Module: MS

Included in:
Fragmenter
Defined in:
lib/fragmenter.rb,
lib/charge_calculator.rb,
lib/fragmenter/masses.rb

Defined Under Namespace

Classes: ChargeCalculator, Fragmenter

Constant Summary collapse

Proton = 
1.00782503207
IonTypeMassDelta = 
{
	a:  (- 29.00273),
	a_star: (-(29.00273+17.02654)),
	a_not:	(-(17.02654 + 29.00273+18.01056)),
	b: (-1.00782),
	b_star: ( - 1.00782 - 17.02654),
	b_not: (-17.02654 - 1.00782 - 18.01056),
	c: (16.01872),
	x: (27.99491 - 1.00782),
	y: (1.00782),
	y_star: (1.00782  - 17.02654),
	y_not: (1.00782 - 18.01056),
	z: (- 16.01872)
}
NTerm = 
1.00782
CTerm = 
27.99491 - 10.9742
MonoResidueMasses = 
{
	:A => 71.037114, 
	:R => 156.101111,
	:N => 114.042927,
	:D => 115.026943,
	:C => 103.009185,
	:E => 129.042593,
	:Q => 128.058578, 
	:G => 57.021464,
	:H => 137.058912,
	:I => 113.084064,
	:L => 113.084064,
	:K => 128.094963,
	:M => 131.040485,
	:F => 147.068414,
	:P => 97.052764,
	:S => 87.032028,
	:T => 101.047679,
	:U => 150.95363,
	:W => 186.079313,
	:Y => 163.06332,
	:V => 99.068414,
   :* => 118.805716,
   :B => 172.048405,
   :X => 118.805716,
   :Z => 128.550585
}
AvgResidueMasses = 
{
  :* => 118.88603, 
  :A => 71.0779, 
  :B => 172.1405, 
  :C => 103.1429, 
  :D => 115.0874, 
  :E => 129.11398, 
  :F => 147.17386, 
  :G => 57.05132, 
  :H => 137.13928, 
  :I => 113.15764, 
  :K => 128.17228, 
  :L => 113.15764, 
  :M => 131.19606, 
  :N => 114.10264, 
  :O => 211.28076, 
  :P => 97.11518, 
  :Q => 128.12922, 
  :R => 156.18568, 
  :S => 87.0773, 
  :T => 101.10388, 
  :U => 150.0379, 
  :V => 99.13106, 
  :W => 186.2099, 
  :X => 118.88603, 
  :Y => 163.17326, 
  :Z => 128.6231
}

Instance Method Summary collapse

Instance Method Details

#charge_state(mass, charge) ⇒ Object 



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# File 'lib/fragmenter/masses.rb', line 11

def charge_state(mass, charge)
	if charge > 0
		(mass + charge) / charge.to_f
	else
		(mass - charge) / charge.to_f
	end
end

#precursor_mass(seq, charge) ⇒ Object 



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# File 'lib/fragmenter/masses.rb', line 3

def precursor_mass(seq, charge)
	mass = NTerm + CTerm
	seq.chars.map(&:to_sym).each do |residue|
		mass += MS::MonoResidueMasses[residue]
	end
	charge_state(mass, charge)
end