Class: SpectrumQuery

Inherits:
Object
  • Object
show all
Defined in:
lib/protk/spectrum_query.rb

Overview

<spectrum_query spectrum=“mr176-BSA100fmole_BA3_01_8167.00003.00003.2” start_scan=“3” end_scan=“3” precursor_neutral_mass=“1398.7082” assumed_charge=“2” index=“2” experiment_label=“mr176”> <search_result> <search_hit hit_rank=“1” peptide=“SQVFQLESTFDV” peptide_prev_aa=“R” peptide_next_aa=“K” protein=“tr|Q90853|Q90853_CHICK” protein_descr=“Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1” num_tot_proteins=“1” num_matched_ions=“9” tot_num_ions=“22” calc_neutral_pep_mass=“1380.6557” massdiff=“18.053” num_tol_term=“1” num_missed_cleavages=“0” is_rejected=“0”> <search_score name=“hyperscore” value=“23.9”/> <search_score name=“nextscore” value=“19.3”/> <search_score name=“bscore” value=“9.6”/> <search_score name=“yscore” value=“7.6”/> <search_score name=“cscore” value=“0”/> <search_score name=“zscore” value=“0”/> <search_score name=“ascore” value=“0”/> <search_score name=“xscore” value=“0”/> <search_score name=“expect” value=“0.099”/> <analysis_result analysis=“peptideprophet”> <peptideprophet_result probability=“0.9997” all_ntt_prob=“(0.0000,0.9997,0.9999)”> <search_score_summary> <parameter name=“fval” value=“2.3571”/> <parameter name=“ntt” value=“1”/> <parameter name=“nmc” value=“0”/> <parameter name=“massd” value=“18.053”/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query>

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ SpectrumQuery

Returns a new instance of SpectrumQuery.



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# File 'lib/protk/spectrum_query.rb', line 102

def initialize()

end

Instance Attribute Details

#psms ⇒ Object

attr_accessor :index



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# File 'lib/protk/spectrum_query.rb', line 45

def psms
  @psms
end

#retention_time ⇒ Object

Returns the value of attribute retention_time.



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# File 'lib/protk/spectrum_query.rb', line 40

def retention_time
  @retention_time
end

#spectrum_title ⇒ Object

Returns the value of attribute spectrum_title.



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# File 'lib/protk/spectrum_query.rb', line 39

def spectrum_title
  @spectrum_title
end

Class Method Details

.from_mzid(query_node, mzid_doc) ⇒ Object

<SpectrumIdentificationResult spectraData_ref=“ma201_Vp_1-10.mzML.mgf” spectrumID=“index=3152” id=“SIR_1”>

<SpectrumIdentificationItem passThreshold="false"
rank="1" peptide_ref="KSPVYKVHFTR"
calculatedMassToCharge="1360.7615466836999"
experimentalMassToCharge="1362.805053710938"
chargeState="1" id="SII_1_1">
  <PeptideEvidenceRef peptideEvidence_ref="PepEv_1" />
  <Fragmentation>
    <IonType charge="1" index="1 4">
      <FragmentArray measure_ref="Measure_MZ"
      values="175.2081208 560.3388993" />
      <FragmentArray measure_ref="Measure_Int"
      values="94.0459823608 116.2766723633" />
      <FragmentArray measure_ref="Measure_Error"
      values="0.08916864948798775 0.0449421494880653" />
      <cvParam cvRef="PSI-MS" accession="MS:1001220"
      name="frag: y ion" />
    </IonType>
  </Fragmentation>
  <cvParam cvRef="PSI-MS" accession="MS:1002466"
  name="PeptideShaker PSM score" value="0.0" />
  <cvParam cvRef="PSI-MS" accession="MS:1002467"
  name="PeptideShaker PSM confidence" value="0.0" />
  <cvParam cvRef="PSI-MS" accession="MS:1002052"
  name="MS-GF:SpecEValue" value="1.4757611E-6" />
  <cvParam cvRef="PSI-MS" accession="MS:1001117"
  name="theoretical mass" value="1360.7615466836999" />
  <cvParam cvRef="PSI-MS" accession="MS:1002543"
  name="PeptideShaker PSM confidence type"
  value="Not Validated" />
</SpectrumIdentificationItem>
<cvParam cvRef="PSI-MS" accession="MS:1000796"
name="spectrum title"
value="Suresh Vp 1 to 10_BAF.3535.3535.1" />
<cvParam cvRef="PSI-MS" accession="MS:1000894"
name="retention time" value="6855.00001" unitCvRef="UO"
unitAccession="UO:0000010" unitName="seconds" />

</SpectrumIdentificationResult>



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# File 'lib/protk/spectrum_query.rb', line 89

def from_mzid(query_node,mzid_doc)
	query = new()
	query.spectrum_title = mzid_doc.get_cvParam(query_node,"MS:1000796")['value'].to_s
	query.retention_time = mzid_doc.get_cvParam(query_node,"MS:1000894")['value'].to_f
	items = MzIdentMLDoc.find(query_node,"SpectrumIdentificationItem")
	query.psms = items.collect { |item| PSM.from_mzid(item,mzid_doc) }
	query
end

Instance Method Details

#as_pepxml ⇒ Object

<spectrum_query spectrum=“SureshVp1to10_BAF.00833.00833.1” start_scan=“833” end_scan=“833” precursor_neutral_mass=“1214.5937” assumed_charge=“1” index=“3222”> <search_result>



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# File 'lib/protk/spectrum_query.rb', line 110

def as_pepxml()
	node = XML::Node.new('spectrum_query')
	node['spectrum']=self.spectrum_title
	node['retention_time_sec']=self.retention_time.to_s


	# Use the first psm to populate spectrum level values
	first_psm=self.psms.first

	c=first_psm.charge

	node['precursor_neutral_mass']=(first_psm.experimental_mz*c-c*HYDROGEN_MASS).to_s
	node['assumed_charge']=c.to_s


	self.psms.each do |psm|  
		node << psm.as_pepxml
	end
   	node
end