Abstract
Proteomics of human body fluids for pharmaceutical applications covers a broad spectrum of technologies. A major challenge is the integration of data from various omics technologies: proteomics, genomics, and metabolomics. Applications relevant to the pharmaceutical industry include diagnostics, drug discovery, and drug development. Special features of these applications are that they are done on a large commercial scale. Currently, sample volumes require large-scale separation prior to analysis by mass spectrometry. Several new technologies, particularly those on the nanoscale, are refining this process and reducing the volume of samples required as well as expense. Refinements of technologies for fluid proteomics, including microfluidics and nanobiotechnology, for detection of biomarkers have applications in clinical diagnostics as well as drug discovery. Analysis of body fluids by metabolomic technologies may uncover biomarkers of drug toxicity that may help in avoiding clinical trials for such drugs, which are then discontinued after considerable expense. Finally, by facilitating the integration of diagnostics with therapeutics, these technologies will allow the development of personalized medicine.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Jain KK. Proteomics and drug discovery. Contrib Nephrol 2004;141:308–327.
Jain KK. Proteomics: Technologies, Markets and Companies. Basel: Jain PharmaBiotech Publications, 2007:1–536.
Verhelst SH, Bogyo M. Chemical proteomics applied to target identification and drug discovery. Biotechniques 2005;38:175–177.
Berger AB, Vitorino PM, Bogyo M. Activity-based protein profiling: applications to biomarker discovery, in vivo imaging and drug discovery. Am J Pharmacogenomics 2004;4:371–381.
Wada Y, Tajiri M, Yoshida S. Hydrophilic affinity isolation and MALDI multiple-stage tandem mass spectrometry of glycopeptides for glycoproteomics. Anal Chem 2004;76:6560–6565.
Fiehn O. Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp Funct Genom 2001;2:155–168.
Kiernan UA, Tubbs KA, Gruber K, et al. High-throughput protein characterization using mass spectrometric immunoassay. Anal Biochem 2002;301:49–56.
Watkins SM, German JB. Metabolomics and biochemical profiling in drug discovery and development. Curr Opin Mol Ther 2002;4:224–228.
Nicholson JK, Connelly J, Lindon JC, Holmes E. Metabonomics: a platform for studying drug toxicity and gene function. Nat Drug Discov 2002;1:153–161.
Gosalia DN, Diamond SL. Printing chemical libraries on microarrays for fluid phase nanoliter reactions. Proc Natl Acad Sci U S A 2003;100:8721–8726.
Cutillas PR. Principles of nanoflow liquid chromatography and applications to proteomics. Curr Nanosci 2005;1:65–71.
Jain KK. Nanobiotechnology: Applications, Markets and Companies. Basel: Jain PharmaBiotech Publications, 2007:1–605.
Omenn GS. Advancement of biomarker discovery and validation through the HUPO plasma proteome project. Dis Markers 2004;20:131–134.
Chromy BA, Gonzales AD, Perkins J, et al. Proteomic analysis of human serum by two-dimensional differential gel electrophoresis after depletion of high-abundant proteins. J Proteome Res 2004;3:1120–1127.
Kozak KR, Amneus MW, Pusey SM, et al. Identification of biomarkers for ovarian cancer using strong anion-exchange ProteinChips: potential use in diagnosis and prognosis. Proc Natl Acad Sci U S A 2003;100:12,343–12,348.
Petricoin EF, Ardekani AM, Hitt BA, et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002;359:572–577.
Baggerly KA, Morris JS, Edmonson SR, Coombes KR. Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J Natl Cancer Inst 2005;97:307–319.
Li J, Zhang Z, Rosenzweig J, et al. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 2002;48:1296–1304.
Varnum SM, Covington CC, Woodbury RL, et al. Proteomic characterization of nipple aspirate fluid: identification of potential biomarkers of breast cancer. Breast Cancer Res Treat 2003;80:87–97.
Pusztai L, Gregory BW, Baggerly KA, et al. Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma. Cancer 2004;100:1814–1822.
Sidransky D, Irizarry R, Califano JA, et al. Serum protein MALDI profiling to distinguish upper aerodigestive tract cancer patients from control subjects. J Natl Cancer Inst 2003;95:1711–1717.
Drake RR, Cazare LH, Semmes OJ, Wadsworth JT. Serum, salivary and tissue proteomics for discovery of biomarkers for head and neck cancers. Expert Rev Mol Diagn 2005;5:93–100.
Noel-Georis I, Bernard A, Falmagne P, Wattiez R. Proteomics as the tool to search for lung disease markers in bronchoalveolar lavage. Dis Markers 2001;17:271–284.
Xiao X, Liu D, Tang Y, et al. Development of proteomic patterns for detecting lung cancer. Dis Markers 2003–2004;19:33–39.
Li J, White N, Zhang Z, et al. Detection of prostate cancer using serum proteomics pattern in a histologically confirmed population. J Urol 2004;171:1782–1787.
Chen R, Pan S, Brentnall TA, Aebersold R. Proteomic profiling of pancreatic cancer for biomarker discovery. Mol Cell Proteomics 2005;4:523–533.
Comunale MA, Mattu TS, Lowman MA, et al. Comparative proteomic analysis of de-N-glycosylated serum from hepatitis B carriers reveals polypeptides that correlate with disease status. Proteomics 2004;4:826–838.
Liao H, Wu J, Kuhn E, et al. Use of mass spectrometry to identify protein biomarkers of disease severity in the synovial fluid and serum of patients with rheumatoid arthritis. Arthritis Rheum 2004;50:3792–3803.
Avasarala JR, Wall MR, Wolfe GM. A distinctive molecular signature of multiple sclerosis derived from MALDI-TOF/MS and serum proteomic pattern analysis. J Mol Neurosci 2005;25:119–126.
Lewin DA, Weiner MP. Molecular biomarkers in drug development. Drug Discov Today 2004;9:976–983.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc., Totowa, NJ
About this chapter
Cite this chapter
Jain, K.K. (2007). Integrative Omics, Pharmacoproteomics, and Human Body Fluids. In: Thongboonkerd, V. (eds) Proteomics of Human Body Fluids. Humana Press. https://doi.org/10.1007/978-1-59745-432-2_9
Download citation
DOI: https://doi.org/10.1007/978-1-59745-432-2_9
Publisher Name: Humana Press
Print ISBN: 978-1-58829-657-3
Online ISBN: 978-1-59745-432-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)