Hello,
I have been using ProteinPilot to analyze a purified protein digest. I am seeing really good coverage of the protein with the software, but the experiments that I will be performing moving forward involve modification of a particular cysteine residue with electrophilic small molecules. Is there a way to add a custom cysteine modification to protein pilot for detection (similar to how one would select iodoacetamide for cysteine alkylation)? For example, one molecule that I am testing as an electrophilic addition to the cysteine residue is sulforaphane, which has a monoisotopic mass of 177.0282. Is there a way that I could put that mass into ProteinPilot as a detectable protein modification?
Thanks,
Matt
Hi Matt,
There are ways to modify ProteinPilot software to incorporate new small molecule binders in your database search if you are using the desktop version of the software. With your software installer in documentation, there should be a document title “Advanced Configuration of ProteinPilot Software.pdf”. This walks you through how you can modify your Parameter Translation file to add new modifications (substitution sets) and modulate probabilities of binding and which residues they are likely to bind too. If you try this, make sure you save a backup of the original un-modified so you can always go back! Also, it is good to have a test dataset where you know the answer, to test that your modifications of the Parameter Translation file are doing what you expect.
Also, our technical support team are very savvy on helping users with adapting the software for novel workflows, so feel free to reach out to support for help!
Christie
Thanks for the reply! Could you point me in the direction of the technical support? I’m having trouble finding it. Thanks!