimal places of precision.
- Outcome (Custom Column)– IF(quanresults.calcAmount= “N/F”, “Absent”, IF(VALUE(quanresults.calcAmount)>= VALUE(compound.LOR), “Present”, “Absent”))
- This function sets the cell to show “Absent” in case of a peak not being found. The next if statement sets the VALUE of the stored results to number. At times in reports, the results may be a string or text, by using VALUE the text is set to a number. The number of the results for Calculated Amount is compared to the Limit of Reporting value set in the method. If it is greater than the LOR value then “Present” is reported in the cell. In all other cases “Absent” is reported. This function could simply report the presence or absence of the compound utilizing the LOR flag as being TRUE or FALSE. However, that flag is only present for Unknown/Specimen sample types. This function allows the statements to be utilized across all sample types.
- Library Score % – quanresults.libraryMatchScore
- Lib Score Threshold – compound.CASNumber
- Library Flag (Custom Column)– IF(INT(quanresults.libraryMatchScore)>= INT(compound.CASNumber), “Pass”,”Fail”)
- This statement converts the values of the Library Match Score and the value entered into the Case Number to Integers. The value then can be utilized to evaluate for being above the threshold value which the Case Number value was utilized for. If it’s above the value then the flag is “Pass”, otherwise the cell will reflect “Fail”.
- Comment – compound.LIMSID
The RED text in the Outcome column utilizes the settings below.
The Power of Reporting – Is it Magic or Tracefinder3.1?…. New Preview of Report Designer with TF 3.1
One of the most requested features is to have an easier way to create custom reports.
Though TF has some great Standard Reports, and a really powerful VBA-Excel custom reporting tool. We’ve been investigating ways to make it easier to create custom reports.
The new Report Designer that will be in Preview form, debuts at ASMS 2013.
The learning curve is low, because it looks and feels like Microsoft Excel . Yet it is powerful, because you can do many the same special functions as Microsoft Excel.
Even if the Report Designer doesn’t have quite the feature you need, but Excel does, simply open the template in Excel from within the Designer. There you can make edits and save the template.
When you use the Excel edited template to create reports those edits are used.
As stated previously, this is a PREVIEW. This means that anyone can use the designer, but it is not a final commercial version.
If you wish to use it for reporting data, as with any custom report template, YOU must validate that the report template generates the correct information.
We will be looking for feedback on issues found or features to be added. Starting soon there will be a page on mytracefinder.com just for the Designer, where updates and feedback will be available.
Below is a video of how to use the Report Designer to create a simple report from a blank page.
The Report Designer uses the data from the currently opened Batch of Samples and results to model the data. This allows you to see exactly what the final report will look like when it’s produced within the application.
The video is a bit longer than usual but shows how simple it is to create a report which uses special features, such as formulas and conditional formating.
If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.
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.
Importing a new custom report template
There have beena few request lately that once a customer recieved their newly created custom report from our Report Service that it wasn’t clear right off the bat how to get the template into TraceFinder for use.
The video below shows how to import the xmlt file which is a VBA enabled template written by our “Professional Service” group when you make a request via the blog or sales team.
It then shows how to make sure you can can use it in the application once you’ve imported it.
The video is from the soon to be released TF 3.0 but the workflow is the same.
If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.
The results can be seen below.
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.
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.
Stop Bouncing Around When Reviewing Data
In Tracefinder you have the ability to review your data in the form of you final report in Report View.
By selecting the report you want to see and the data you want see it from, as long as its a Standard Report shipped with TraceFinder, you can see a preview of the report without actually creating the pdf or paper.
This is a virtual report help in memory while you review it. It allows the user to see the end result but still be able to make some changes.
A feature of many of the Standard reports that are sample centric is the Active View tab.
This tab allows the user to stay in the reporting area and make data review type changes. It will display the results found in the text of the report, but give you the ability to perform chromatographic editing just like in Data Review. Once all the changes are made then simply press an Update Report button that will appear above the virtual reports and the data on the report will be updated and the results in the Data Review Screen will be too.
This keeps you from clicking around from Report View and Data Review.
TraceFinder: Direct Knowledge 