Methods for identifying bioagents

A method of identifying a eukaryotic organism bioagent in a sample, comprising:

• (a) amplifying a nucleic acid from said eukaryotic organism bioagent with at least one pair of oligonucleotide primers to form at least one amplification product, wherein one member of said pair of primers hybridizes to a first conserved region of a nucleic acid and the other member of said pair of primers hybridizes to a second conserved region, wherein said conserved regions are present in three or more bioagents, and wherein said first and second conserved regions flank a variable nucleic acid region which varies among at least three bioagents;
• (b) analyzing said amplification product or fragments thereof by mass spectrometry to obtain one or more molecular masses;
• (c) determining a base composition of said amplification product from said one or more molecular masses of said amplification product or fragments thereof wherein said base compositions identify the number of, but not the nucleic acid gene sequence order of, A residues, C residues, T residues, G residues, and base analogs thereof;
• and
• (d) comparing said one or more base compositions to calculated or measured base compositions of amplification products produced using said pair of oligonucleotide primers, or fragments of said amplification products, thereby identifying said bioagent.