Class: Ms::Mascot::Dat::Peptides::PeptideHit

Inherits:
Struct
  • Object
show all
Defined in:
lib/ms/mascot/dat/peptides.rb

Overview

PeptideHit

Represents peptide hit data, infered by inspection of the MS/MS sample results, esp F981123.dat.

# str: 0,499.300598,-0.051862,2,LAVPT,10,0000000,3.87,0001002000000000000,0,0

index  example              meaning
0      0                    n Missed Cleavages
1      499.300598           Monoisotopic mass of neutral peptide Mr(calc)
2      -0.051862            actual - theoretical delta mass
3      2
4      LAVPT                matched sequence
5      10
6      0000000              modification sites (including n,c residues; number indicates mod)
7      3.87                 peptide score
8      0001002000000000000
9      0
10     0

The dat file is said to be generate by Mascot version 1.0, but the headers section records 2.1.119.

Modification Sequence

The modification sequence indicates which residues are modified and includes the n and c-terminal residues. The index at each location indicates the modification used (0 indicates no modification).

Unaccounted for data

Peptide data known to exist in the dat file:

Homology threshold
Identity threshold
Frame number
Number of fragment ion matches
Experimental charge

Instance Attribute Summary collapse

Instance Attribute Details

#delta_mass ⇒ Object

Returns the value of attribute delta_mass

Returns:

  • (Object) —

    the current value of delta_mass



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def delta_mass
  @delta_mass
end

#hit_num ⇒ Object

Returns the value of attribute hit_num

Returns:

  • (Object) —

    the current value of hit_num



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def hit_num
  @hit_num
end

#modifications ⇒ Object

Returns the value of attribute modifications

Returns:

  • (Object) —

    the current value of modifications



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def modifications
  @modifications
end

#n_missed_cleavages ⇒ Object

Returns the value of attribute n_missed_cleavages

Returns:

  • (Object) —

    the current value of n_missed_cleavages



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def n_missed_cleavages
  @n_missed_cleavages
end

#peptide_mass ⇒ Object

Returns the value of attribute peptide_mass

Returns:

  • (Object) —

    the current value of peptide_mass



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def peptide_mass
  @peptide_mass
end

#protein_maps ⇒ Object

Returns the value of attribute protein_maps

Returns:

  • (Object) —

    the current value of protein_maps



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def protein_maps
  @protein_maps
end

#query_num ⇒ Object

Returns the value of attribute query_num

Returns:

  • (Object) —

    the current value of query_num



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def query_num
  @query_num
end

#score ⇒ Object

Returns the value of attribute score

Returns:

  • (Object) —

    the current value of score



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def score
  @score
end

#sequence ⇒ Object

Returns the value of attribute sequence

Returns:

  • (Object) —

    the current value of sequence



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def sequence
  @sequence
end

#unknown10 ⇒ Object

Returns the value of attribute unknown10

Returns:

  • (Object) —

    the current value of unknown10



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def unknown10
  @unknown10
end

#unknown3 ⇒ Object

Returns the value of attribute unknown3

Returns:

  • (Object) —

    the current value of unknown3



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def unknown3
  @unknown3
end

#unknown5 ⇒ Object

Returns the value of attribute unknown5

Returns:

  • (Object) —

    the current value of unknown5



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def unknown5
  @unknown5
end

#unknown8 ⇒ Object

Returns the value of attribute unknown8

Returns:

  • (Object) —

    the current value of unknown8



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def unknown8
  @unknown8
end

#unknown9 ⇒ Object

Returns the value of attribute unknown9

Returns:

  • (Object) —

    the current value of unknown9



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# File 'lib/ms/mascot/dat/peptides.rb', line 72

def unknown9
  @unknown9
end