Table 1.

Summarized Comparison of Immunohistochemical Method and Liquid Chromatography-Mass Spectrometry (LC-MS) in Tissue Proteomics

Method of Protein Detection	Advantages	Drawbacks
Immunohistochemistry	Protein location and distribution seen Detectable in small and large tissue biopsies and fixed tissues Validation of other highthroughput studies ( DNA microarray)	Limited ability to quantitate protein content Problems with antibody types, limited ability to detect protein modifications Limited or lack of Evidence based Criteria Single or dual detection ability Variable scoring methods and reproducibility No normalization methods Limited throughput Limited capacity for clinical biomarker profiling( only with tissue microarrays)
Other Proteomics (i.e LC-MS)	100's to 1000's of peptides and proteins detected Can peruse databases for protein function and Gene ontology Robust Bioinformatics High throughput High level quantitation Can detect modified proteins Great potential for use in detecting clinical biomarkers	Cannot locate identified peptides to cell type(s) Need fresh or frozen tissue samples