Bahuvrihi mspire

Mascot does not do it's parent ion mass calculation in an obvious way, leading to misidentifications I want to look into. In order to do so I plan to use the data mascot produces for it's matches (ie the data in a peptide_view).

I'd like to use the export xml, but it looks like the ion masses calculated by Mascot are not available as an option. As a result the data will have to be parsed from the html directly.

It appears tabular, and the FIRST table on the page:

  <TR ALIGN="RIGHT">
    <TD><B><FONT COLOR=#0000FF>1</FONT></B></TD>
    <TD>  72.0444</TD>
    <TD>  36.5258</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD ALIGN="CENTER"><B><FONT COLOR=#0000FF>A</FONT></B></TD>
    ...
  </TR>

  indicates predicted value for that series/fragment. The ALIGN="CENTER" TD shows the fragment residue. And there is a header row:

  <TR BGCOLOR=#cccccc>
    <TH>#</TH>
    <TH>b</TH>
    <TH>b<SUP>++</SUP></TH>
    <TH>b*</TH>
    <TH>b*<SUP>++</SUP></TH>
    <TH>b<SUP>0</SUP></TH>
    <TH>b<SUP>0++</SUP></TH>
    <TH>Seq.</TH>
    ...
   </TR>

The monoisotopic mass is in these tags:

<PRE>
<B>Monoisotopic mass of neutral peptide Mr(calc):</B> 832.3828
<B>Ions Score:</B> 45  <B>Expect:</B> 0.016  
<B>Matches (<FONT COLOR=#FF0000>Bold Red</FONT>):</B> 9/58 fragment ions using 18 most intense peaks
</PRE>