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      • Nano-LC FTICR Tandem MassSpectrometry for Top-DownProteomics: Routine Baseline Unit Mass Resolution of Whole Cell LysateProteins up to 72 kDa

        Tipton, JeremiahD.,Tran, John C.,Catherman, Adam D.,Ahlf, Dorothy R.,Durbin, Kenneth R.,Lee, Ji Eun,Kellie, John F.,Kelleher, Neil L.,Hendrickson, ChristopherL.,Marshall, Alan G. American ChemicalSociety 2012 ANALYTICAL CHEMISTRY - Vol.84 No.5

        <P>Current high-throughput top-down proteomic platformsprovide routineidentification of proteins less than 25 kDa with 4-D separations.This short communication reports the application of technologicaldevelopments over the past few years that improve protein identificationand characterization for masses greater than 25 kDa. Advances in separationscience have allowed increased numbers of proteins to be identified,especially by nanoliquid chromatography (nLC) prior to mass spectrometry(MS) analysis. Further, a goal of high-throughput top-down proteomicsis to extend the mass range for routine nLC MS analysis up to 80 kDabecause gene sequence analysis predicts that ∼70% of the humanproteome is transcribed to be less than 80 kDa. Normally, large proteinsgreater than 50 kDa are identified and characterized by top-down proteomicsthrough fraction collection and direct infusion at relatively lowthroughput. Further, other MS-based techniques provide top-down proteincharacterization, however at low resolution for intact mass measurement.Here, we present analysis of standard (up to 78 kDa) and whole celllysate proteins by Fourier transform ion cyclotron resonance massspectrometry (nLC electrospray ionization (ESI) FTICR MS). The separationplatform reduced the complexity of the protein matrix so that, at14.5 T, proteins from whole cell lysate up to 72 kDa are baselinemass resolved on a nano-LC chromatographic time scale. Further, theresults document routine identification of proteins at improved throughputbased on accurate mass measurement (less than 10 ppm mass error) ofprecursor and fragment ions for proteins up to 50 kDa.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/ancham/2012/ancham.2012.84.issue-5/ac202651v/production/images/medium/ac-2011-02651v_0004.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ac202651v'>ACS Electronic Supporting Info</A></P>

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