Towards Global Proteomics, All Ions All the Time: A Proof-of-Principle of the Qualitative Ion Mapping Technology

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Jeffrey C. Silva, Keith Richardson, Phillip Young, Richard Denny, Kieran Neeson, Therese McKenna, Craig Dorschel, Guo-Zhong Li, Marc Gorenstein, Timothy Riley, and Scott Geromanos
Waters ASMS 2004 poster
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Traditional tandem mass spectrometry (MS/MS) is a method of mass spectrometry whereby intact peptides (parent ions) generated from an enzymatic digest of a protein sample are mass filtered and collisionally dissociated to yield product or fragment ions which are subsequently mass analyzed. The resulting product ion spectra can be used to determine the sequence of the parent peptide and, through a database search, the identity of the originating protein. This method of analysis can be automated and it is generally performed in conjunction with a real time liquid chromatography separation system. Although this methodology is quite powerful, it has been shown to have limitations when characterizing complex protein mixtures. Many of these limitations are associated with the serial nature of the MS/MS data acquisition process which limits both the qualitative and the quantitative reproducibility of the information generated. A new method of protein characterization of proteolytically-generated peptides has been developed which is based on coupling the alternate scanning of peptides at low and elevated energy1,2 with a robust accurate mass LC/MS data acquisition mode3. This mode of data acquisition is very high in duty cycle and provides exact mass MS analysis of both the precursor and product ions for every detectable peptide. Chromatographic retention time is used to associate fragments to their corresponding precursors as a unique attribute of the Waters® Protein Expression System technology. Proprietary Protein Expression System Informatics software has been developed which allows this information to be processed in a quantitative and qualitative manner. This poster will focus on the qualitative identification capabilities of this software. Poster TPR 357 (Geromanos et al., “Towards Global Proteomics by Analysis of Exact Mass Retention Time Pairs: A proof-of-principle of the Quantitative Ion Mapping Technology”) addresses the quantitative capabilities of the software and Poster TPY 458 (C. Dorschel et al., “Protocols to Assure Reproducible Quantitative and Qualitative Analysis of Tryptic Digests of Complex Protein Mixtures for Global Proteomic Experiments”) highlights the reproducibility of the Protein Expression System platform.

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