Table 2.

Number of strain–level assignments by metaproteomics in each infant. These numbers are based on assignments of each MS/MS (tandem mass spectrometry) fragmentation spectrum to a peptide sequence and the assignment of that sequence uniquely to a particular bacterial strain.

Subject	Spectral Counts
	C	T	B	P	M	N	E	R
Total number of strains assigned with ≥1 unique spectrum 1	45	67	78	99	75	76	64	64
Number of strains assigned with ≥2 spectra	25	43	49	71	45	42	39	42
Number of strains assigned with ≥5 spectra	9	14	20	32	18	18	19	10

¹ Level of confidence increases with the number of spectra assigned to the same strain.