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Biotech / Medical : Ciphergen Biosystems(CIPH): -- Ignore unavailable to you. Want to Upgrade?

To: tuck who wrote (156)	10/9/2003 1:55:26 PM
From: tuck	Read Replies (1) \| Respond to of 510

[identifying the proteins fingerprinted by SELDI] >>Anal Biochem. 2003 Oct 1;321(1):116-24. Methods for on-chip protein analysis. Caputo E, Moharram R, Martin BM. Unit on Molecular Structures, LNT, NIMH, NIH, DHHS, 10 Center Drive, Bldg. 10 3N309, Bethesda, MD 20892-1262, USA. The unambiguous identification of peptides/proteins is crucial for the definition of the proteome. Using ProteinChip Array technology also known as surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS), we developed experimental protocols and probed test conditions required for the protein identification on ProteinChip surfaces. We were able to directly digest peptides/proteins on-chip surfaces by specific proteases, such as trypsin, and to obtain the peptide mass fingerprint of the sample under investigation by its direct analysis on a simple laser desorption/ionization mass spectrometer. Furthermore, tandem mass spectrometry was performed on several of the resulting tryptic peptides by using collision quadrupole time of flight (Qq-TOF) MS/MS via the ProteinChip interface, thus allowing the unambiguous identification of the protein(s) within the sample. In addition, we were able to identify the C-terminal sequence of peptides by their digestion with carboxypeptidase Y directly on ProteinChip surfaces coupled with SELDI-TOF MS analysis of the resulting peptide mass ladders employing the instrument's protein ladder sequence software. Moreover, the removal of up to nine amino acid residues from the C-terminal end of a peptide extends the functional range of Qq-TOF MS/MS sequence determination to over 3000 m/z. The utility of these procedures for the proteome exploration are discussed.<< Cheers, Tuck

To: tuck who wrote (156)	1/22/2005 2:56:04 PM
From: tuck	Respond to of 510

This full text of this study on the use of SELDI for finding biomarkers for ovarian cancer is now free: pnas.org Cheers, Tuck

To: tuck who wrote (156)	10/22/2005 2:51:55 PM
From: tuck	Read Replies (1) \| Respond to of 510

The UCLA team, after 2 years, has identified its markers for ovarian cancer, and guess what? They're pretty similar to the ones Ciphergen is commercializing: >>Proteomics. 2005 Oct 20; [Epub ahead of print] Characterization of serum biomarkers for detection of early stage ovarian cancer. Kozak KR, Su F, Whitelegge JP, Faull K, Reddy S, Farias-Eisner R. Department of Obstetrics and Gynecology, University of California, Los Angeles, CA, USA. We have previously reported the identification of three ovarian cancer biomarker panels comprised of SELDI-TOF-MS peaks representing 14 differentially expressed serum proteins for the diagnosis of ovarian cancer. Using micro-LC-MS/MS, we identified five m/z peaks as transthyretin (TTR 13.9 kDa, TTR fragment 12.9 kDa), beta-hemoglobin (Hb, 15.9 kDa), apolipoprotein AI (ApoAI, 28 kDa) and transferrin (TF, 79 kDa). Western and/or ELISA methods confirmed the differential expression of TTR, Hb, and TF, and multivariate analyses resulted in improving the detection of early stage ovarian tumors (low malignant potential and malignant; receiver operating characteristic, ROC 0.933) as compared to cancer antigen CA125 alone (ROC 0.833). Interestingly, when CA125 was included with our markers in the multivariate analysis, the ROC increased to 0.959. Furthermore, multivariate analysis with only the mucinous subtype of early stage ovarian tumors, showed our markers to greatly improve the detection of disease (ROC 0.959) as compared to CA125 alone (ROC 0.613). Interestingly, the combination of CA125 with our markers did not seem to further improve the detection of mucinous tumors (ROC 0.955). We conclude that TTR, Hb, ApoAI and TF, when combined with CA125 should significantly improve the detection of early stage ovarian cancer.<< Cheers, Tuck