<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<!-- DTD for polymer definitions, used by the
'massXpert' mass spectrometry application.
Copyright 2006,2019 Filippo Rusconi
Licensed under the GNU GPL -->
<!DOCTYPE polchemdefinition [
<!ELEMENT polchemdefinition (polchemdefdata)>
<!ATTLIST polchemdefinition version NMTOKEN #REQUIRED>
<!ELEMENT polchemdefdata (name , leftcap , rightcap , codelen , ionizerule , monomers , modifs , crosslinkers , cleavageagents , fragmentationpathways)>
<!ELEMENT ionizerule (formula , charge , level)>
<!ELEMENT monomers (mnm)*>
<!ELEMENT modifs (mdf)*>
<!ELEMENT crosslinkers (clk)*>
<!ELEMENT cleavageagents (cla)*>
<!ELEMENT fragmentationpathways (fgp)*>
<!ELEMENT mnm (name , code , formula)>
<!ELEMENT mdf (name , formula , targets , maxcount)>
<!ELEMENT clk (name , formula , modifname*)>
<!ELEMENT cla (name , pattern , clr*)>
<!ELEMENT fgp (name , end , formula , sidechaincontrib , comment? , fgr*)>
<!ELEMENT clr (name , (le-mnm-code , le-formula)? , (re-mnm-code , re-formula)?)>
<!ELEMENT fgr (name , formula , prev-mnm-code? , curr-mnm-code? , next-mnm-code? , comment?)>
<!ELEMENT leftcap (#PCDATA)>
<!ELEMENT rightcap (#PCDATA)>
<!ELEMENT codelen (#PCDATA)>
<!ELEMENT charge (#PCDATA)>
<!ELEMENT maxcount (#PCDATA)>
<!ELEMENT level (#PCDATA)>
<!ELEMENT name (#PCDATA)>
<!ELEMENT modifname (#PCDATA)>
<!ELEMENT code (#PCDATA)>
<!ELEMENT formula (#PCDATA)>
<!ELEMENT sidechaincontrib (#PCDATA)>
<!ELEMENT targets (#PCDATA)>
<!ELEMENT pattern (#PCDATA)>
<!ELEMENT end (#PCDATA)>
<!ELEMENT le-mnm-code (#PCDATA)>
<!ELEMENT re-mnm-code (#PCDATA)>
<!ELEMENT le-formula (#PCDATA)>
<!ELEMENT re-formula (#PCDATA)>
<!ELEMENT comment (#PCDATA)>
<!ELEMENT prev-mnm-code (#PCDATA)>
<!ELEMENT curr-mnm-code (#PCDATA)>
<!ELEMENT next-mnm-code (#PCDATA)>
]>
<polchemdefinition version="1">
  <polchemdefdata>
    <name>protein-3-letters</name>
    <leftcap>"N-term amine" +H</leftcap>
    <rightcap>"C-term carboxylic acid" +OH</rightcap>
    <codelen>3</codelen>
    <ionizerule>
      <formula>+H</formula>
      <charge>1</charge>
      <level>1</level>
    </ionizerule>
    <monomers>
      <mnm>
        <name>Glycine</name>
        <code>Gly</code>
        <formula>C2H3NO</formula>
      </mnm>
      <mnm>
        <name>Alanine</name>
        <code>Ala</code>
        <formula>C3H5NO</formula>
      </mnm>
      <mnm>
        <name>Valine</name>
        <code>Val</code>
        <formula>C5H9NO</formula>
      </mnm>
      <mnm>
        <name>Leucine</name>
        <code>Leu</code>
        <formula>C6H11NO</formula>
      </mnm>
      <mnm>
        <name>DiaminoPimelic</name>
        <code>Dap</code>
        <formula>C7H12N2O3</formula>
      </mnm>
      <mnm>
        <name>Isoleucine</name>
        <code>Ile</code>
        <formula>C6H11NO</formula>
      </mnm>
      <mnm>
        <name>Serine</name>
        <code>Ser</code>
        <formula>C3H5NO2</formula>
      </mnm>
      <mnm>
        <name>Threonine</name>
        <code>Thr</code>
        <formula>C4H7NO2</formula>
      </mnm>
      <mnm>
        <name>Cysteine</name>
        <code>Cys</code>
        <formula>C3H5NOS</formula>
      </mnm>
      <mnm>
        <name>Methionine</name>
        <code>Met</code>
        <formula>C5H9NOS</formula>
      </mnm>
      <mnm>
        <name>Arginine</name>
        <code>Arg</code>
        <formula>C6H12N4O</formula>
      </mnm>
      <mnm>
        <name>Lysine</name>
        <code>Lys</code>
        <formula>C6H12N2O</formula>
      </mnm>
      <mnm>
        <name>Aspartate</name>
        <code>Asp</code>
        <formula>C4H5NO3</formula>
