Table 1.

Comparison of immunostaining and chemical tag-based staining approaches

Characteristic	Immunostaining	Chemical labeling
Duration*	Hours–days	Minutes–hours
User interactions	>15†	8
Substrate size kDa	150	1
Staining steps	2‡	1
Blocking	Yes	No
Background	Often high	Low
Epitope stability	Variable	High
Cell permeable	No	Yes/No
No. of channels	Many	4 (currently)
Transgenics	No	Yes
Stoichiometry§	Variable (> 1:1)	1:1

^*Staining durations indicated are typical for thick tissue samples (hundreds of micrometers to several millimeters).

^†Using standard immunostaining protocol for Drosophila brains (see text for references).

^‡Fluorophore-coupled primary antibodies are sometimes used, reducing the number of staining steps to one.

^§I.e., fluorescent label-to-protein tag ratio. For immunohistochemistry, this ratio cannot be easily quantified.