Table 2.

Summary of anticipated results from peptide identification strategies.

Method	Result	Advantage	Disadvantage
Extraction from whole tissue section	Database of all peptides generated by on-tissue digestion	Database can be used to search peptides extracted from small target regions	Ambiguity from homologous or isobaric peptides
	Ability to calculate bioinformatic processes
Extraction from target region	Target peptides from region	Enrichment of distinct peptides from a region	Poor sequence coverage; missing peptide information due to sensitivity issues
On-tissue MS/MS	On-tissue peptide sequence information	Direct link to sequence information from tissue	May require a high number of averaged scans to produce an interpretable MS/MS