Category Archives: Configuration

Wizards and Batches… Removing the Warlock….

In TF there are three main choices to create batches. Each of these come from historical markets that TF is serving.

To start there is a selection of the type of creation you want to see. This is located in the Configuration mode under the Optional features section.

This allows the user to choose between the LabForms style wizard and the TraceFinder Acqustion Mode.

The TraceFinder Mode was made to make a wizard like workflow that naturally fit inside the application, and had a bit more intellegent checking of criteria before submitting a batch for Acqusition. This is the reason, that there are four mode buttons when it is enabled.

The Historical LabForms wizard was left in place to allow for users of that product to transition their existing workflow into the new application of TraceFinder.

Thereby, reducing the cost of the move. This view is more of a popup window and has some unique features. Eirther one allows for templates to be made and utilized in batch creation.

Finally Batches can just be made in a regular, non-templeted fashion by using the Batch View new batch selection.


Method General Setting Page – Hmmm.. I missed that setting

One thing that TF has as part of its DNA is to be flexible. Method development is a complex process and we are always looking at ways to reduce the effort, but to give flexibility in our approach.

One page that has alot of power, but is over looked many times is the General Setting Page.

These settings are the general setting for properties in the method.

These settings overide the default settings in the Application and apply to the Method and consiquently all the data that is processed with the method. These settings can be changed in at both the Master and Local Method levels.

Two points to look at.

1) Mass precision – This applies to all the masses used in producing results. It does not apply to the reporting    properties of thethings like RT, or calcualted amounts.

2) Instrument Method Edit/Update – In the master method you have a copy of the selected instrument method, which the ultimate Master instrument method is located in the Xcaliber/Methods directory. When you select edit, you are editing the copy that is located in the Master Method folder. When you select update you are overwriting the changes you made in the Master Method Copy, to the ultimate Instrument Master method in the Xcaliber/Methods directory. When you use these button in the local method you edit the Local Method copy of the instrument method that was copied to the Local Method directory, and the update button copies those changes to the Master Method instrument method. This isolated the Ultimate Master instrument method from batch level changes that you may not want to be inherited by other Master Methods produced in the furture.

Now that I have a CDS, what do I do with it?

Well, the end game of the CDS is to supply information that can be used to create methods and acquire data.

Here we’ll look at the Acquisition List side of the equation.


Here in the data we retrieved from a CDS or PMD file is stored.

Note that PMD files do not contain all instrument information but this can be added to a CDS and then adjusted.

From here you can select the export SRM data in the Method View tab and an Xml file containing the instrument specific data will be produced.


If you open this file in a text editor such as note pad it will contain the information in the Acquisition List in a format that can be imported into the Instrument Method editor.



If on the Batch View section or the final page of the Acquisition Mode wizard you select Auto-TSRM update this information is passed to the mass spec at the time of acquisition. This allows the user to collect only the data needed to be processed and allows for manual updates in the batch to be automatically loaded to the mass spec at run time. This does not monitor the RT of peaks and automatically update the mass spec controller, but allows for user input to occur in on place versus having to open the instrument editor for a second adjustment.

Compound Data Store or Compound Database – Kinda the same thing….

TF has the concept of bring in a data you know about compounds and storing it for later use.

This we call the Compound Data Store (CDS), but what’s in a name… Its a an XML file that contains information about the compound.

The picture above shows this data in excel. It contains information like the compound name, experiment type, collicion energy, retention time, fragments relationships.

Attached here is a copy of the csv template TEMPLATE.

This information can be edited in excel and uploaded into TF to add to a database or to alter the data base. The changes will be reflected in the TF CDS module.

Once the data is in the CDS, a method developer can utilize it to create processing methods which in turn can be used in syncing acquistion methods in the Master Method.

A blog post to come later this week will highlight the use of the information in the Auto-SRM feature.

A quick note is that the CDS is not automatically turned on at installation.

The user will have to configure the option and restart TF to take advantage of this feature.



Converting From Old to New… Methods, Data and Templates

TraceFinder provides an executable application the top level menu “Go” item, that will allow you to convert all of your old stuff to the latest versions of TraceFinder for use.

This includes all previous versions of TraceFinder and back to the LabForms 2.5.x application.

This allows you to reproduce your data and methods you currently use in the newer platform without having to recreate everything.


It also allows you to browse to any stored TF or LabForms directories to pull in the information even if,  it has been archived on a remote disk.

After you have opened the directory the contents for the selected data type will be listed below.

You can select individual files or right click and select all. the simply press the “Start Converting” button in the lower right corner.

If any issues occur the Status column will contain an entry and the log file will record the issues with conversion.

A Quick Note on OneNote and Report Printing?

Is Microsoft OneNote hijacking your print jobs?

on April 25

While we don’t usually focus on tech support issues here on the Office Blog (that’s what the Microsoft Answers forums are for), let me shine a quick light on a recurring issue that has caused some of you to scratch your heads and write in about.

In a nutshell, the problem appears to be that OneNote 2010 (or OneNote 2007) intercepts all of your print jobs whenever you try to send any information from your other programs or your Web browser to your trusty printer. While you must admit that this is a great way to save paper and finally “go green,” it’s no laughing matter when your boss expects you to hand him or her a printed report and you can’t seem to do that.

What’s happening?

Until recently, you’ve always been able to print anything from your computer to your printer. Now, your print jobs seem to suddenly bypass your printer completely and go straight into Microsoft OneNote, where they appear like scanned images. You really want things to go back to the way things were and have your print jobs sent to your actual printer once again.

What’s causing it?

