Targeted protein-omic methods are bridging the gap between proteomic and hypothesis-driven protein analysis approaches

Abstract

While proteomic methods have illuminated many areas of biological protein space, many fundamental questions remain with regard to systems-level relationships between mRNAs, proteins, and cell behaviors. While mass spectrometric methods offer a panoramic picture of the relative expression and modification of large numbers of proteins, they are neither optimal for the analysis of pre-defined targets across large numbers of samples nor for assessing differences in proteins between individual cells or cell compartments. Conversely, traditional antibody-based methods are effective at sensitively analyzing small numbers of proteins across small numbers of conditions, and can be used to analyze relative differences in protein abundance and modification between cells and cell compartments. However, traditional antibody-based approaches are not optimal for analyzing large numbers of protein abundances and modifications across many samples. In this perspective article, we will review recent advances in methodologies and philosophies behind several microarray-based, intermediate-level, “protein-omic” methods including a focus on reverse phase lysate arrays and micro-western arrays that have been helpful for bridging gaps between large- and small-scale protein analysis approaches and have provided insight into the roles that protein systems play in several biological processes.

Caffeic Acid Phenethyl Ester Suppresses the Proliferation of Human Prostate Cancer Cells through Inhibition of p70S6K and Akt Signaling Networks

“…To determine the global short-term effects of CAPE on the changes in cellular signaling proteins related to Akt signaling, cell stress, and cell proliferation in LNCaP 104-S cells, we performed Micro-Western Array analysis (MWA) (21, 22, 30, 31) of 28 protein abundances and modifications in LNCaP 104-S cells at six time points from 0 to 480 min following replenishment of serum- and androgen-containing medium in the absence or presence of 10 μM CAPE (Fig. 3; Supp.…”

The application of modular protein domains in proteomics

“…Antibodies are meant to recognize an epitope on target molecules; so off target cross-reactivity can badly affect quantitative results. Therefore, multiple validation and nor-malization steps are necessary to eliminate false positive signals in antibody-based proteomics [9,10]. On the other hand, modular domains naturally have wide-ranging specificity; promiscuity in ligand selection is considered a physiological propensity rather than experimental noise.…”

Cholestane-3β, 5α, 6β-triol Suppresses Proliferation, Migration, and Invasion of Human Prostate Cancer Cells

“…Micro-Western Arrays (MWAs) represent a new method for proteomic analyses [19]. The MWA is a modification of the antibody-based modified reverse phase protein array.…”