Frozen tissue biobanks. Tissue handling, cryopreservation, extraction, and use for proteomic analysis

References

• Qualman SJ, France M, Grizzle WE, LiVolsi VA, Moskaluk CA, Ramirez NC, et al. Establishing a tumour bank: Banking, informatics and ethics. Br J Cancer 2004; 90: 1115–9
   PubMed Web of Science ®Google Scholar
• Vortmeyer AO, Weil RJ, Zhuang Z. Proteomic applications for differential diagnosis of histologically identical tumors. Neurology 2003; 61: 1626–7
   PubMed Web of Science ®Google Scholar
• Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 2005.
   PubMed Web of Science ®Google Scholar
• Anderson NL, Anderson NG. The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics 2002; 1: 845–67
   PubMed Web of Science ®Google Scholar
• Craven RA, Banks RE. Use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis. Methods Enzymol 2002; 356: 33–49
   PubMed Web of Science ®Google Scholar
• Franzen B, Linder S, Okuzawa K, Kato H, Auer G. Nonenzymatic extraction of cells from clinical tumor material for analysis of gene expression by two-dimensional polyacrylamide gel electrophoresis. Electrophoresis 1993; 14: 1045–53
   PubMed Web of Science ®Google Scholar
• Omenn GS. The Human Proteome Organization Plasma Proteome Project pilot phase: Reference specimens, technology platform comparisons, and standardized data submissions and analyses. Proteomics 2004; 4: 1235–40
   PubMed Web of Science ®Google Scholar
• Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, et al. 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. Proteomics 2005; 5: 3226–45
   PubMed Web of Science ®Google Scholar
• Banks RE, Stanley AJ, Cairns DA, Barret JH, Clarke PC, Thompson D, et al. Influences of blood sample processing on low-molecular-weight proteome identified by surface-enhanced laser desorption/ionization mass spectrometry. Clin Chem 2005; 51: 1637–49
   PubMed Web of Science ®Google Scholar
• Hulmes JD, Bethea D, Ho K, Huang S-P, Ricci DL, Opiteck GJ, et al. An investigation of plasma collection, stabilization, and storage procedures for proteomic analysis of clinical samples. Clin Proteomics J 2004; 1: 17–31
   Google Scholar
• Rai AJ, Gelfand CA, Haywood BC, Warunek DJ, Yi J, Schuchard MD, et al. HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples. Proteomics 2005; 5: 3262–77
   PubMed Web of Science ®Google Scholar
• Tammen H, Schulte I, Hess R, Menzel C, Kellmann M, Mohring T, et al. Peptidomic analysis of human blood specimens: Comparison between plasma specimens and serum by differential peptide display. Proteomics 2005; 5: 3414–22
   PubMed Web of Science ®Google Scholar
• Muller A, MacCallum RM, Sternberg MJE. Structural characterization of the human proteome. Genome Research 2002; 12: 1625–41
   PubMed Web of Science ®Google Scholar
• Pieper R, Gatlin CL, Makusky AJ, Russo PS, Schatz CR, Miller SS, et al. The human serum proteome: Display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics 2003; 3: 1345–64
   PubMed Web of Science ®Google Scholar
• Shmueli O, Horn-Saban S, Chalifa-Caspi V, Shmoish M, Ophir R, Benjamin-Rodrig H, et al. GeneNote: Whole genome expression profiles in normal human tissues. C R Biol 2003; 326: 1067–72
   PubMed Web of Science ®Google Scholar
• Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA 2002; 99: 4465–70
   PubMed Web of Science ®Google Scholar
• Righetti PG, Castagna A, Herbert B, Reymond F, Rossier JS. Prefractionation techniques in proteome analysis. Proteomics 2003; 3: 1397–407
   PubMed Web of Science ®Google Scholar
• Perrot M, Sagliocco F, Mini T, Monribot C, Schneider U, Shevchenko A, et al. Two-dimensional gel protein database of Saccharomyces cerevisiae (update 1999). Electrophoresis 1999; 20: 2280–98
   PubMed Web of Science ®Google Scholar
• Washburn MP, Wolters D, Yates JR 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001; 19: 242–7
   PubMed Web of Science ®Google Scholar
• Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J Proteome Res 2003; 2: 43–50
   PubMed Web of Science ®Google Scholar
• Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, et al. Global analysis of protein expression in yeast. Nature 2003; 425(6959)737–41
   PubMed Web of Science ®Google Scholar
• Jacobs JM, Mottaz HM, Yu LR, Anderson DJ, Moore RJ, Chen WN, et al. Multidimensional proteome analysis of human mammary epithelial cells. J Proteome Res 2004; 3: 68–75
   PubMed Web of Science ®Google Scholar
• Humphery-Smith I. A human proteome project with a beginning and an end. Proteomics 2004; 4: 2519–21
   PubMed Web of Science ®Google Scholar
• Nilsson P, Paavilainen L, Larsson K, Odling J, Sundberg M, Andersson AC, et al. Towards a human proteome atlas: High-throughput generation of mono-specific antibodies for tissue profiling. Proteomics 2005.