Microsoft OneNote comes with a nifty little utility called the Send to OneNote print driver. A print driver is a small piece of software that directs output from a computer to a printer. Typically, the operating system controls such software, so it can monitor how a computer talks to hardware devices like a printer. In the case of OneNote, a special print driver is installed that lets you send your print jobs as images into your OneNote notebooks.

The OneNote print driver wasn’t designed to override your printer settings and assume you want every print job sent to OneNote 2010. Instead, it’s intended to be waiting in the wings, available whenever you want to use it, and taking a backseat again whenever you’re done sending a particular print job to OneNote.

However, the OneNote print driver may have accidentally promoted itself to top dog in any of the following conditions:

  • You installed OneNote 2010 or Office 2010 with no physical printer installed or selected at the time, causing the Send to OneNote print driver to act as your default (preferred) printer.
  • You installed a new physical printer on your computer after installing OneNote 2010 or Office 2010, without promoting the printer to act as your default printer.
  • You share your computer with someone else who installed OneNote 2010 or Office 2010 and set the Send to OneNote print driver to act as the default printer.
  • Your printer software is incompatible with your operating system version and Windows has reverted to the Send to OneNote print driver as the default printer.

Even if you’re not really sure how it may have happened, there’s an easy solution.
Setting a default printer in Windows Control Panel

When the Send to OneNote 2010 print driver is marked as shown, print jobs will be sent to OneNote as images.
If you have a real printer installed, right-click its icon, and then click Set as Default Printer on the shortcut menu.
Your printer is recognized as the preferred printer for future print jobs when it has the check mark icon next to it.

How can I fix it?

On any edition of Windows 7, do the following:

  1. On the Windows taskbar, click the Start button.
  2. On the right side of the Start menu, click Control Panel.
  3. When Control Panel opens, click View Devices and Printers (if you’re in Category view) or click Devices and Printers (if you’re in Icon view).
  4. Right-click the printer icon that represents your physical printer, and then click Set as Default Printer on the shortcut menu.

If you’re using Windows Vista, the steps are nearly identical:

  1. On the Windows taskbar, click the Start button.
  2. On the right side of the Start menu, click Control Panel.
  3. When Control Panel opens, click Printer (if you’re in Category view) or click Printers (if you’re in Classic view).
  4. Right-click the printer icon that represents your physical printer, and then click Set as Default Printer on the shortcut menu.

If you do not see an icon for your actual printer, it’s likely that your printer is not correctly installed. Check the printer manufacturer’s website for any updated drivers that are specific to your version of Windows (for example, a 64-bit edition of Windows) and make sure that the printer is properly connected to your computer.

Don’t be hatin’!

Even if you had a bad first impression of the OneNote print driver hogging all of your print jobs, don’t be too quick to dismiss it even after you demote it from being your default “printer.” You might be surprised how useful it is to have the ability to print certain information right into OneNote.

Although digital printouts in OneNote are image files that you can’t edit, you can right-click such images in OneNote 2010 and extract the text from them with the Copy Text from Picture command. As long as the text in the image is large enough and legible, this works really well. You can then paste and use the copied text into your notes or elsewhere in your work.

When you’re properly introduced to it, the OneNote print driver is a pretty cool feature!  😉

Remember, whenever you have a technical support issue, head on over to Microsoft Answers — the official Support forums for OneNote and Office. It is monitored daily by knowledgeable and helpful members of the Microsoft MVP community, Microsoft Support, and the Office product teams.

— Michael C. Oldenburg

Multiplexing… The old and the new.

TF can be used with Aria MX and AriaOS.

Linked below is a guide on how to work with Aria OS and TraceFinder.

This allows the user to make use of his Aria OS system that has been certified for chemical analysis, but would want to take advantage of the superior TF quantitative properties. This relies on the fact that analysis is performed in a batch processing manner.

Aria OS TraceFinder Walkthrough

The Birthplace of Peaks… Peak Detection Parameters

So after all is said and done, in the routine world, data really relies on the basic two dimensions.

Time and Response.

To put it all together we need to setup a way to detect what is really meaningful out of a line of connected dots using these two dimensions.

There are a plethora of detections alogrithms out there. We at Thermo typically use Two (ICIS and Genesis), sometimes a third. As in anything we need a starting place.

In TF we give you the ability to set up what you want your Default detector to be.

This also gives you the option to set the default conditions. Hint: I gave you my preferred default settings in an earlier post.

You use these settings when you make a new compound/peak in a method.

But you can also set up default conditions for you’re other alogrithms. So, if you find the need to change one that has already been assigned to a peak, you’ll have your preferred setting right off the bat.

So this is one place where you can defind your freedom of choice.

Designated Driver?????

One of the issues that many new users have is making sure all the different pieces of software are compatible with each other.

TraceFinder installers guarantee the system has the right Foundation, Xcalibur and TF versions.
In the release notes on the installation disks, we list the appropriate instrument drivers for that particular TraceFinder release version.

An example of this would be an incompatible mass spec driver, with all the other pieces being correctly paired. The instruments may not respond,or the instrument editor may not open because it can not detect the instrument.

So a word to the wise always make sure that if you’re taking TraceFinder out for a spin, you bring along the designated driver.

Processing Across A Network

TraceFinder can store batches on a remote mapped drive on a companies network.

One issue that may arise is latency/slowness of the network itself. Remeber the processing occurs on the local PC, so files and results have to read and written to disk by passing through the network.

If the storage disk is very far away or the network has heavy traffic, processing will slow down.

A remendy of this is to locate the storage server within the building of the laboratory or have a dedicated line.

Also TraceFinder 2.0 and above can be installed in a Cloud configuration where the processing and storage are on a remote server, with multiple instances capable of being hosted. This allows the user to see via a browser the application and process and review results without the latency issue.