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> </TD>
<TD> </TD>
<TD> </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>