calculate theoretical isotope distribution give the AA sequence
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Entering edit mode
Oliver • 0
@ollymcrook
Last seen 4.0 years ago
oxford

I am looking for an R package preferably Bioconductor that will compute the theoretical isotope spectra given the amino acid sequence. For example

AYARATAYT

should return these details.

Most likely isotope combination: 12C44 1H66 14N12 16O14 Exact mass is 986.482 Probability of combination is 56.118%

  • 986.48 1.000000000
  • 987.48 0.552510687
  • 988.48 0.177857196
  • 989.48 0.042054957
  • 990.48 0.008026484 etc

another example where the major isotope is [M+1]/Z

AYARATAYTRYTNNPPY

Most likely isotope combination: 12C89 13C1 1H129 14N25 16O27 Exact mass is 1992.952 Probability of combination is 31.025%

  • 1991.95 0.884750727
  • 1992.95 1.000000000
  • 1993.95 0.607872385
  • 1994.95 0.261239673
  • 1995.95 0.088463730
  • 1996.95 0.025004454 etc

It would also be great if we could return isotope distributions for label incoperation could also be supported such as 15N or 2H. I'm sure a good package must exist somewhere.

Metabolomics proteomics MassSpectrometry • 1.5k views
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@laurent-gatto-5645
Last seen 8 weeks ago
Belgium
  • In section Working with peptide sequences in the RforProteomics vignette, I used OrgMassSpecR to calculate the the isotope distributions for different 15N incorportations.
  • Otherwise, the BRAIN package might be useful: Baffling Recursive Algorithm for Isotope distributioN calculations.
  • Finally, the camera package has a vignette about Isotope pattern validation with CAMERA.
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Oliver • 0
@ollymcrook
Last seen 4.0 years ago
oxford

OrgMassSpecR seems to have the required code in IsotopicDistributionHDX.R, seems worth slightly rewriting to make it a little more general. Thanks Laurent

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