Recent progress in protein profiling of clinical tissues for next-generation molecular diagnostics

Abstract

Differences in protein levels and the activation of signaling pathways have been extensively studied in tumor tissues, but the implementation of protein profiling methods in routine hospital workflows lags far behind that of nucleic acid-based approaches. In this review, major technologies that are currently used for measuring protein abundances in human tissues are highlighted, and for each method several examples are provided. We differentiate between extract-based and section-based methods that are each further divided into targeted- and discovery-based approaches (i.e., when the proteins to be analyzed are known or for finding promising new biomarker candidates, respectively). Current problems in protein profiling are addressed and ways in which protein profiling can successfully be implemented in routine clinical workflows are shown.

Analysis of Reverse Phase Protein Array Data: From Experimental Design towards Targeted Biomarker Discovery

“…As outlined previously, antibody validation presents a fundamental prerequisite. Thus, antibody cross-reactivity must be kept at a minimum for RPPA [7,8]. To verify antibody specificity, it is also possible to calculate a correlation factor between Western blot signals and array-based signals for a particular set of samples.…”

Addition of CsCl reduces ion suppression effects in the matrix‐assisted laser desorption/ionization mass spectra of triacylglycerol/phosphatidylcholine mixtures and adipose tissue extracts

“…Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) is an increasingly used analytical method due to the simple performance, the considerable sensitivity and the high‐throughput capacity . MALDI MS was initially used for the analysis of “large” molecules such as proteins . In the last decades there has been an increased awareness about the crucial role of lipids in cell, tissue and organ physiology .…”