      </mnm>
      <mnm>
        <name>Glutamate</name>
        <code>Glu</code>
        <formula>C5H7NO3</formula>
      </mnm>
      <mnm>
        <name>Asparagine</name>
        <code>Asn</code>
        <formula>C4H6N2O2</formula>
      </mnm>
      <mnm>
        <name>Glutamine</name>
        <code>Gln</code>
        <formula>C5H8N2O2</formula>
      </mnm>
      <mnm>
        <name>Tryptophan</name>
        <code>Trp</code>
        <formula>C11H10N2O</formula>
      </mnm>
      <mnm>
        <name>Phenylalanine</name>
        <code>Phe</code>
        <formula>C9H9N1O</formula>
      </mnm>
      <mnm>
        <name>Tyrosine</name>
        <code>Tyr</code>
        <formula>C9H9N1O2</formula>
      </mnm>
      <mnm>
        <name>Histidine</name>
        <code>His</code>
        <formula>C6H7N3O</formula>
      </mnm>
      <mnm>
        <name>Proline</name>
        <code>Pro</code>
        <formula>C5H7N1O1</formula>
      </mnm>
    </monomers>
    <modifs>
      <mdf>
        <name>Acetylation</name>
        <formula>C2H2O1</formula>
        <targets>;Lys;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>AmidationAsp</name>
        <formula>H1N1-O1</formula>
        <targets>;Asp;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>AmidationGlu</name>
        <formula>H1N1-O1</formula>
        <targets>;Glu;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>Carbamidomethylation</name>
        <formula>C2H3N1O1</formula>
        <targets>;Cys;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>Carbamylation</name>
        <formula>C1H1N1O1</formula>
        <targets>;Lys;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>CarboxyMethylation</name>
        <formula>C2H2O2</formula>
        <targets>;Cys;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>Chromo-O</name>
        <formula>-O1</formula>
        <targets>;Thr;Ser;Gly;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>Chromo-H</name>
        <formula>-H1</formula>
        <targets>;Gly;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>Chromo-H3</name>
        <formula>-H3</formula>
        <targets>;Tyr;Phe;Trp;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>Dehydroalanine</name>
        <formula>-H2S1</formula>
        <targets>;Cys;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>DTNB (adsorbed)</name>
        <formula>C14H8N2O8S2</formula>
        <targets>;Cys;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>Dehydroxylation</name>
        <formula>-H1O1</formula>
        <targets>;Asp;Glu;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>Formylation</name>
        <formula>C1O1</formula>
        <targets>*</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>GlcNAcMurNAc(R)</name>
        <formula>C19H32N2O12</formula>
        <targets>*</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>Glutamylation</name>
        <formula>C5H7N1O3</formula>
        <targets>;Glu;</targets>
        <maxcount>6</maxcount>
      </mdf>
      <mdf>
        <name>Glycylation</name>
        <formula>C2H3N1O1</formula>
        <targets>;Glu;</targets>
        <maxcount>34</maxcount>
      </mdf>
      <mdf>
        <name>Hydroxylation</name>
        <formula>H1O1</formula>
        <targets>;Phe;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>LysMethylation</name>
        <formula>C1H2</formula>
        <targets>;Lys;</targets>
        <maxcount>3</maxcount>
      </mdf>
      <mdf>
        <name>Methylation</name>
        <formula>C1H2</formula>
        <targets>;Lys;Arg;</targets>
        <maxcount>2</maxcount>
