A New Software Tool for Interpretation of Accurate Mass LC/MS Peptide Maps

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Beth L. Gillece-Castro, Thomas E. Wheat, Scott Berger, Marc Gorenstein, Keith Richardson, Kieran Neeson, Barry Dyson, Phillip Young, Jeff Mazzeo, and Diane Diehl, Waters
Mass Spec 2007 Sept. 5-7 Montreal Canada
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Protein characterization requires efficient tools to establish a complete chemical structure.  Ideally, the analysis would be sensitive to minor changes in the structure.   Peptide mapping by liquid chromatography linked to high mass accuracy mass spectrometry (LC/MS) has the benefit of chemical structure identification.  During protein characterization comparisons are made between batches and a control or reference standard.  A software tool which makes visual and quantitative comparisons readily reported and exported can provide efficient data interpretation.  We have developed prototype software, MassLynx Software's customized BioPharmaLynx Application Manager, to address the large data sets found in protein characterization laboratories.   The peaks are detected by the Apex3D/Peptide3D algorithms to deconvolute multiply-charged ions and combine isotopes.  Apex3D and Peptide3D are specifically designed to interpret the resolved isotope clusters produced by oa-Tof mass spectrometers.   The results can be viewed as a table, as a combined spectrum, or as a processed chromatogram. This poster was shown at Mass Spec 2007: Fourth Symposium on the Practical Applications of Mass Spectrometry in the Biotechnology and Pharmaceutical Industries.

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