Analysis of Complex Protein Digest Samples by Off-Line Strong Cation Exchange Chromatography in Combination with LC/MS/MS on a Hybrid Quadrupole Orthogonal Acceleration Time-Of-Flight (Q-Tof) Mass Spectrometer

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Waters Poster
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Advances in both LC and MS instrumentation have allowed the analysis of protein complexes which have not been separated on a two-dimensional gel. These experiments involve separation of a complex digest mixture by nanoscale liquid chromatography connected to an instrument capable of data directed switching between the MS and MS/MS modes. Protein identification is then achieved via databank searching of the ESI/MS/MS spectra, providing qualitative information on the proteins that are present. Hundreds of MS/MS spectra can be acquired in a fully automated fashion, resulting in the identification of significant numbers of proteins, including low copy number proteins, from a single LC/MS/MS experiment.

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