Mass spectrometry analysis of microorganisms in samples

A microorganism identification system, the system comprising:

• a capture module configured to capture an unknown microorganism from a sample and generate ions of the unknown microorganism, wherein the capture module comprises a porous substrate;
• a mass analyzer operably coupled to the capture module to receive the generated ions of the unknown microorganism;
• and
• a central processing unit (CPU) and storage coupled to the CPU for storing instructions that when executed by the CPU cause the CPU to:
• accept as input from the mass analyzer, at least one mass spectrum of the unknown microorganism;
• annotate the at least one mass spectrum of the unknown microorganism to generate one or more annotated mass spectra;
• compare the one or more annotated mass spectra to a database comprising annotated mass spectra of known organisms;
• and
• output an identification of the unknown organism based on results of the comparison.