\renewcommand{\sectitle}{The Protein Chemistry Definition File}
\section*{\sectitle}
\addcontentsline{toc}{section}{\numberline{}\sectitle}

\begin{verbatim}
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<!-- DTD for polymer definitions, used by the
'GNU polyxmass' suite of mass spectrometry applications.
Copyright 2003, 2004 Filippo Rusconi - Licensed under the GNU GPL -->
<!DOCTYPE polchemdefdata [
<!ELEMENT polchemdefdata (type,leftcap,rightcap,codelen,ionizerule,
                          monomers,modifs,cleavespecs,fragspecs)>
<!ELEMENT ionizerule (actform,charge,level)>
<!ELEMENT monomers (mnm*)>
<!ELEMENT modifs (mdf*)>
<!ELEMENT cleavespecs (cls*)>
<!ELEMENT fragspecs (fgs*)>
<!ELEMENT mnm (name,code,formula)>
<!ELEMENT mdf (name,actform)>
<!ELEMENT cls (name,pattern,clr*)>
<!ELEMENT fgs (name,end,actform,comment?,fgr*)>
<!ELEMENT clr ((le-mnm-code,le-actform)?,(re-mnm-code,re-actform)?)>
<!ELEMENT fgr (name,actform,prev-mnm-code?,this-mnm-code?,next-mnm-code?,comment?)>
<!ELEMENT type (#PCDATA)>
<!ELEMENT leftcap (#PCDATA)>
<!ELEMENT rightcap (#PCDATA)>
<!ELEMENT codelen (#PCDATA)>
<!ELEMENT actform (#PCDATA)>
<!ELEMENT charge (#PCDATA)>
<!ELEMENT level (#PCDATA)>
<!ELEMENT name (#PCDATA)>
<!ELEMENT code (#PCDATA)>
<!ELEMENT formula (#PCDATA)>
<!ELEMENT pattern (#PCDATA)>
<!ELEMENT end (#PCDATA)>
<!ELEMENT le-mnm-code (#PCDATA)>
<!ELEMENT re-mnm-code (#PCDATA)>
<!ELEMENT le-actform (#PCDATA)>
<!ELEMENT re-actform (#PCDATA)>
<!ELEMENT comment (#PCDATA)>
<!ELEMENT prev-mnm-code (#PCDATA)>
<!ELEMENT this-mnm-code (#PCDATA)>
<!ELEMENT next-mnm-code (#PCDATA)>
]>
<polchemdefdata>
  <type>protein</type>
  <leftcap>+H</leftcap>
  <rightcap>+OH</rightcap>
  <codelen>1</codelen>
  <ionizerule>
    <actform>+H</actform>
    <charge>1</charge>
    <level>1</level>
  </ionizerule>
  <monomers>
    <mnm>
      <name>Glycine</name>
      <code>G</code>
      <formula>C2H3NO</formula>
    </mnm>
    <mnm>
      <name>Alanine</name>
      <code>A</code>
      <formula>C3H5NO</formula>
    </mnm>
    <mnm>
      <name>Valine</name>
      <code>V</code>
      <formula>C5H9NO</formula>
    </mnm>
    <mnm>
      <name>Leucine</name>
      <code>L</code>
      <formula>C6H11NO</formula>
    </mnm>
    <mnm>
      <name>Isoleucine</name>
      <code>I</code>
      <formula>C6H11NO</formula>
    </mnm>
    <mnm>
      <name>Serine</name>
      <code>S</code>
      <formula>C3H5NO2</formula>
    </mnm>
    <mnm>
      <name>Threonine</name>
      <code>T</code>
      <formula>C4H7NO2</formula>
    </mnm>
    <mnm>
      <name>Cysteine</name>
      <code>C</code>
      <formula>C3H5NOS</formula>
    </mnm>
    <mnm>
      <name>Methionine</name>
      <code>M</code>
      <formula>C5H9NOS</formula>
    </mnm>
    <mnm>
      <name>Arginine</name>
      <code>R</code>
      <formula>C6H12N4O</formula>
    </mnm>
    <mnm>
      <name>Lysine</name>
      <code>K</code>
      <formula>C6H12N2O</formula>
    </mnm>
    <mnm>
      <name>Aspartate</name>
      <code>D</code>
      <formula>C4H5NO3</formula>
    </mnm>
    <mnm>
      <name>Glutamate</name>
      <code>E</code>
      <formula>C5H7NO3</formula>
    </mnm>
    <mnm>
      <name>Asparagine</name>
      <code>N</code>
      <formula>C4H6N2O2</formula>
    </mnm>
    <mnm>
      <name>Glutamine</name>
      <code>Q</code>
      <formula>C5H8N2O2</formula>
