This page provides protein annotations from InsPecT and MS-Alignment, run against
various peptide MS/MS data-sets.  

<h3>Annotated Mod Spectra</h3>
<br>
We have gathered high-confidence annotations of modified peptides as a publicly-accessible
resource for other mass spectrometrists. The archive contains .dta files from an ion trap
mass spectrometer, and a table of
annotations.  Modifications include deamidaition (net mass shift +1Da), oxidation (+16Da),
methylation of cysteine (+14Da, annotated as -43 since it blocks the +57Da protecting group),
and others.
<br><br>
For further information on the sample, please refer to Wilmarth et. al.,
"Analyzing Age-Related Changes in Human Eye by Comparative Analysis of
Post-Translational Modifications in Young and Aged Lens: Do Modifications
Contribute to Age-Related Loss of Solubility in Senile Cataracts?" (in preparation)
<br>
<a href="AnnotatedModSpectra.20051217.zip">AnnotatedModSpectra archive</a>
<br><a href="AnnotatedModSpectraPlots.20051217.zip">Annotated spectrum plots</a>

<h3>Blind Search Results</h3>

<hr>
The following annotated spectra and search results are supplemental material for the
paper "Identification of post-translational modifications by blind search of mass spectra",
Tsur et. al., Nature Biotechnology, Dec 2005.  
<hr>
Representative spectra for modification types:
<li><a href="MSAlignmentExamples/Lens/index.html">Lens</a>
<li><a href="MSAlignmentExamples/IKKB/index.html">IKKB</a>
<li><a href="MSAlignmentExamples/ISB/index.html">ISB</a>
<hr>

MS-Alignment blind search results:
<li><a href="SearchResults/LensBlind.zip">Lens</a>
<li><a href="SearchResults/IKKBBlind.zip">IKKB</a>
<li><a href="SearchResults/ISBBlind.zip">ISB</a>
<hr>
InsPecT restrictive search results:
<li><a href="SearchResults/LensModList.zip">Lens</a>
<li><a href="SearchResults/IKKBModList.zip">IKKB</a>
<li><a href="SearchResults/ISBModList.zip">ISB</a>
<hr>
Spectra (in .dta format)
<li><a href="SearchResults/IKKB.zip">IKKB</a>
<hr>
Click <a href="index.html">here</a> to return to the supplemental data index,
or <a href="http://peptide.ucsd.edu">here</a> to visit our lab webpage.