InSilicoSpectro-Databanks

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t/insilicodef-test.xml  view on Meta::CPAN

      <loss name="H2O" repeat="1"/>
    </oneFragType>
    <oneFragType name="y-H2O*" series="y" charge="1">
      <loss name="H2O" repeat="-1"/>
    </oneFragType>
    <oneFragType name="y-H2O*-NH3*" series="y" charge="1">
      <loss name="H2O" repeat="-1"/>
      <loss name="NH3" repeat="-1"/>
    </oneFragType>
    <oneFragType name="y++-NH3" series="y" charge="2">
      <loss name="NH3" repeat="1"/>
    </oneFragType>
    <oneFragType name="y++-NH3*" series="y" charge="2">
      <loss name="NH3" repeat="-1"/>
    </oneFragType>
    <oneFragType name="y++-H2O" series="y" charge="2">
      <loss name="H2O" repeat="1"/>
    </oneFragType>
    <oneFragType name="y++-H2O*" series="y" charge="2">
      <loss name="H2O" repeat="-1"/>
    </oneFragType>
    <oneFragType name="z" series="z" charge="1"/>
    <oneFragType name="z-NH3" series="z" charge="1">
      <loss name="NH3" repeat="1"/>
    </oneFragType>
    <oneFragType name="z-NH3*" series="z" charge="1">
      <loss name="NH3" repeat="-1"/>
    </oneFragType>
    <oneFragType name="z-H2O" series="z" charge="1">
      <loss name="H2O" repeat="1"/>
    </oneFragType>
    <oneFragType name="z-H2O*" series="z" charge="1">
      <loss name="H2O" repeat="-1"/>
    </oneFragType>
    <oneFragType name="z++" series="z" charge="2"/>
    <oneFragType name="z++-NH3" series="z" charge="2">
      <loss name="NH3" repeat="1"/>
    </oneFragType>
    <oneFragType name="z++-NH3*" series="z" charge="2">
      <loss name="NH3" repeat="-1"/>
    </oneFragType>
    <oneFragType name="z++-H2O" series="z" charge="2">
      <loss name="H2O" repeat="1"/>
    </oneFragType>
    <oneFragType name="z++-H2O*" series="z" charge="2">
      <loss name="H2O" repeat="-1"/>
    </oneFragType>
  </fragTypes>

  <internalFragType>
    <oneInternFragType name="immo">
      <residues>HFILYPV</residues>
      <delta monoisotopic="-26.9871" average="-26.9871"/>
    </oneInternFragType>
  </internalFragType>

 </fragTypeDefSet>
</fragTypeDescriptions>

<modRes>
  <oneModRes type="ptm" name="ACET_nterm">
    <description>Acetylation_nterm</description>
    <site>
      <residue>^NKHFW</residue>
      <nterm/>
    </site>
    <residues aa="^NKHFW" nterm="yes"/>
    <delta monoisotopic="42.0106" average="42.0373"/>
    <sprotFT><![CDATA[(N-acetylalanine|N-acetylaspartate|N-acetylcysteine|N-acetylglutamate|N-acetylglycine|N-acetylmethionine|N-acetylproline|N-acetylserine|N-acetylthreonine|N-acetyltyrosine|N-acetylvaline).*]]></sprotFT>
  </oneModRes>
  <oneModRes type="ptm" name="ACET_core">
    <description>Acetylation_core</description>
    <site>
      <residue>KR</residue>
    </site>
    <residues aa="KR"/>
    <delta monoisotopic="42.0106" average="42.0373"/>
    <sprotFT><![CDATA[(N2-acetylarginine|N6-acetyllysine).*]]></sprotFT>
  </oneModRes>
  <oneModRes type="ptm" name="PHOS">
    <description>Phosphorylation</description>
    <site>
      <residue>STYHD</residue>
    </site>
    <residues aa="STYHD"/>
    <delta monoisotopic="79.9663" average="79.9799" />
    <sprotFT><![CDATA[(4-aspartylphosphate|Phosphoarginine|Phosphocysteine|Phosphohistidine|Phosphoserine|Phosphothreonine|Phosphotyrosine|Pros-phosphohistidine|Tele-phosphohistidine).*]]></sprotFT>
  </oneModRes>
  <oneModRes type="ptm" name="AMID">
    <description>Amidation</description>
    <siteRegexp cterm="yes">.(?=G)</siteRegexp>
    <residues aa="." aaAfter="G" cterm="yes"/>
    <delta monoisotopic="-0.9840" average="-0.9847"/>
    <sprotFT><![CDATA[(Alanine amide|Arginine amide|Aspartic acid 1-amide|Asparagine amide|Cysteine amide|Glutamic acid 1-amide|Glutamine amide|Glycine amide|Histidine amide|Isoleucine amide|Leucine amide|Lysine amide|Methionine amide|Phenylalanine a...
  </oneModRes>
  <oneModRes type="ptm" name="DEAMID" description="Deamidation">
    <description></description>
    <site>
      <residue>NQ</residue>
    </site>
    <residues aa="NQ"/>
    <delta monoisotopic="0.9840" average="0.9847"/>
    <sprotFT><![CDATA[(Deamidated asparagine|Deamidated glutamine).*]]></sprotFT>
  </oneModRes>
  <oneModRes type="ptm" name="DEAM_N">
    <description>Deamidation_N</description>
    <siteRegexp>N(?=G)</siteRegexp>
    <residues aa="N" aaAfter="G"/>
    <delta monoisotopic="0.9840" average="0.9847"/>
    <sprotFT><![CDATA[(Deamidated asparagine).*]]></sprotFT>
  </oneModRes>
  <oneModRes type="ptm" name="DEAM_Q">
    <description>Deamidation_Q</description>
    <site>
      <residue>Q</residue>
    </site>
    <residues aa="Q"/>
    <delta monoisotopic="0.9840" average="0.9847"/>
    <sprotFT><![CDATA[(Deamidated glutamine).*]]></sprotFT>
  </oneModRes>
   <oneModRes type="ptm" name="BIOT">
    <description>Biotin</description>
    <site>
      <residue>K</residue>
      <cterm/>
    </site>
    <residues aa="K" cterm="yes" prositeRule="PDOC00167"/>
    <prositeRule>PDOC00167</prositeRule>
    <delta monoisotopic="226.0776" average="226.2934"/>
  </oneModRes>
  <oneModRes type="ptm" name="CAM_nterm">



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