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ProMass for Xcalibur Getting Started

In this short tutorial we will get you up and running processing data automatically using ProMass for Xcalibur.  In order to run this example, you will need the example data file and processing method.  These were not distributed with early versions of ProMass.  If you do not have them, we suggest you download and install the latest ProMass package.

In this tutorial we will show you how to:

• Open a template sequence
• Add a data file and processing method
• Process a data file
• Look at the results

How do you want to process your data?  If you want to process spectra manually (i.e., one at a time), you use the process spectrum from the clipboard method.  If you want to process spectra automatically, continue to the next step below.

Open a template sequence:  Let's get started.  Go to the Xcalibur home page. Click on the Sequence Setup button.  Choose File | Open... or click on the folder icon to open an existing sequence.  Locate your ProMass install directory.  Usually this is C:\Program Files\ProMassXcali if you selected the defaults during the installation.  There should be a subdirectory called TestData (e.g., C:\Program Files\ProMassXcali\TestData).  Open the sequence file called test.sld.  You should see a blank sequence.  Also note the three fields that were added called ZNova Params, BioSequence, and Target Info.  These fields are used for adding ZNova parameter strings, protein or oligonucleotide sequences, and other bio-sequence related parameters, respectively.  We'll get to those later.

Add a data file and processing method:  Within the Xcalibur Sequence setup view, double-click on the blank File Name field to add a data file to the template sequence.  Select the myolcmsdata.raw file in the TestData directory.  The Path field in the Xcalibur sample list should have updated with the data file path.  Double click on the empty Proc Method field to add a processing method to the sequence.  Select the test.pmd processing method in the TestData directory.  Now save your Xcalibur sequence as a different name (e.g., File | Save As... myoglobin.sld) in case you want to recall test.sld later and repeat the exercise.

Process a data file: Highlight the sequence row and choose Actions | Batch Reprocess... or click on from the Xcalibur sequence setup window.  Make sure you have the same options checked as shown in the dialogue box below.  Note: your Process Rows entry should only indicate 1, since we are only processing row 1 in the sequence.

Click on OK.

You should see a console window pop up that indicates that ZNova processing is occurring.  When the processing finishes, the Xcalibur processing que will beep to indicate that it is done.

Look at the results:  The easiest way to navigate to the latest results is to open the ProMassXcali HomePage and click on the ProMass Browser button (note: this is a feature that was added in version 1.2).  The ProMass Browser will always display the latest summary report that was created.  Clicking on the links in the top-level summary report will take you to the chromatogram-level summary, where you can browse the spectra from each chromatographic run.

How ProMass results are organized:  We probably need to tell you a bit more about how ProMass results are organized.  When we processed our data file, ProMass created a bunch of results files and automatically put them in a directory called promass_results in the data file path.  Use Windows Explorer to locate your C:\Program Files\ProMassXcali\TestData\promass_results directory.  Double click on the index.html file summary report. You should see an HTML table with an entry for the myoglobin LC/MS data set.  If you would have processed multiple files, you would see a separate row entry for each data file.   In this same directory you'll also see a myolcmsdata.html file which is what we call the chromatogram-level report. Clicking on any link on the summary page will take you to the chromatogram-level summary.  As you scroll through the file you should see LC/MS and LC/UV chromatograms, a raw ESI mass spectrum, a deconvoluted spectrum, and another deconvoluted spectrum zoomed around the biggest peak.  Congratulations!  You just learned the basics of using ProMass.

Oops, what if it did not work?  You followed all of the directions above and no console window came up and you got no index.html file.  Well, probably what happened is that you installed ProMass somewhere other than the default directory and the template processing method does not know about it.  Not a problem.  Open the ProMass home page and click the Check Processing Method button.  Locate the test.pmd processing method that we discussed above.  Follow the directions to fix the test.pmd processing method and repeat the batch reprocess steps above to see if this fixed the problem.

What next?  If you've completed these steps successfully, we would suggest that you explore ProMass Xcali Processing Overview then How to run ProMass Xcali.