Open a template Xcalibur sequence In this short tutorial we will get you up and running processing data automatically using ProMass. In order to run these examples, you will need the example data file and processing method. The example files are in the subdirectory called TestData in the install directory (e.g., C:\Program Files\ProMassXcali\TestData). The data file is an LC/MS run of myoglobin with a single chromatographic peak. This example will demonstrate automatic selection of the largest TIC peak from an LC/MS chromatogram, deconvolution of the spectrum, and reporting of the results.
In this tutorial we will show you how to:
Open a template Xcalibur sequence
Add a data file and processing
method
Process a data file
View 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 dialog 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, as shown below:
When the processing finishes, the Xcalibur processing queue will beep to indicate that it is done.
View the results: The easiest way to navigate to the latest results is to open the ProMass Home Page and click on the ProMass Browser button. The ProMass Browser will always display the latest summary report that was created. Clicking on the links in the ProMass Browser 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: 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 should also see a myolcmsdata.html file, which is the chromatogram-level summary for the data set. Clicking on any link on the ProMass Browser 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.
What if it did not work? If you followed all of the directions above and no console window popped up and there was no index.html file, there is a likely remedy. If you installed ProMass somewhere other than the default directory (C:\Program Files\ProMassXcali ), the template processing method does not have the correct path to the ProMass program. Open the ProMass home page and click the Check Processing Method button. Locate the test.pmd processing method that we used in the example 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 have completed these steps successfully, we would suggest that you explore ProMass Processing Overview then Automated Processing with ProMass. A more advanced example of ProMass automated processing is also available highlighting the use of the program for oligonucleotide MW confirmation.