\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}