LEADER 05190nam 2200661Ia 450 001 9911019536703321 005 20200520144314.0 010 $a9786610722952 010 $a9781280722950 010 $a1280722959 010 $a9783527609482 010 $a3527609482 010 $a9783527609420 010 $a3527609423 035 $a(CKB)1000000000377132 035 $a(EBL)482214 035 $a(OCoLC)78232861 035 $a(SSID)ssj0000152378 035 $a(PQKBManifestationID)11157452 035 $a(PQKBTitleCode)TC0000152378 035 $a(PQKBWorkID)10322978 035 $a(PQKB)10168028 035 $a(MiAaPQ)EBC482214 035 $a(Perlego)2759980 035 $a(EXLCZ)991000000000377132 100 $a20061020d2006 uy 0 101 0 $aeng 135 $aur|n|---||||| 181 $ctxt 182 $cc 183 $acr 200 00$aExploring the human plasma proteome /$fedited by Gilbert S. Omenn 210 $aWeinheim $cWiley-VCH$dc2006 215 $a1 online resource (396 p.) 300 $aCollection of articles published previously in the journal Proteomics. 311 08$a9783527317578 311 08$a3527317570 320 $aIncludes bibliographical references and index. 327 $aExploring the Human Plasma Proteome; Table of Contents; Preface; List of Contributors; 1 Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database; 1.1 Introduction; 1.2 PPP reference specimens; 1.3 Bioinformatics and technology platforms; 1.3.1 Constructing a PPP database for human plasma and serum proteins; 1.3.2 Analysis of confidence of protein identifications; 1.3.3 Quantitation of protein concentrations 327 $a1.4 Comparing the specimens1.4.1 Choice of specimen and collection and handling variables; 1.4.2 Depletion of abundant proteins followed by fractionation of intact proteins; 1.4.3 Comparing technology platforms; 1.4.4 Alternative search algorithms for peptide and protein identification; 1.4.5 Independent analyses of raw spectra or peaklists; 1.4.6 Comparisons with published reports; 1.4.7 Direct MS (SELDI) analyses; 1.4.8 Annotation of the HUPO PPP core dataset(s); 1.4.9 Identification of novel peptides using whole genome ORF search 327 $a1.4.10 Identification of microbial proteins in the circulation1.5 Discussion; 1.6 References; 2 Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project; 2.1 Introduction; 2.2 Materials and methods; 2.2.1 Development of the data model; 2.2.1.1 Laboratory; 2.2.1.2 Experimental protocol; 2.2.1.3 Protein identification data set; 2.2.1.4 Peak list; 2.2.1.5 Summary of technologies and resources; 2.2.1.6 MS/MS spectra; 2.2.1.7 SELDI peak list; 2.2.2 Data submission process; 2.2.3 Design of the data repository; 2.2.4 Receipt of the data 327 $a2.3 Inference from peptide level to protein level2.4 Summary of contributed data; 2.4.1 Cross-laboratory comparison, confidence of the identifications; 2.5 False-positive identifications; 2.6 Data dissemination; 2.7 Discussion; 2.8 Concluding remarks; 2.9 Computer technologies applied; 2.10 References; 3 HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples; 3.1 Introduction; 3.2 Materials and methods; 3.2.1 HUPO reference sample collection protocol; 3.2.2 Differential peptide display 327 $a3.2.3 Stability studies and SELDI analysis3.2.4 SDS-PAGE analysis for stability studies; 3.2.5 2-DE for stability studies; 3.2.6 SELDI-TOF analysis for protease inhibitor studies; 3.2.7 2-DE for plasma protease inhibition studies; 3.2.8 Tryptic digestion and protein identification for protease inhibition studies; 3.2.9 Antibody microarray analysis using two-color rolling circle amplification; 3.3 Results; 3.3.1 Comparisons of specimen types; 3.3.1.1 Analysis of serum; 3.3.1.2 Analysis of plasma; 3.3.2 Evaluation of storage and handling conditions 327 $a3.3.3 Evaluations of the use of protease inhibitors 330 $aOn the cutting edge of medical diagnostics, plasma proteomics promises to generate a new wave of technologies to help identify many different diseases and disease risks.Plasma and serum are the preferred non-invasive specimens to test normal individuals, at-risk groups, and patients for protein biomarkers discovered and validated to reflect physiological, pathological, and pharmacological phenotypes. These specimens present enormous challenges due to extreme complexity, huge dynamic range in protein concentrations, non-standardized methods of sample processing, and intra- and inter-individ 606 $aProteomics 606 $aMolecular biology 615 0$aProteomics. 615 0$aMolecular biology. 676 $a572.6 701 $aOmenn$b Gilbert S$01842458 801 0$bMiAaPQ 801 1$bMiAaPQ 801 2$bMiAaPQ 906 $aBOOK 912 $a9911019536703321 996 $aExploring the human plasma proteome$94422588 997 $aUNINA