I've reading about proteomics and how it can be used with mass spectrometry to sequence digested peptides.

Reading this paper the author states (in box 2):

peptide fragmentation induced by collisions with residual gas, and bond breakage mainly occurs through the lowest energy pathways - that is, cleavage of the amide bonds

Why is cleavage predominately at the amide bond? What makes the amide bond the lowest energy pathway?

  • 1
    $\begingroup$ This question is probably better suited to Chemistry.SE $\endgroup$
    – MattDMo
    Mar 11, 2014 at 20:49
  • 2
    $\begingroup$ @MattDMo While this is a chemistry question, it is also about biologically important molecules, so it is still on-topic here. $\endgroup$ Mar 11, 2014 at 21:34
  • 1
    $\begingroup$ @MadScientist Even though it is about a biological relevant molecule the principle behind this question is chemistry. Note that this is not about peptide formation and degradation in-vivo; it is about collision induced decay (nothing biological here). $\endgroup$
    Dec 8, 2014 at 12:29


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