Obtaining Maximum Information from a Peptide Map using Alternative MS and Global Multiplexed MS/MS Data Acquisition

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A. Chakraborty, C. Dorschel, S.J. Berger, J.C. Gebler
Presented at: ABRF 2005; Association of Biomolecular Resource Facilities Annual Meeting; February 5-8; Savannah GA
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The peptide map is a basic tool for the identification and characterization of proteins and their modifications. Developing an effective peptide map requires analytical technologies for characterizing all the components within a sample, and tracking them as the method is developed. The combination of accurate mass and MS/MS information can uniquely identify digested peptides, even from closely related peptides containing deamidations, oxidations, and other modifications. Although data directed MS/MS analysis (DDA) on a TOF based MS detector can provide effective qualitative information, multiple runs may be required, and peptide quantitative information is lost. We have developed an alternative approach (termed “Protein Expression”) where alternating cycles of MS and multiplexed MS/MS analysis provide quantitative and qualitative information from asingle run. This approach is illustrated using a yeast enolase peptide map.

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