Intact-protein-based High-resolution Three-dimensional Quantitative Analysis System for Proteome Profiling of Biological Fluids

Wang, Hong; Clouthier, Shawn G.; Galchev, Vladimir; Misek, David E.; Duffner, Ulrich; Min, Chang Ki; Zhao, Rong; Tra, John; Omenn, Gilbert S.; Ferrara, James L.M.; Hanash, Samir M.

doi:10.1074/mcp.m400126-mcp200

Cited by 124 publications

(89 citation statements)

References 23 publications

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“…In addition, separations of intact proteins on the basis of their different masses or other properties can be used to identify different protein isoforms. 5,17 Quantitative analysis based on the number of peptides identified per protein is increasingly used. [6][7][8][9][10] An important consideration with spectrum counting is the fact that small proteins tend to have fewer peptides identified per protein compared with large proteins.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive and quantitative proteome profiling of the mouse liver and plasma

2008

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We report a comprehensive and quantitative analysis of the mouse liver and plasma proteomes. The method used is based on extensive fractionation of intact proteins, further separation of proteins based on their abundance and size, and high-accuracy mass spectrometry. This analysis reached a depth in proteomic profiling not reported to date for a mammalian tissue or a biological fluid, with 7099 and 4727 proteins identified with high confidence in the liver and in the corresponding plasma, respectively. This method allowed for the identification in both compartments of low-abundance proteins such as cytokines, chemokines, and receptors and for the detection in plasma of proteins in the pg/mL concentration range. This method also allowed for semiquantitation of all identified proteins. The calculated abundance scores correlated with the abundance of the corresponding transcripts for the large majority of the proteins identified in the liver. Finally, comparison of the liver and plasma datasets demonstrated that a significant number of proteins identified in the liver can be detected in plasma. These included proteins involved in complement and coagulation, in fatty acid, purine and pyruvate metabolism, in gluconeogenesis and glycolysis, in protein ubiquitination, and in insulin, interleukin-4, epidermal growth factor, and platelet-derived growth factor signaling. Conclusion: This in-depth analysis of the mouse liver and corresponding plasma proteomes provides a strong basis for investigations of liver pathobiology and biology that employ mouse models of hepatic diseases in an effort to better understand, diagnose, treat, and prevent human hepatic diseases. (HEPATOLOGY 2008;47: 1043-1051.)

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Section: Discussionmentioning

confidence: 99%

Comprehensive and quantitative proteome profiling of the mouse liver and plasma

2008

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“…Differences in the abundance of resolved proteins are determined based on Cy dye ratios. IPAS provides a highly sensitive and quantitative approach for the analysis of serum and plasma proteins [14,101].…”

Section: Quantitative Analysis and Profilingmentioning

confidence: 99%

Human body fluid proteome analysis

2006

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The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, and amniotic fluid, as well as its applications to human disease biomarker discovery. We aim to summarize the proteomics technologies currently used for global identification and quantification of body fluid proteins, and elaborate the putative biomarkers discovered for a variety of human diseases through human body fluid proteome (HBFP) analysis. Some critical concerns and perspectives in this emerging field are also discussed. With the advances made in proteomics technologies, the impact of HBFP analysis in the search for clinically relevant disease biomarkers would be realized in the future.

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“…Besides the ultrahigh resolving power of CIEF-based multidimensional separations, initial proteome studies [46,47] have supported the ability to perform comprehensive analysis of yeast cell lysates while requiring the amount of yeast peptides or proteins that are two to three orders of magnitude less than those utilized in a multidimensional LC system [33][34][35][36][37][49][50][51]. Such an increase in proteome sensitivity resulting from IEF concentration and separation of peptides and proteins is further supported by the study of Cargile et al [52] using IPG gels.…”

Section: Cief-based Multidimensional Separationsmentioning

confidence: 71%

Capillary separations enabling tissue proteomics‐based biomarker discovery

et al. 2006

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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.

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Intact-protein-based High-resolution Three-dimensional Quantitative Analysis System for Proteome Profiling of Biological Fluids

Cited by 124 publications

References 23 publications

Comprehensive and quantitative proteome profiling of the mouse liver and plasma

Comprehensive and quantitative proteome profiling of the mouse liver and plasma

Human body fluid proteome analysis

Capillary separations enabling tissue proteomics‐based biomarker discovery

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