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FAQ

Frequently asked questions about ProMass for Xcalibur

• Does ProMass for Xcalibur support data from the LTQ-FT and Orbitrap instruments?  Yes, ProMass does work on data from these instruments.  However, ProMass has not yet been optimized to take advantage of the resolution afforded by these instruments.  As a result, your deconvoluted spectra will look like those from a standard LTQ.
  
  
• Does ProMass work on Vendor X data?  ProMass will process any comma or tab-delimited mass-intensity formatted data set.  However, ProMass for Xcalibur requires an installation of Xcalibur.   Contact us if you are interested in running ProMass on other platforms.
  
  
• I've just installed ProMass and I'm getting an error message, when I click on the Build Params button.  What do I do?   Go to our update page and download the latest version and install it.  This should fix the problem.
  
  
• When I click on the ProMass Browser button I get an error message stating, "Error: ProMass summary file could not be found."  What is causing this?  There's really nothing wrong.  The ProMass Browser summary is only created after you do automated processing.  If you have not done any automated processing you will get this error message if you click the ProMass Browser button.
  
  
• Where can I find examples of how your program works on different samples?  Try our applications page.
  
  
• I am having a problem getting good deconvolution of my data set.  What do I do?  Your ProMass parameters are probably not optimized.  Check here if there's an example parameter file that matches your application.  Otherwise, the easiest thing to do is send us your data file.  That way, we can generate an optimized parameter file and send it back to you.  Contact us to discuss this option.
  
  
• How can I zoom deconvoluted spectra within the ProMass report?  You cannot zoom the spectra directly in the ProMass report web pages because the spectra are static gif or jpg images.  However, ProMass versions later than v. 2.3 utilize ProMass DecView to allow interactive manipulation of the spectra, by double clicking the spectra or clicking the [View Data] web link within the ProMass web report in Internet Explorer.   If you do not have this feature, download the latest version of ProMass and you will be able to view your deconvoluted spectra in ProMass DecView.  See the next FAQ for configuring Firefox to work with DecView.
  

• How can I configure Firefox to open deconvolution results (.dec) files with ProMass DecView?

  By default Firefox does not automatically open .dec files in DecView.  This is because Firefox treats .dec files as plain text by default.   You will need to install and configure a Firefox Add-on called Mime Edit to be able to easily open .dec files with Firefox.  The Mime Edit Firefox extension can be obtained here:

  https://addons.mozilla.org/en-US/firefox/addon/4498 

1. Download and install the Mime Edit extension.
2. Restart Firefox.  If the installation was successful, you should see the Mime Edit... option in the Firefox Tools menu.
3. From the Firefox Tools menu, select Mime Edit...
4. Click on the Edit tab.
   
5. Click the New Type... button.
6. In the Edit Type box, enter the following:
1. Mime Type: application/promass
2. Description: ProMass DecView file
3. Extension: dec  (Note: enter dec NOT .dec)
   
4. Select the Open it with the default application option
5. Deselect the Always ask me before handling files of this type option
   
7. Click on OK to exit the Edit Type box
8. The ProMass application should now be displayed in the list of supported file types.
   
9. Click on OK to exit the Mime Edit configuration.  Spectra can now be opened from Firefox in ProMass web reports using the [View Data] link above the mass spectra.