Table 3.

Comparison of different methods (histology, immuno-histochemistry (IHC) and proteomics (fractionation coupled to mass spectrometry (MS) and direct tissue MS) for peptide/protein analysis in tissue samples.

	Histology	IHC	Proteomics
			Fractionation-MS	Direct tissue MS
Methods	Cellular staining	Antibody directed staining of specific proteins	Liquid phase separation (i.e., liquid chromatography)	Direct measurement of peptides and proteins from tissue section
Analysis	Tissue morphology assessment by light microscopy	Protein distribution across tissue sections	MS protein identification	MS profiles of tissue sections
			Quantitation using protein labelling	Peptide and protein intensity maps showing distribution across tissue sections
Advantages	Easy staining methods	Highly specific	Highly sensitive	Rapid
	Cellular microscopy resolution	Cellular microscopy resolution	Thousands of proteins analysed at a time	Spatial proteome information
	Well established	Well established	Heavily automated	Measurement of hundreds of molecular features at a time
	Clinical personnel already available	Clinical personnel already available	Highly modular workflows	No antibodies required
Disadvantages	Reproducibility issues	Time consuming	Time consuming	Expensive equipment
	Based on visual assessment of morphology	Labor intensive	Labor intensive	Novel technology
	Non-specific	Limited to 3–4 proteins	Removes spatial information	Requires fraction-MS based proteomics to identify peptide and protein features
	Analysis is subjective	Dependent on antibody quality	Requires specialist personnel	Analytical resolution limited to a maximum of 20–50 μm