The sample is injected onto a reversed phase column (75 μm × 150 mm Zorbax SB300 C-18, Agilent Technologies) connected to a Dionex Ultimate 3000 HPLC system and a Thermo Finnigan LTQ-FT mass spectrometer equipped with an nanospray interface. The samples are chromatographed using a binary solvent system consisting of A: 0.1% formic acid and 5% acetonitrile and B: 0.1% formic acid and 95% acetonitrile at a flow rate of 200 nL/min. A gradient is run from 15% B to 55%B over 60 minutes. The mass spectrometer is operated in positive ion mode with the trap set to data dependent MS/MS acquisition mode. The instrument is set to complete a mass scan from 400-1800 daltons in one second. Peaks eluting from the LC column that have ions above 1,000 arbitrary intensity units trigger the ion trap to isolate the ion and perform an MS/MS experiment scan after the MS full scan. The instrument’s dynamic ion exclusion filter is set to allow the instrument to record 2 MS/MS spectra for each detected ion to optimize the acquisition of quantitative data in MS mode as well as qualitative data in MS/MS mode and in addition after every MS scan in the ion trap, ions are then transferred to the isolation cell of the 7T magnet in the FT where a high resolution (up to 500,000 at m/z 400) and high mass accuracy (1 ppm) mass spectrum of the precursor ions is obtained. Data files created are then processed to produce an intermediate file containing the peaks detected and fragmented and these intermediate files are transferred to a server where sequence database searching and de-novo sequencing may be performed.