Author Archives: humphrjk

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

TF 3.3 – Example Of How To Create a Highly Customized Report Template

TraceFinder has a Excel-like report template creation tool. It was first introduced as a plug-in beta release in TF 3.1 and a final product in TF 3.2. After feedback from the user based we made some modifications that should allow for easier template editing and creation. The more feedback we receive the better we can make this tool in the future.

The example below goes into detail how to create some very custom data table information and flagging. This includes taking values that are stored as numbers or TRUE/FALSE text and changing then to read PASS/FAIL with highlighted, bolded and color changed text. It also includes setting up test range criteria for the information to be flagged against without the number having to appear in the data table as being read directly from the results table in the batch to give the PASS/FAIL flag.

The report is a Batch report that shows only compounds that were found to be positive in a concentration above the limit of reporting used set in the Master Method template. It uses typical fields in the header and contains a blend of regular data columns and custom columns in the table. It is separated by the Sample ID as a line unto itself between each set of sample results.

Custom Report page

Below is shown the data fields used to create the table.

The statement in the Table Filter ensures that only compounds that have result greater than the Limit of Reporting (LOR) value, set in the Master Method template, will be displayed in the report.

Setting the sorting by the Sample ID and having it be the top most data field in the selector, allows for that value to be used as the Repeat Header Per Group field. By unchecking the box, the field won’t display on the row, but will appear in the separation row above only.

Custom Report page data feild table

The listings below are the custom fields created to do the special flagging a show data. If you notice these are all the same small scripts that you would use in Excel to create the information. The difference is that the underlying individual results don’t have to be on the sheet, in a hidden column or a second worksheet. It just reflective of the results in the batch. The functions are entered into the Formula text cell when the data field is selected.

Custom Report page data feild table formula field

The way these statements work is whatever is designated as the “=” state(True or False) the first text will be set to display for that state. All other states will render the second text.

To get the data field to use in the functions below simply click on a data element in the selector, highlight the text in the Formula cell and copy/paste it into a custom column’s formula text field and then edit the function around it.

IS Flag

IF(quanresults.ISTDAreaOutOfRangeFlag=False, “Pass”, “Fail”)

This function looks at the internal standard out of range flag. It creates the condition that if the flag is FALSE, meaning it is not indicating a failure of the flag criteria, the show “Pass” in the cell. If the flag is TRUE, meaning that the criteria indicates it has failed, the show “Fail” in the cell.

IR Flag

IF(quanresults.irFlag=False, “Pass”, “Fail”)

This function shows that if the Ion Ratio criteria has been meet by all confirming ions then the flag will be False. This state will then display “Pass” in the cell. If the flag is True then “Fail” will be displayed. The way these statements work is whatever is designated as the “=” state(True or False) the first text will be set for that state. All other states will render the second text.

IR2

quanresults.ionRatio(1,2)

One limit of the tool is that the table builder can only natively create one column for a set of information. However, you can create a custom column to show 2nd, 3rd, etc… of a data entry. One instance of this is a second confirming ion ratio. The setting (1,2) will display the result for quantitative peak 1, confirming peak 2.

mz Flag

if(quanresults.mzDelta(“Report”) > “2.5”,”Fail”, “Pass”)

This function sets the high precision number of the delta mass, derived from the expected mass minus the actual measured mass, which is always an abolute number, to display “Fail” if its greater than 2.5. If not or less then display “Pass”.

RT Flag

IF(ABS(quanresults.RTDelta(1,0)) >=0.06, “Fail”,”Pass”)

This function declares with the ABS statement that the RT delta result number which can be positive or a negative number will be evaluated by its positive equivalent. If it’s greater than or equal to 0.06 then display “Fail”, in all other cases display “Pass”.

Ion CoE Flag

IF(AND(quanresults.RTDelta(1,1) < 0.01,quanresults.RTDelta(1,1) > -0.01),  “Fail”,”Pass”)

This function combines two conditions the value of these two confirming ions, designated by the values (1,1), must fall outside these two conditions to display “Fail”, if it falls between them then display “Pass”.

Lastly I set conditional formats for each column separately for the custom flagging that if the cell value was “Fail” that it would change the Font to bold and red and the borders of the cell red.

Custom Report page conditional format