Characterizing Proteins with High Sequence Coverage Using an Alternate Scanning (LC/MS) Data Acquisition Strategy

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Asish B. Chakraborty , Scott J. Berger, and John C. Gebler
HUPO 2006, March 12-15, 2006 Boston, MA; HUPO 2006 October 28 - November 1 Long Beach, Ca
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Protein was identified with high sequence coverage (92%) using a single Protein Expression analysis run. Processing of peptide map data from Protein Expression analysis can be accomplished using fully automated informatics tools. Peptide map data in both the MS and MSE (multiplexed MS/MS) scans were shown to be reproducible from run to run. Both qualitative (components within a run) and quantitative (component intensity differences between runs) peptide map analysis can be accomplished using this approach. It was demonstrated that clear and concise MS/MS data could be obtained from peptides with overlapping elution profiles. This approach should prove valuable for developing better peptide mapping methods.

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