Discovery of Biomarker Candidates within Disease by Protein Profiling:  Principles and Concepts

Abstract

Proteins and peptides present within clinical samples represent a valuable library of information regarding the ongoing processes within cells and tissues in health and disease. We have developed and validated novel technology applications that can be used to characterize the patterns of global protein expression in tissue and biofluids in either gel-based systems or by automated multidimensional nanocapillary liquid chromatography. Mass spectrophotometry platforms using MALDI MS and MS/MS or LTQ ion trap MS were capable of delivering sensitive and accurate identifications of hundreds of proteins contained in individual samples including individual forms of processing intermediates such as phospho peptides. The Systems Biology approach of integrating protein expression data with clinical data such as histopathology, clinical functional measurements, medical imaging scores, patient demographics, and clinical outcome provides a powerful tool for linking biomarker expression with biological processes that can be segmented and linked to disease presentation.

Biomarkers of Cardiovascular Disease

“…Third, there is increased recognition that diseases arise out of the dynamic dysregulation of several gene regulatory networks, proteins, and metabolic alterations, reflecting complex perturbations (genetic and environmental) of the "system." 131,132 The expectation that single biomarkers can capture these intricate derangements and can unambiguously identify disease or that targeting single molecules or signaling pathways is adequate for treating complex pathology is simplistic. Rather, a "systems biology" approach that investigates multiple components of malfunctioning regulatory networks (referred to as multiparameter analysis of tens of hundreds of molecules) may provide better insights into disease diagnosis, prognosis, and treatment.…”

“…Rather, a "systems biology" approach that investigates multiple components of malfunctioning regulatory networks (referred to as multiparameter analysis of tens of hundreds of molecules) may provide better insights into disease diagnosis, prognosis, and treatment. 131 The development of biomarkers in CVD can be thought of as consisting of 2 potential approaches: the first strategy is "knowledge-based" (deductive method), and the second one is more "unbiased" (inductive strategy). These 2 approaches Bias: A quantitative measure of inaccuracy or departure from accuracy.…”

“…131 Table 4 provides an overview of some key techniques used for identifying putative CVD biomarkers. 133 Table 5 defines broadly these "Omics" tools.…”

Prefractionation of Cerebrospinal Fluid to Enhance Glycoprotein Concentration Prior to Structural Determination with FT−ICR Mass Spectrometry

“…To discover biomarkers the measurements need to be reproducible in larger subject groups. Ideally, a study protocol associated with the collection of samples with clearly defined inclusion and exclusion critera designed in collaboration with medical expertise within the disease area would facilitate the discovery (19).…”

Quantitative proteomic strategies for the identification of microRNA targets

“…When combined with MS and advanced image analysis software, 2-DE can provide important information on protein expression, post-translational modifications and splice variants [40,41]. The advantage of 2-DE is that it can be used for the identification of many protein isoforms and post-translational modifications.…”