calculate theoretical isotope distribution give the AA sequence
2
0
Entering edit mode
Oliver • 0
@ollymcrook
Last seen 9 months 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 • 227 views
ADD COMMENT
1
Entering edit mode
@laurent-gatto-5645
Last seen 1 day 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.
ADD COMMENT
0
Entering edit mode
Oliver • 0
@ollymcrook
Last seen 9 months 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

ADD COMMENT

Login before adding your answer.

Traffic: 486 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6