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High resolution, high mass accuracy analysis of peptide digests and proteins using hybrid instruments such as the Thermo Finnigan LTQ-FT Ultra instrument allow for faster unambiguous computer identification of proteins from peptide digests, accurate measurement of intact protein MW and detection of post translational modifications by top down methods and the use of auxiliary dissociation methods such as ECD to study disulfide bonds and crosslinked peptides as well as post-translational modifications such as phosphorylation. User demand for these instruments remains high in shared facilities like ours and efforts are always being made to improve sample throughput to increase instrument availability. Several vendors have released microfluidic based integrated chromatographic systems in the last few years that allow for relatively easy use in nanospray mode along with reductions in delay volumes and significant improvement in sample throughput and sensitivity. The current work reports on the successful integration of one such system, the Agilent Chip Cube system, originally designed to work only on MS instruments from that manufacturer, so that it will function routinely on the LTQ-FT Ultra MS. Using the chip cube's nanocolumn cartridge “chips”, our facility has been able to significantly shorten runtimes for digest based analyses of simple and complex fractionated samples while obtaining excellent peptide detection using smaller sample injection volumes. Details of the adaptation will be provided and examples will be shown using data from both CID and ECD based proteolytic workflows. In addition, we will present data generated using an online electrochemical potentiostat, the ROXY EC system, along with the chip cube on the LTQ FT Ultra allowing the detection of electrochemically generated peptide fragments from intact proteins as an adjunct/replacement for proteolysis in specific analytical problems where the use of nano-LC/MS/MS proteolytic analysis is normally required due to low picomolar and femtomolar protein levels.