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Topic: Output particular peptide fragments -mass and intensity

My research focus on studing new type of peptide fragmentaion ions. Is there any way that I can define the particular product ions, like b/y product ions, and tell the software to only output the found definded fragments with m/z and intensity information?

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Re: Output particular peptide fragments -mass and intensity

Hi, I am not sure I understand your question correctly. Once you have your peptide sequence defined in your document, you can use Peptide Fragmentation tool to generate theoretical fragments. In the tool GUI you can define which fragments you want to generate. You can then Match the fragments to your measured data and Annotate matched peaks. If you then generate a Report, it provides a table of all the annotations with intensity, error etc.

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Re: Output particular peptide fragments -mass and intensity

Thank you very much for the reply. I was wondering if we could define a new type of fragmentation ion in peptide fragmentation tool by ourselves, not just select the types of fragmentation we want to label.

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Re: Output particular peptide fragments -mass and intensity

Hi,
technically, in the source code it is possible to define a new fragment definition and use it later on. Unfortunately, there is not an option in the UI to use this new fragment.