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This tutorial will guide you through the interpretation of a typical SUMmOn analysis.

SUMmOn Analysis Quickstart

The first part of a SUMmOn analysis consists of running the data generated by the MS instrument through the SUMmOn algorithm. The data must first be converted to mzXML format.

After acquiring and converting the data do the following:

• Create a new directory.
• Copy (or create a symbolic link to) the mzXML file in the directory you just created.
• Copy a condition file in the new directory and edit it to match your experimental setup. Some condition files that can be used as templates can be found in the SUMmOn/CondidtionFiles/ directory. These files define the ion series that SUMmOn will search for. For example, if you are working with human SUMO1 on an LCQ instrument, you should choose the condition file called sumo-1_sapiens_trypsin_avg.
• Create a file called subDB.fasta containing the list of all the target proteins you would like SUMmOn to scan for. The file should be in fasta format and the amino acids one letter code must be capital.
• From a shell type "summon -c <conditionFileName> <msFile.mzXM>"

This instructs SUMmOn to use the parameters defined in "conditionFileName" to analyze the MS run "msFile.mzXML".

Condition files for SUMmOn are simple XML files regulated by this Schema. This is the documentation for the Schema.

Here is an example condition file for mouse SUMO-1:

<?xml version="1.0" encoding="UTF-8"?>
<SUMmOnCondition xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 xsi:noNamespaceSchemaLocation="http://summon.sf.net/SUMmOnCondition/1.0/SUMmOnCondition.xsd" 
 description="Tryptice fragment from mouse SUMO-1 ELGMEEEDVIEVYQEQTGG">
    <fragmentMasses type="S">
        130.1234
        113.1594
        57.0519
        131.1926
        129.1155
        129.1155
        129.1155
        115.0886
        99.1326
        113.1594
        129.1155
        99.1326
        163.1760
        128.1307
        129.1155
        128.1307
        101.1051
        57.0519
        57.0519
        0
    </fragmentMasses>
    <modifiedResidue residue="K" notTerminal="0"/>
    <modify residue="M" mass="15.9994" static="0"/>
    <digestC residue="K" notResidue="P"/>
    <digestC residue="R" notResidue="P"/>
    <missCleaveC residue="K" value="1"/>
    <getMissCleaveC residue="K" notResidue="P" value="1"/>
    <digestionTolerance value="3"/>
    <massTolerance value="1"/>
    <endCharge value="5"/>
    <centroiding type="0"/>
    <normalization type="-2"/>
    <targetMs level="2"/>
    <output type="1"/>
    <nonInteractive value="0"/>
</SUMmOnCondition>

This condition file will instruct SUMmOn to run a search for Mouse SUMO-1 assuming that the sample was digested with trypsin (with one missed cleavage at the site of SUMOylation). Methionine oxidation is turned on as a variable modification. The precursor mass tolerance is 3 Da, while the fragment ions tolerance is 1 Da. The program will quickly read through the data and display a multiple choice menu. For this quick start tutorial simply select 5 to save the results of the analysis into an XML file.

Congratulations, you have just finished the first part of the analysis!! Now click here to learn how to interpret the results.