A sampling probe based on ambient desorption ionization was designed for in-vivo chemical analysis by mass spectrometry in surgical and endoscopic procedures. Sampling ionization of analytes directly from tissue was achieved by sealing the sampling tip against the tissue surface without allowing leakage of the auxiliary gas used for desorption ionization. The desorbed charged species were transferred over a long distance (up to 4 m) through a flexible tube of internal diameter as small as 1/16 inch to the inlet of the mass spectrometer used for analysis. The conditions used for desorption electrospray ionization (DESI) were optimized to achieve biocompatibility for clinical applications while obtaining adequate efficiency for the analysis. This optimization involved removal of high voltage and use of pure water as spray solvent instead of the organic solvents or aqueous mixtures normally used. Improved sensitivity was achieved under these conditions by increasing the gas flow rate in the transfer tube. The destructive effect on tissue surfaces associated with typical desorption ionization was avoided by altering the local gas dynamics in the sample area without compromising the overall analysis efficiency.