Monthly Archives: March 2012

Brief description of flagging colors

NO Flag – Criteria for flagging on a compound was not met or flagging criteria was defaulted as off by being set to zero. No criteria or no level beyond the set threshold, No flag

Green Flag – Certain compounds, such as those designated as internal standards have default criteria that is not defaulted as off. Green flag means all the criteria is meet.

Yellow Flag – A compound did not have a peak defined peak detected as a quan peak.

Orange Flag – Used to designate that a value of the calculated amount lies between the LOD and The LOQ as set in the QC/Limits section of the master/local method.

Red Flag – Used to designate the failure of a set limit in the QAQC/Limits section of the master/local method, including threshold failures, ratio failures, etc..

Recommended Minimum Computer system requirements For TF 2.x


 • 2 GHz dual core processor enabled

• 4 GB RAM with system-managed memory enabled

• CD-ROM/DVD drive

• Resolution display 1280 ×1024 (XGA)

• 100 GB available on the C: drive

• NTFS format


 • Microsoft™ Windows™ 7 or Windows XP Professional with Service Pack 3 operating system

• Microsoft Office 2010 (Customers can use Office 2007 SP2 if they own it)

• Thermo Scientific software:

Xcalibur™ 2.2 SP1

TSQ Series 2.3 SP3

 LC Devices 2.5

 LTQ™ 2.6

Aria™ MUXVi 1.0

ToxID™ 2.1.2 SP2

Foundation™ 2.0 SP1

Exactive™ 1.1 SP4

Exactive Series 2.0

How to Create a Master Method and Batch From DrugX

This attachment breifly describes how to make a batch with already acquired data using drugx demo data from the xcaliburexamples folder

DrugX workflow tutorial

Preferred setup diagram for LIMS with TraceFinder

LIMS integration

If a customer wishes to interface TraceFinder with a LIMS (or “LIS” in clinical accounts) there is a preferred configuration. The setup diagrammed in the attached file has worked successfully with past LCQuan systems, and may be used as a model for forthcoming TraceFinder interfaces.

When the TraceFinder user clicks Import in Analysis tab, the last used folder will show up. This can be a designated drop folder to which the LIMS sends sample list .csv files. After the run is complete, TraceFinder will post the result as an xml file in a newly created batch folder. The LIMS sniffer program should be set to check for a “newly created” folder within C:ThermoTraceFinder[version#]Projects. The Data folder within that folder will contain files ending in .rsx, which are xml files. The LIMS sniffer program would then import the required accession numbers, calculated result, time stamp, etc directly from those xml files.

Creating a Master Method from an Xcalibur PMD file

Here’s a quick way to turn your old xcalibur processing methods into TraceFinder Methods.

Click on the link to a word docx file below

Creating a Master Method From a PMD

Exact mass XIC database for TF Compound Datastore

The attachment link is for an Exact Mass XIC database.  The downloaded file must be changed from an .xlsx file to an .csv file before it can be imported into TraceFinder 2.x for a Compound Datastore.


Custom Report Request Template and Workflow

TraceFinder Custom Report Lifecycle Process flow

The attached files outline the workflow of submitting and working through the custom report process.

Custom Report Request Template

Also the template for gathering requirements for the custom report being requested.

TraceFinder 2.0SP1 Installation Guide


Click Link above to open PDF file

Ion Ratio Settings and the uneditable percent

In TraceFinder under the General Tab you can set select:

  • Manual – typed in and manual adjusted for each confirming peak
  • Average – calculates the average of the ratios across the calibration curve and uses that as the percent entry for the ratio
  • Weighted Average – calculates the average of the ratios across the calibration curve with a weighting and uses that as the percent entry for the ratio
  • Level – Uses a level that the use selects for calcualtion of the ratio

IF the user selects anything other manual, those values are not editable.

If the Curve or the level have not been completed, then with all other selections results for the samples before either the last calibration sample or the selected level will not have a ratio defined to flag against.

Uneditable ion ratios

Video For manual and other settings for ion range calculation

Disappearing Peaks – Master Method and Instrument Method not set correctly together

Last week at a customer site, the system was collecting information but no peaks were being detected and displayed.

If you opened the Raw files up in Qual browser and applied a layout AND selected autofilter the peaks for the compounds would appear correctly.

The issue was that the instrument method that had been updated in the master method did not collect information for the set quan mass. that is the filters in the rawfile looked something like this MS + SRM 906.01 [59.2-60.2] but the filter selection stored in the master method looked like this  MS + SRM 906.01 [59.3-60.3], and the extracted mass set in grid was set to 59.27.

Update scan filters

Video of update filter