Class: Ms::Mascot::Fragment

Inherits:
InSilico::Fragment
  • Object
show all
Defined in:
lib/ms/mascot/fragment.rb

Overview

Ms::Mascot::Fragment::manifest calculates a theoretical Mascot ms/ms spectrum

Calculates the parent ion mass and theoretical ms/ms spectrum for a peptide sequence. Configurations allow the specification of one or more fragmentation series to include, as well as charge, and intensity.

% rap fragment TVQQEL --+ dump --no-audit
# date: 2008-09-15 14:37:55
---
ms/mascot/fragment (:...:):
- - 717.3777467
  - - 102.054955
    - 132.1019047
    - 201.123369
    - 261.1444977
    - 329.181947
    - 389.2030757
    - 457.240525
    - 517.2616537
    - 586.283118
    - 616.3300677

In the output, the parent ion mass is given first, followed by an array of the sorted fragmentation data.

Instance Method Summary collapse

Instance Method Details

#spectrum(peptide) ⇒ Object 



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# File 'lib/ms/mascot/fragment.rb', line 33

def spectrum(peptide)
  Mascot::Spectrum.new(peptide, nterm, cterm)
end