    </mnm>
    <mnm>
      <name>Tryptophan</name>
      <code>W</code>
      <formula>C11H10N2O</formula>
    </mnm>
    <mnm>
      <name>Phenylalanine</name>
      <code>F</code>
      <formula>C9H9N1O</formula>
    </mnm>
    <mnm>
      <name>Tyrosine</name>
      <code>Y</code>
      <formula>C9H9N1O2</formula>
    </mnm>
    <mnm>
      <name>Histidine</name>
      <code>H</code>
      <formula>C6H7N3O</formula>
    </mnm>
    <mnm>
      <name>Proline</name>
      <code>P</code>
      <formula>C5H7N1O1</formula>
    </mnm>
  </monomers>
  <modifs>
    <mdf>
      <name>Phosphorylation</name>
      <actform>-H+H2PO3</actform>
    </mdf>
    <mdf>
      <name>Acetylation</name>
      <actform>-H+C2H3O</actform>
    </mdf>
    <mdf>
      <name>Amidation</name>
      <actform>-OH+NH2</actform>
    </mdf>
    <mdf>
      <name>SulfideBond</name>
      <actform>-H2</actform>
    </mdf>
  </modifs>
  <cleavespecs>
    <cls>
      <name>CyanogenBromide</name>
      <pattern>M/</pattern>
      <clr>
        <re-mnm-code>M</re-mnm-code>
        <re-actform>-CH2S+O</re-actform>
      </clr>
    </cls>
    <cls>
      <name>Trypsin</name>
      <pattern>K/;R/;-K/P</pattern>
    </cls>
    <cls>
      <name>Chymotrypsin</name>
      <pattern>W/;V/</pattern>
    </cls>
    <cls>
      <name>EndoLysC</name>
      <pattern>K/</pattern>
    </cls>
    <cls>
      <name>EndoAspN</name>
      <pattern>/D</pattern>
    </cls>
    <cls>
      <name>GluC</name>
      <pattern>E/</pattern>
    </cls>
  </cleavespecs>
  <fragspecs>
    <fgs>
      <name>a</name>
      <end>LE</end>
      <actform>-C1O1</actform>
      <fgr>
        <name>a-fgr-1</name>
        <actform>+H200</actform>
        <prev-mnm-code>E</prev-mnm-code>
        <this-mnm-code>D</this-mnm-code>
        <next-mnm-code>F</next-mnm-code>
        <comment>comment here!</comment>
      </fgr>
      <fgr>
        <name>a-fgr-2</name>
        <actform>+H100</actform>
        <prev-mnm-code>F</prev-mnm-code>
        <this-mnm-code>D</this-mnm-code>
        <next-mnm-code>E</next-mnm-code>
        <comment>comment here!</comment>
      </fgr>
    </fgs>
    <fgs>
      <name>b</name>
      <end>LE</end>
      <actform>-H0</actform>
    </fgs>
    <fgs>
      <name>c</name>
      <end>LE</end>
      <actform>+N1H2+H1</actform>
      <comment>that's just a comment</comment>
    </fgs>
    <fgs>
      <name>z</name>
      <end>RE</end>
      <actform>-N1H1</actform>
      <comment>Not in CID high En. frag</comment>
    </fgs>
    <fgs>
      <name>y</name>
      <end>RE</end>
      <actform>+H2</actform>
    </fgs>
    <fgs>
      <name>x</name>
      <end>RE</end>
      <actform>+C1O1</actform>
      <fgr>
        <name>x-fgr-1</name>
        <actform>+H100</actform>
        <prev-mnm-code>E</prev-mnm-code>
        <this-mnm-code>D</this-mnm-code>
        <next-mnm-code>F</next-mnm-code>
        <comment>comment here!</comment>
      </fgr>
      <fgr>
        <name>x-fgr-2</name>
        <actform>+H200</actform>
        <prev-mnm-code>F</prev-mnm-code>
        <this-mnm-code>D</this-mnm-code>
        <next-mnm-code>E</next-mnm-code>
        <comment>comment here!</comment>
      </fgr>
    </fgs>
    <fgs>
      <name>imm</name>
      <end>NE</end>
      <actform>-C1O1+H1</actform>
    </fgs>
  </fragspecs>
</polchemdefdata>
\end{verbatim}