Proteomics Biomarker discovery

Jacobs JM, Adkins JN, Qian WJ, Liu T, Shen Y, Camp DG, 2nd, Smith RD (2005) Utilizing human blood plasma for proteomic biomarker discovery. J Proteome Res 4 1073—1085. 

Puroliit S, Podolsky R, Schatz D, Muir A, Hopkins D, Huang YH, She JX (2006) Assessing tire utility of SELDI-TOF and model averaging for serum proteomic biomarker discovery. Proteomics 6(24) 6405-6415. 

While the above study utilized urine, probably no biofluid has attracted the attention of the proteomic biomarker discovery field as serum and plasma. Although the analysis of serum by RPLC-MS has almost become routine, such is not the case for CE-MS. In a proof of principle study to show the efficacy of using CE-MS to find differentially abundant proteins in serum, the group of Sassi et al. analyzed groups of sera that were spiked with different concentrations of known standard peptides. The groups of sera were analyzed by CE-MS and the standard peptides were successfully identified as being differentially abundant with a success rate of 95%. 

Meistermann H, Norris J, Aerni H, et al. Biomarker discovery by imaging mass spectrometry transthyretin is a biomarker for gentamicin-induced nephrotoxicity in rat. Mol. Cell. Proteomics 2006 5 1876-1886. 

Gronborg, M., Kristiansen, T.Z., Iwahori, A., Chang, R., Reddy, R, Sato, N., Molina, H., Jensen, O.N., Hruban, R.H., Coggins, M.G., et al, (2006) Biomarker Discovery from Pancreatic Cancer Secretome Using a Differential Proteomic Approach. Mol Cell Proteomics, 5, 157-171. 

Reyzer, M. L., and Caprioli, R. M. (2005b). MALDI mass spectrometry for direct tissue analysis A new tool for biomarker discovery. J. Proteome Res. 4 1138-1142. 

Melle, C., Ernst, G., Schimmel, B., Bleul, A, Koscielny, S., Wiesner, A., Bogumil, R., Moller, U., Osterloh, D., Halbhuber, K.J., and F. Von Eggling, 2003, Biomarker Discovery and Identification in Laser Microdissected Head and Neck Squamous Cell Carcinoma with ProteinChip(R) Technology, Two-dimensional Gel Electrophoresis, Tandem Mass Spectrometry, and Immunohistochemistry. Mol Cell Proteomics. 2(7) 443-52. 

Radulovic D, Jelveh S, Ryu S, et al. Informatics platform for global proteomic profiling and biomarker discovery using liquid-chromatography-tandem mass spectrometry. Mol Cell Proteomics 2004 21 21. 

Srinivas PR, Verma M, Zhao Y, Srivastava S. Proteomics for cancer biomarker discovery. Clin Chem 2002 48(8) 1160—1169. 

He QY, Chiu JF. Proteomics in biomarker discovery and drug development. J Cell Biochem 2003 89 868-886. 

Krieg RC, Paweletz CP, Liotta LA, Petricoin EF 3rd. Clinical proteomics for cancer biomarker discovery and therapeutic targeting. Technol Cancer Res Treat 2002 1 263-272. 

McDonald WH, Yates JR 3rd. Shotgun proteomics and biomarker discovery. Dis Markers 2002 18 99-105. 

Aleo MD, Navetta KA, Emeigh Hart SG et al. (2002) Mechanism-based urinary biomarkers of aminoglycoside-induced phospholipidosis. Comp Clin Pathol 11 193-194 Aleo MD, Navetta KA, Emeigh Hart SG et al. (2003) Mechanism-based urinary biomarkers of renal phospholipidosis and injury. Toxicol Sci 72 (Suppl) 243 Bandara LR, Kennedy S (2002) Toxicoproteomics - a new pre-clinical tool. Drug Disc Today 7 411—418 Chapman K (2002) The ProteinChip biomarker system from Ci-phergen Biosystems a novel proteomics platform for rapid biomarker discovery and validation. Biochem Soci Trans 30 82-87... 

Yasui Y, Pepe M, Thompson ML, Adam BL, Wright GL, Qu Y, Potter JD, Winget M, Thornquist M, Feng Z (2003) A data-analytic strategy for protein biomarker discovery profiling of high-dimensional proteomic data for cancer detection. Biostatistics 4 449-463... 

Omenn, G. S. (2004a). Advancement of biomarker discovery and validation through the HUPO plasma proteome project. Dis. Markers 20, 131-134. 

Biomarker Discovery in Renal Cell Carcinoma Applying Proteome-Based Studies in Combination with Serology... 

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