. Author manuscript; available in PMC: 2009 Mar 30.

Published in final edited form as: Int J Mass Spectrom. 2007 Jan 1;259(1-3):105–116. doi: 10.1016/j.ijms.2006.08.004

Table 1.

Experimental design for two internalized bacteria/control comparisons and four methods for calculating protein expression ratios. The variable ScRatio1 thus represents the ratio of internalized PG and PG controls grown under normal culture conditions (see 2.1) calculated using the protein level spectral count method. The other seven conditions are defined analogously according to their position in the table.

	PG_PP/PG_nm		PG_PP/PG_PPC
	Protein level	Peptide level	Protein level	Peptide level
Spectral count	ScRatio1	ScRatio3	ScRatio2	ScRatio4
Signal intensity	PiRatio1	PiRatio3	PiRatio2	PiRatio4