Improved proteomic characterization of highly complex samples, such as intact proteins, continually demands higher performance from mass spectrometric instrumentation. Innovations that improve the detection of intact proteins, add new and different fragmentation modalities, increase dynamic range and reduce scan time are all required to make accessible the data needed by clinicians and researchers to generate the major impacts on human health envisaged in each and every one of the eight DBPs proposed. With mass analysis being central to proteomics, the impact of these innovations on the proposed DBPs is difficult to understate. In two specific aims, we present two new instruments. The first is a modified Orbitrap Fusion instrument with reduced vacuum pressure and the addition of an ultraviolet excimer laser for 193nm photodissociation. The second instrument builds upon the Exactive platform, adding a time-of-flight separator in place of the quadrupole for high-efficiency, parallel isolation and dynamic range enhancement to analyze more ions simultaneously. The DBPs proposed by the resource demand the development of new instrumentation specifically tailored to the challenges of whole protein analysis in applications where sample is limited. New and fast fragmentation approaches, combined with selective accumulation and an already impressive fragmentation tool box, will yield an instrument unsurpassed in the ability to thoroughly characterize protein targets (Orbitrap Fusion-based instrument). Functioning as a complement to these capabilities, a TOF-Orbitrap, with parallel selection and dynamic range enhancement will uncover and identify proteins never before seen. The coupling of these instruments with the separation approaches described in TR&D 1 will produce the foundation of the analytical platform required to extract the best possible outcomes for the DBP collaborators.
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