This tutorial is going to address the PTM Finder tool. Using the PTM finder, you can identify any additional PTMs and increase the coverage of the proteins already found. It is important to note that the PTM Finder can only be applied to a Protein ID results file. As it is very time consuming to run Protein ID with many PTMs, this allows searching for more PTMs in less time. Make sure that you click on a Protein ID result before performing a PTM Finder search.

1) Click the PTM Finder toolbar icon or select “PTM Finder” from the “Tools” menu.
2) Enter the settings as shown:

• Parent ion error tolerance to 0.1 daltons using monoisotopic mass
• Fragment mass error tolerance to 0.8 daltons
• Enzyme to trypsin
• Carboxymethyl as our fixed PTM
• Oxidation M and Deamidation as variable
• Search through the sample db database

Note here we can use decoy database validation if we wanted. As previously mentioned, saving the parameters for future reference is achieved by clicking on the “Save Parameter” button.

Click “OK” to commence analysis.

After the PTM Finder search is complete, double click on the result node. The “Peptide View” window will appear.

The results will be displayed in the same format as was seen for Protein ID. Recall that the Protein ID search identified spectra 1, 3, 4 and 5. The PTM finder search also displayed spectra 2 with the addition of deamidation on N.

Click here to continue on to the next tutorial, dedicated to inChorus multi-engine protein ID.