Implementing the ISB program t2x for the conversion of Xcalibur raw files to the new universal mzXML format. Your new mzXML file can then be viewed with the free Insilicos viewer and searched on the public version of the Phenyx Search Engine.

1.) Go to the START menu on your computer, and click on the "Run..." tab. 
2.) Click on RUN, a dialog box will come up, type cmd  
3.) Type cd\
4.) Type cd "your path to the folder"  mzXML is the folder in this example.
5.) Type, t2x yourrawfilename.raw, as shown in Figure 1 and hit return
6.) Wait until the converting process is finished, this can take minutes, 5, 10, or 20, depending on the size of your file and the speed of your computer.  Your can go to the task manager by typing control-alt-delete and then click on the processes tab to see if t2x is done running.

(Yes, we tried to just click on the t2x icon to launch the program but that did not work on our computer, you need to tell the program which file to convert from the run command line.)

Here is a screen shot of the run dialog and the folder.  Notice in the folder view that the created mzXML file is 1.4 times bigger.

Figure 1
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Download the free Insilicos Viewer at http://www.insilicos.com/products.html

Figure 2

The free viewer comes with an installer and installs painlessly.  It is a small program and very efficient so it launches quickly and also opens files quickly.

Once the viewer is installed open the program and open the file you just converted to mzXML format.  It is as easy as that!  It is a revolution I think.  Now anyone can read native Finnigan Xcalibur files.  Thank you Insilicos and ISB!  Here are a few screen shots of the program.

Figure 3

Figure 3: This is a screen shot of the viewer with a base peak plot in the upper left hand frame and a full MS spectrum in the bottom plot.  Notice the tabs at the bottom, the first tab is the full MS followed by the three MS2s that were performed.

Figure 4

Figure 4: Shows a screen shot of the viewer with a base peak plot in the upper left hand frame and an MS2 spectrum in the bottom plot. 

Now that you have your data in the new common file format, mzXML, you can submit your files to those proteoimc search engines that accept mzXML.  If your vendor does not support mzXML tell them that you want it. 

Figure 5
This is the Public Phenyx data submission page.  Browse to your new mzXML file to begin your search.

Figure 6

This is the Phenyx Results Page.  Look at how well the horse myoglobin hit differentiates itself from the second hit, scores 108.87 and 31.0 respectively.   Pretty amazing!  That OLAV scoring must be doing something  right!  The protein coverage is 66%.  Click on the details link to see the protein details page.  If you would like to do your own Phenyx search click here to download the mzXML file.

This is the protein match details page.  All of the peptides identified are listed here as well as the protein sequence coverage map.

Shown below is the sequence coverage map.  Notice the half cleaved peptides and those matches that were deemed invalid.

Figure 7

Below is the peptide match details page.  Remember this was all from an mzXML file generated from a native Xcalibur raw file.  Also remember that you can download tools from SourceForge and ISB that can convert other MS formats to mzXML!   We have also noticed that Phenyx does a very good job at identifying, scoring, and correlating difficult spectra.