Class: Ms::Mascot::Fragment

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

Overview

:startdoc::manifest calculates a theoretical Mascot ms/ms spectrum

Calculates the theoretical Mascot ms/ms spectrum for a peptide sequence. A Mascot spectrum differs from the standard in-silico spectrum only in the masses that get used. By default Mascot::Fragment uses masses with 6 significant digits, the same masses that Mascot uses by default, and generates spectra with an intensity of 1.

In addition, Mascot::Fragment supports several alternative series notations.

Notation     Translation    Example
series+<n>   series + Hn    a++, y0++
series*      series - NH3   b*
series0      series - H2O   y0
Immon.       immonium       Immon.

See Ms::Mascot::Spectrum for more details.

Instance Method Summary collapse

Instance Method Details

#headers(spec) ⇒ Object

Generates some MGF-specific headers.



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# File 'lib/ms/mascot/fragment.rb', line 29

def headers(spec)
  {
    :charge => charge,
    :parent_ion_mass => spec.parent_ion_mass(charge),
    :title => "#{spec.sequence.gsub(/\s+/, "")} (#{series.join(', ')})"
  }
end

#spectrum(peptide) ⇒ Object

Returns a Mascot::Spectrum for the peptide.



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# File 'lib/ms/mascot/fragment.rb', line 38

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