HDMSE for Quantitative and Qualitative Profiling of Complex Protein Samples

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January 26, 2012

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  • The presentation describes the analytical challenges we face in bottom-up proteomics today. Proteome analyses are often performed on incredibly complex mixtures, and this poses a significant analytical challenge. When examined, it is evident that, unfortunately, many peptides are unevenly distributed across mass and chromatographic space, giving rise to areas of extreme analyte density. The dynamic range of peptide abundance from a biological sample can be very high, often more so than the capability of the mass spectrometer alone. Chimericy is also a likely phenomenon, where 2 precursor ions have similar masses and similar chromatographic retention times. The final issue is the widely documented poor reproducibility of DDA-type experiments, due largely to the almost random selection of precursor ions for MS/MS analysis. A brief introduction into the data-independent MSE process, how it addresses these challenges, and how it compares with the more traditional data-dependent acquisition strategies will be discussed. The enhancement of the MSE process with the addition of ion-mobility separations, a technique that we call High Definition or HD-MSE, will be illustrated with experimental examples.

    Flow Chemistry

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