Class: Mascot::DAT::PSM

Inherits:
Object
  • Object
show all
Defined in:
lib/mascot/dat/psm.rb

Overview

A single Peptide Spectrum Match (PSM) result. In Mascot parlance, this is a match from a query (e.g. a single MS2 spectrum from a MGF file) to a given peptide. A query may match more than one peptide at a given score, and Mascot will report these in order of descending significance, or “rank”.

From the Mascot documentation, the following represents a reasonably complete PSM entry

q1_p1_db=01  # two digit integer of the search DB index, zero filled and retarded.
q1_p1=missed cleavages, (-1 indicates no match)
      peptide Mr,
      delta,
      number of ions matched,
      peptide string,
      peaks used from Ions1,
      variable modifications string,
      ions score,
      ion series found,
      peaks used from Ions2,
      peaks used from Ions3;
      "accession string":frame number:start:end:multiplicity, # data for first protein
      "accession string":frame number:start:end:multiplicity, # data for second protein, etc.
q1_p1_et_mods=modification mass,
              neutral loss mass,
              modification description
q1_p1_primary_nl=neutral loss string
q1_p1_drange=startPos:endPos
q1_p1_terms=residue,residue:residue,residue # flanking AA for each protien, in order

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(psm_entry) ⇒ Mascot::DAT::PSM

Parameters:

  • psm_entry (Array) —

    The multi-line string entry from the Mascot DAT file



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# File 'lib/mascot/dat/psm.rb', line 51

def initialize(psm_entry)
  parse_entry(psm_entry)
end

Instance Attribute Details

#attrs ⇒ Object

Returns the value of attribute attrs.



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# File 'lib/mascot/dat/psm.rb', line 47

def attrs
  @attrs
end

#dbs ⇒ Object

Returns the value of attribute dbs.



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# File 'lib/mascot/dat/psm.rb', line 45

def dbs
  @dbs
end

#delta ⇒ Object

Returns the value of attribute delta.



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# File 'lib/mascot/dat/psm.rb', line 35

def delta
  @delta
end

#ion_series_str ⇒ Object

Returns the value of attribute ion_series_str.



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# File 'lib/mascot/dat/psm.rb', line 41

def ion_series_str
  @ion_series_str
end

#ions1 ⇒ Object

Returns the value of attribute ions1.



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# File 'lib/mascot/dat/psm.rb', line 38

def ions1
  @ions1
end

#ions2 ⇒ Object

Returns the value of attribute ions2.



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# File 'lib/mascot/dat/psm.rb', line 42

def ions2
  @ions2
end

#ions3 ⇒ Object

Returns the value of attribute ions3.



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# File 'lib/mascot/dat/psm.rb', line 43

def ions3
  @ions3
end

#missed_cleavages ⇒ Object

Returns the value of attribute missed_cleavages.



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# File 'lib/mascot/dat/psm.rb', line 33

def missed_cleavages
  @missed_cleavages
end

#mr ⇒ Object

Returns the value of attribute mr.



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# File 'lib/mascot/dat/psm.rb', line 34

def mr
  @mr
end

#num_ions_matched ⇒ Object

Returns the value of attribute num_ions_matched.



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# File 'lib/mascot/dat/psm.rb', line 36

def num_ions_matched
  @num_ions_matched
end

#pep ⇒ Object

Returns the value of attribute pep.



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# File 'lib/mascot/dat/psm.rb', line 37

def pep
  @pep
end

#proteins ⇒ Object

Returns the value of attribute proteins.



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# File 'lib/mascot/dat/psm.rb', line 44

def proteins
  @proteins
end

#query ⇒ Object

Returns the value of attribute query.



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# File 'lib/mascot/dat/psm.rb', line 31

def query
  @query
end

#rank ⇒ Object

Returns the value of attribute rank.



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# File 'lib/mascot/dat/psm.rb', line 32

def rank
  @rank
end

#score ⇒ Object

Returns the value of attribute score.



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# File 'lib/mascot/dat/psm.rb', line 40

def score
  @score
end

#terms ⇒ Object

Returns the value of attribute terms.



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# File 'lib/mascot/dat/psm.rb', line 46

def terms
  @terms
end

#var_mods_str ⇒ Object

Returns the value of attribute var_mods_str.



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# File 'lib/mascot/dat/psm.rb', line 39

def var_mods_str
  @var_mods_str
end