z ion-type masses

Issue #28 resolved
Anonymous created an issue

Hello, Pyteomics Team

I am a current chemsitry graduate student at the University of Michigan using pyteomics for top-down sequencing. I used one of your combined examples: https://pythonhosted.org/pyteomics/examples/example_msms.html

I obtain the list of z-ions from a sequence, but when I compare them to the z-ions obtained from the same sequence from the MS-Product section of Protein-Prospector (http://prospector.ucsf.edu/prospector/mshome.htm), the z-ions produced by pyteomics are one hydrogen mass lower. Has somebody else experience this? Is this related to z'+ vs z(superscript dot) +, radical/even-electron pairs for c and z ions?

Thanks for your attention,

Carolina Rojas Ramirez

Graduate Student

Department of Chemistry

University of Michigan

Comments (4)

  1. Lev Levitsky repo owner

    Hi Carolina,

    indeed, Protein-Prospector calculates z-dot ion m/z, while pyteomics calculates regular z ions. This was briefly discussed on our mailing list as long as 5 years ago. Nothing changed since then, apparently I forgot to add "z-dot" to std_ion_comp. I will add it now.

    However, you don't need to wait. The linked discussion shows how you can add your own ion_comp and use it for m/z calculation.

    Let me know if you have any follow-up questions.

    Best regards,

    Lev

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