Table I. Methods used to identify menstrual blood proteins and the number of protein groups and entries identified at >95% confidence.

Method (see Figure 1)		Sample	Depletion (Hb, Alb, IgG)	μg Protein processed (after treatment)	Protein groupsa identified (>95% Confidence)	Protein entriesa (>95% Confidence)
1	LC MALDI TOF/TOF	S2	No	50 μg	67	84
2	LC MALDI TOF/TOF	S2	Yes	50 μg	129	168
3	SDS PAGE + 1C MALDI TOF/TOF	S2	Yes	200 μg	243	327
4	IEF + LC MALDI TOT/TOF	S1 Supernatant	Yes	600 μg	275	470
5	SDS PAGE + LC MALDI TOF/TOF	S1 Pellet	No	50 μg	626	722

^a Protein entries represent all possible proteins identified in a database search that possess one or more of the peptides found in the sample. Protein groups combine proteins that share common peptides, for example splice variants.