An apparatus for monitoring a surgical procedure includes a MALDI-TOF mass spectrometer comprising a load lock, an ionization chamber, and an ion detector. A first video camera produces an optical image of an operating field of the surgical procedure. A sample extracting device extracts the tissue sample at the location within the optical image of the operating field. A sample preparation system prepares MALID-TOF samples by depositing an extract of the extracted tissue sample on a sample plate together with a MALDI matrix. A sample plate loading mechanism loads the sample plate into the MALDI-TOF mass spectrometer. A second video camera produces an optical image of the sample plate and records a location of the extracted tissue sample. A computer records the images from first and second video cameras, correlates the location of the tissue sample in the operating field with the location of the tissue sample on the sample plate, acquires mass spectra data from the MALDI-TOF mass spectrometer, and compares the mass spectrum data to known mass spectrum data.
