Automated sample analysis system and methods of use thereof

A method for automated sample analysis, the method comprising:

• providing an automated sample analysis system comprising a desorption electrospray ionization (DESI) probe;
• a substrate for holding one or more samples;
• a mass spectrometer;
• and one or more controllers, wherein the one or more controllers are operably associated with each other and at least one of the DESI probe, the substrate, and/or the mass spectrometer, and the one or more controllers are each configured to execute one or more programs that cause acquisition of two-dimensional tandem mass spectrometry (2D-MS/MS) data domains via synchronous operation of the DESI probe with movement of the substrate along with the 2D-MS/MS data acquisition, thereby ensuring automated correct time and position for 2D-MS/MS data acquisition;
• and
• operating the system to analyze one or more samples and generated a 2D-MS/MS image for each sample in an automated and synchronized manner.