TraceFinder 4.0 – Easy Triple Quad Master Method Template Creation

TraceFinder 4.0 – QExactive Easy Master Method Template Creation

TraceFinder 4.0 – Master Method Template

iOrbi Webinar – Q Exactive Targeted Quan using TraceFinder

TraceFinder Webinar series in Begins in October


please click the link below for more information.

http://www.thermoscientific.com/content/tfs/en/about-us/events/tracefinder-webinar-series.html

Links to each webinar listed below:

 

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.

Capture

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.

Internal Standard plot series settings

Video – How to create NIST 2014 custom libraries with FreeStyle

To make custom libraries for use in TraceFinder 3.3 Unknown Analysis, the easiest way is to curate your spectra with FreeStyle and send to the NIST 2014 application which comes with the purchase of any NIST 2014 library.

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

Grouped Sample Report

UnGrouped Sample Report

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.

Sample table

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.

condition1

condition2

condition3

Interesting Article on Drugs of Abuse Analysis using TraceFinder

Detection of drugs of abuse in exhaled breath using a device for rapid collection: comparison with plasma, urine and self-reporting in 47 drug users

by: Olof Beck, Niclas Stephanson, Sren Sandqvist and Johan Franck

link:
http://m.iopscience.iop.org/1752-7163/7/2/026006

Example of Simple Physician Office Style Report – TF 3.3

Below is a simple report that converts raw data to plain language text.

The example is of a style that has been dubbed, the Physicians report, as it simply states if a component is found and above a value. If the calculated amount is above the Cutoff amount, a custom “Outcome” column will state that the value is “Positive”, otherwise its “Negative”.

It also has a custom column, that will display the calculated amount if the value is above the Cutoff and a peak was detected. If a peak is detected, but the value is below the cutoff the cell will display “< Cutoff”, otherwise if a peak is not detected it will display either NA or NF.

Click here to download the Template: Physicians Report

Simply unzip into the folder C:\TraceFinderData\3.3\Templates\ReportTemplates

or unzip into the folder C:\TraceFinderData\32\Templates\ReportTemplates

Physicians Report

The excel like script for the Calculated Amount (AMT) column is:

if(quanresults.calcamount(“Report”) <= compound.LOR,”<Cutoff”, quanresults.calcamount)

It simply takes the calculated value and compares to the LOR (Limit of Reporting) value in the method if is equal to of less than the set limit it will show “<Cutoff”, otherwise it will report the calculated value.

The script for the “Outcome” column is very simple.

IF(quanresults.LORFlag= TRUE, “Positive”, “Negative”)

If the value triggers the flag, the flag value is TRUE. IF true show “Positive” in the cell, otherwise show “Negative”

For the function of the LOR flag to work in the case of all reports, the setting to report a value above a set limit and not to show components that didn’t meet that criteria, two setting mu be activated in the method as shown below.

Physicians Report1

The setting in the table filter text field limit the reporting components in to only be Target Compounds and not display Internal Standards.

quanresults.compoundtype= “eTargetCompound”

Physicians Report2