We present a surface assisted laser desorption ionization (SALDI) technique, coupled with fluorocarbon coating, to achieve selective segregation of ionic and/or hydrophilic analytes from background biofluid electrolytes for quantiatve mass spectrometric analysis. By controlling the contact angle of (1H,1H,2H,2H-perfluorooctyl) trichlorosilane or (1H,1H,2H,2H-perfluorooctyl) dimethylchlorosilane to a specific range (105-120°), background electrolytes can be made to segregate from hydrophilic analytes during a drying step on the surface of a highly nanoporous thin film. Nanoporous silicon films were prepared using glancing angle deposition (GLAD) thin film technology, then coated with fluorcarbon. This desalting method directly separates highly polar, ionic metabolites, such as amino acids, from salty biofluids such as aritificial cerebrospinal fluid (aCSF) and serum. Derivatization, extraction and rinsing steps are not required to separate the analytes from the bioelectrolytes. With on-chip desalting, the limit of quantitation for histidine spiked in aCSF is ∼1 μM, and calibration curves with internal standards can achieve a precision of 1-9% within a 1 to 50 μM range. Five highly polar organic acids in serum were successfully quantified, and the SALDI-MS results obtained on the desalted serum sample spots show both good reproducibility and compare well to results from NMR and liquid chromatography-mass spectrometry. Putative identification of a total of 32 metabolites was accomplished in blood using time-of-flight MS with perfluoro coated Si-GLAD SALDI, by comparison to tabulated data.