Nanoscale liquid chromatography coupled to electrospray ionization Fourier transform ion cyclotron mass spectrometry (FTICR MS) was performed on an Agilent 1100 nanoflow system (Agilent Technologies, Santa Clara, CA, USA) hyphenated to a LCQ-FT 7.0 (Thermo Scientific). A volume of 5 mL from the reconstituted SCX fraction was injected automatically and loaded onto a C18 PicoFrit column (75 mm ID/15 mm tip ID, New-Objective, Woburn, MA) packed directly inside the electrospray needle tip using specially designed nanospray emitter tips. A water/formic acid (FA)/acetonitrile (ACN) solvent system was used where solvent A was 0.1% FA and solvent B was 100% ACN, 0.1% FA. Gradient elution was performed: 0% B for 10 min, 0% B to 50% B for 100 min, 50% B to 90% B for 5 min, 90%B for 5 min. Peptide elution was followed by ESI FTICR MS and tandem mass spectrometry (MS/MS) for peptide sequencing. A fullscan spectrum was acquired at high resolution (FWHM = 100000) using the FT analyzer. Data dependant acquisition was applied for MSMS precursor selection, where the 5 most intense mass peaks were subjected to subsequent isolation and collisioninduced fragmentation in the ion trap. Annotated fragment spectra were subjected to a database containing sequences of known rat neuropeptides (SwePep peptides, 245 peptide entries, www.swepep.org,) and neuropeptide precursor proteins (Swepep precursor, 123 protein entries) using the Mascot search engine (v 2.2, matrixscience, London, UK). For peptide identification the search was made with the following specifications: no enzyme specificity; 10 ppm precursor tolerance and 1.2 Da fragment tolerance; no fixed modifications; variable modifications: C-term. amidation, deamidation, oxidation (M); precursor charges: 2+ and 3+; instrument: ESI trap. Peptide matches with a score above the confidence threshold (p,0.05) were considered to be a significant hit. The false positive identification rate (FPR) was estimated by searching the **data** against a decoy database, where the FPR threshold was set to ,1%.