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Fully Automated Nano-Electrospray Coupled with a Finnigan LCQ Deca XP Plus for Sub-fmol Proteomic Analysis

e Nunc International, Rochester, NY, USA). The plate was sealed with plastic film to minimize evaporation and inserted into the autosampler of a Finnigan Surveyor HPLC system (Thermo Electron, San Jose, CA, USA), where it was kept at 4C while waiting for analysis. The injected peptides were first loaded onto a reversed-phase poly(styrene-divinylbenzene) peptide trap (Michrom BioResources, Auburn, CA, USA) with a flow rate of 10 μL/min for 3 minutes (Figure 1). The peptides were eluted from the trap and separated on a reversed-phase capillary column (PicoFritTM; 5 μm BioBasic C18 [Thermo Electron], 300 pore size; 75 μm 10 cm; tip 15 μm, New Objective, Woburn, MA, USA) with a 30-min linear gradient of 060% acetonitrile in 0.1% formic acid/water at a flow rate of approximately 0.1 μL/min after split. The HPLC was directly coupled to a Finnigan LCQ Deca XP Plus ion trap mass spectrometer equipped with a nanospray ionization source. The spray voltage was 2.0 kV and the capillary temperature was 150C. The ion-trap collisional fragmentation spectra were obtained using collision energies of 35%. Each full-scan mass spectrum was followed by three Data DependentTM MS/MS spectra of the three most intense peaks. The Dynamic ExclusionTM feature was enabled (Repeat Counts: 2, Repeat Duration: 0.2 minutes, Exclusion Duration: 5 minutes and Exclusion Mass width: 2 Da).

Data Analysis
Peptides and proteins were identified automatically by the computer program BioWorksTM version 3.1 (Thermo Electron, San Jose, CA, USA) which correlated the experimental tandem mass spectra against theoretical tandem mass spectra using the SEQUEST algorithm. The protein database used for this analysis was obtained from the National Center for Biotechnology Information (NCBI). Peptide identification was evaluated using the Xcorr vs. Charge State fil
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