ProtMax was mentioned in a new paper this month in MCP, and Google helped me find it. It is a really quick, simple, and extremely useful application provided by the University of Vienna and written by Dr. V. Egelhofer.
You upload the processed MzXML file and it automatically gives you quan data by spectral counting. It can take into account retention time and link your spectral counts to your protein. You can also make it search a specific target list, rather than the full scan data. At the site it is also possible to download test data to verify that your formats are correct. Hopefully there will be instructions soon for this handy little tool!
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