      </mdf>
      <mdf>
        <name>Oxidation</name>
        <formula>O1</formula>
        <targets>;Met;Tyr;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>Phosphorylation</name>
        <formula>H1O3P1</formula>
        <targets>;Ser;Thr;Tyr;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>ProtonLoss</name>
        <formula>-H1</formula>
        <targets>;Cys;Tyr;Lys;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>SulfideBond</name>
        <formula>-H2</formula>
        <targets>;Cys;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>Sulphation</name>
        <formula>O3S1</formula>
        <targets>;Ser;Thr;Tyr;</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>SPITC</name>
        <formula>C7H5N1O3S2</formula>
        <targets>*</targets>
        <maxcount>1</maxcount>
      </mdf>
      <mdf>
        <name>TNB</name>
        <formula>C7H3N1O4S1</formula>
        <targets>;Cys;</targets>
        <maxcount>1</maxcount>
      </mdf>
    </modifs>
    <crosslinkers>
      <clk>
        <name>CFP-chromophore</name>
        <formula/>
        <modifname>Chromo-O</modifname>
        <modifname>Chromo-H3</modifname>
        <modifname>Chromo-H</modifname>
      </clk>
      <clk>
        <name>DisulfideBond</name>
        <formula/>
        <modifname>ProtonLoss</modifname>
        <modifname>ProtonLoss</modifname>
      </clk>
    </crosslinkers>
    <cleavageagents>
      <cla>
        <name>EndoAspN+GluN</name>
        <pattern>/Asp;/Glu</pattern>
      </cla>
      <cla>
        <name>Trypsin</name>
        <pattern>Lys/;Arg/;-Lys/Pro</pattern>
      </cla>
      <cla>
        <name>Chymotrypsin</name>
        <pattern>Trp/;Val/</pattern>
      </cla>
      <cla>
        <name>EndoLysC</name>
        <pattern>Lys/</pattern>
      </cla>
      <cla>
        <name>EndoAspN</name>
        <pattern>/Asp</pattern>
      </cla>
      <cla>
        <name>GluC</name>
        <pattern>Glu/</pattern>
      </cla>
      <cla>
        <name>CyanogenBromide</name>
        <pattern>Met/</pattern>
        <clr>
          <name>Homoseryl</name>
          <re-mnm-code>Met</re-mnm-code>
          <re-formula>-CH2S+O</re-formula>
        </clr>
      </cla>
      <cla>
        <name>EndoAspN-Trypsin</name>
        <pattern>/Asp;Lys/;Arg/;-Lys/Pro</pattern>
      </cla>
    </cleavageagents>
    <fragmentationpathways>
      <fgp>
        <name>a</name>
        <end>LE</end>
        <formula>-C1O1H1</formula>
        <sidechaincontrib>0</sidechaincontrib>
      </fgp>
      <fgp>
        <name>b</name>
        <end>LE</end>
        <formula>-H</formula>
        <sidechaincontrib>0</sidechaincontrib>
      </fgp>
      <fgp>
        <name>c</name>
        <end>LE</end>
        <formula>+N1H2</formula>
        <sidechaincontrib>0</sidechaincontrib>
        <comment>that's just a comment</comment>
      </fgp>
      <fgp>
        <name>z</name>
        <end>RE</end>
        <formula>-N1H1</formula>
        <sidechaincontrib>0</sidechaincontrib>
        <comment>Typically in ECD of protonated ions</comment>
      </fgp>
      <fgp>
        <name>y</name>
        <end>RE</end>
        <formula>+H1</formula>
        <sidechaincontrib>0</sidechaincontrib>
      </fgp>
      <fgp>
        <name>x</name>
        <end>RE</end>
        <formula>+C1O1-H1</formula>
        <sidechaincontrib>0</sidechaincontrib>
      </fgp>
      <fgp>
        <name>imm</name>
        <end>NE</end>
        <formula>-C1O1</formula>
        <sidechaincontrib>0</sidechaincontrib>
      </fgp>
    </fragmentationpathways>
  </polchemdefdata>
</polchemdefinition>
