Capillary separations enabling tissue proteomics‐based biomarker discovery

Abstract

Development of the capability to enable large‐scale proteome studies, analogous to comprehensive gene expression analysis, will clearly have far‐reaching impacts on protein biomarker investigations of human diseases such as cancer through interrogation of the archived fresh frozen and formalin‐fixed and paraffin‐embedded tissue collections. This review therefore focuses on the most recent advances in microdissection techniques and proteome platforms for procuring homogeneous subpopulations of tumor cells or structures and performing comprehensive analysis of protein profiles within tissue specimens, respectively. Developments in capillary separations capable of providing extremely high resolving power and selective analyte enrichment are particularly highlighted for their roles within the broader context of a state‐of‐the‐art integrated tissue proteome effort. The capabilities of CIEF‐based multidimensional separations for performing proteome analysis from minute samples create new opportunities in the pursuit of biomarker discovery using enriched and selected cell populations procured from tissue specimens. These proteome technological advances combined with recently developed tissue microdissection techniques provide powerful tools for those seeking to gain a greater understanding at the global level of the cellular machinery associated with human diseases such as cancer.

Capillary electrophoresis of proteins 2005–2007

“…Applications of CE in tissue proteomics-based biomarker discovery [185], system biology [186], and functional and structural studies of Bacillus proteome [187] have been reviewed.…”

What does it need to be a biomarker? Relationships between resolution, differential quantification and statistical validation of protein surrogate biomarkers

“…Expectations to carry MS results directly to clinical profiling [36,37] seem exaggerated [38][39][40]. The views presented in this article are, therefore, only partially in line (or even completely controversial) with regard to a number of recently published reviews, which offer a variety of essentially MS-based technological approaches for the biomarker problem [6,[41][42][43][44][45]. Supplementary and independent confirmation of molecular information from MS-based proteomic studies, e.g., by antibody-based technologies, appears to be highly desirable [46,47].…”

“…The MS used to identify proteins can be integrated into differential quantitative analysis as well in many ways, ranging from surface-enhanced laser desorption and ionization (SELDI), ICAT to multidimensional protein identification technolo-gies (MudPIT) and imaging MS. Moreover, various fractionations, including immunoaffinity depletion and other affinity-based approaches and even protein arrays, contribute to the dynamic range of samples and thus essential considerations necessary for differential analysis [5][6][7][8][9][10][11].…”

Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry

“…The high analyte concentrations in small peak volumes as a result of electrokinetic focusing/stacking and the resolving multidimensional separation results in sensitive proteome analysis by enhancing the dynamic response and detection sensitivity of the coupled MS instruments. Instead of performing multiruns or multidimensional separations, comparable or even better HT proteome results could theoretically be achieved by simply increasing the number of CIEF fractions due to the intrinsic high resolvation nature of electrokinetic focusing, a feature that is particularly important for proteome analysis of limited tissue samples [217].…”