I am trying to study peptide fragmentation in mass spectrometry. My goal is to find software with which I can retrieve the molecular structure of the peptide and see the a,b,c fragments.

I found these two online tools. Pep draw & Fragment Ion Calculator. Ι entered a short sequence and I retrieved the m/z values for the a.b.c and x.y.z values in a table.

Is there any software /online tool that I will add a peptide sequence and automatically generate the chemical structure? I want this image generated but for my peptide sequence instead of the side chains.

enter image description here

  • $\begingroup$ By "generate automatically the chemical structure" do you mean the 3-d structure of the fragment peptide? If you google "predicting 3d structure of peptides from sequence" you'll find references to a bunch of software that attempts to do this, the PEP-Fold server for example. Of course as the fragment gets larger the problem gets harder, and you end up needing Alpha-Fold. $\endgroup$ Feb 9 at 20:45
  • $\begingroup$ @CharlesE.Grant I just edited my post. Maybe now is more clear what I am searching for. $\endgroup$
    – KGee
    Feb 10 at 22:19


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