   PubMed Web of Science ®Google Scholar
• Uhlen M, Ponten F. Antibody-based proteomics for human tissue profiling. Mol Cell Proteomics 2005; 4: 384–93
   PubMed Web of Science ®Google Scholar
• Ficarro SB, McCleland ML, Stukenberg PT, Burke DJ, Ross MM, Shabanowitz J, et al. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol 2002; 20: 301–5
   PubMed Web of Science ®Google Scholar
• Salomon AR, Ficarro SB, Brill LM, Brinker A, Phung QT, Ericson C, et al. Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry. Proc Natl Acad Sci USA 2003; 100: 443–8
   PubMed Web of Science ®Google Scholar
• Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science 2002; 298(5600)1912–34
   PubMed Web of Science ®Google Scholar
• Wang WQ, Sun JP, Zhang ZY. An overview of the protein tyrosine phosphatase superfamily. Curr Top Med Chem 2003; 3: 739–48
   PubMed Web of Science ®Google Scholar
• McCluskey A, Sim AT, Sakoff JA. Serine-threonine protein phosphatase inhibitors: Development of potential therapeutic strategies. J Med Chem 2002; 45: 1151–75
   PubMed Web of Science ®Google Scholar
• Honkanen RE, Golden T. Regulators of serine/threonine protein phosphatases at the dawn of a clinical era?. Curr Med Chem 2002; 9: 2055–75
   PubMed Web of Science ®Google Scholar
• Qian WJ, Goshe MB, Camp DG 2nd, Yu LR, Tang K, Smith RD. Phosphoprotein isotope-coded solid-phase tag approach for enrichment and quantitative analysis of phosphopeptides from complex mixtures. Anal Chem 2003; 75: 5441–50
   PubMed Web of Science ®Google Scholar
• Steinberg TH, Agnew BJ, Gee KR, Leung WY, Goodman T, Schulenberg B, et al. Global quantitative phosphoprotein analysis using Multiplexed Proteomics technology. Proteomics 2003; 3: 1128–44
   PubMed Web of Science ®Google Scholar
• Guy GR, Philip R, Tan YH. Analysis of cellular phosphoproteins by two-dimensional gel electrophoresis: Applications for cell signaling in normal and cancer cells. Electrophoresis 1994; 15: 417–40
   PubMed Web of Science ®Google Scholar
• Wulfkuhle JD, Aquino JA, Calvert VS, Fishman DA, Coukos G, Liotta LA, et al. Signal pathway profiling of ovarian cancer from human tissue specimens using reverse-phase protein microarrays. Proteomics 2003; 3: 2085–90
   PubMed Web of Science ®Google Scholar
• Lowenthal MS, Mehta AI, Frogale K, Bandle RW, Araujo RP, Hood BL, et al. Analysis of albumin-associated peptides and proteins from ovarian cancer patients. Clin Chem 2005; 51: 1933–45
   PubMed Web of Science ®Google Scholar
• Adkins JN, Varnum SM, Auberry KJ, Moore RJ, Angell NH, Smith RD, et al. Toward a human blood serum proteome: Analysis by multidimensional separation coupled with mass spectrometry. Mol Cell Proteomics 2002; 1: 947–55
   PubMed Web of Science ®Google Scholar
• Cho SY, Lee EY, Lee JS, Kim HY, Park JM, Kwon MS, et al. Efficient prefractionation of low-abundance proteins in human plasma and construction of a two-dimensional map. Proteomics 2005; 5: 3386–96
   PubMed Web of Science ®Google Scholar
• Tang HY, Ali-Khan N, Echan LA, Levenkova N, Rux JJ, Speicher DW. A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes. Proteomics 2005; 5: 3329–42
   PubMed Web of Science ®Google Scholar
• Anderson NL, Anderson NG, Haines LR, Hardie DB, Olafson RW, Pearson TW. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J Proteome Res 2004; 3: 235–44
   PubMed Web of Science ®Google Scholar
• Wulfkuhle JD, Sgroi DC, Krutzsch H, McLean K, McGarvey K, Knowlton M, et al. Proteomics of human breast ductal carcinoma in situ. Cancer Res 2002; 62: 6740–9
   PubMed Web of Science ®Google Scholar
• Petricoin EF 3rd, Ornstein DK, Paweletz CP, Ardekani A, Hackett PS, Hitt BA, et al. Serum proteomic patterns for detection of prostate cancer. J Natl Cancer Inst 2002; 94: 1576–8
   PubMed Web of Science ®Google Scholar
• Adam BL, Qu Y, Davis JW, Ward MD, Clements MA, Cazares LH, et al. Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res 2002; 62: 3609–14
   PubMed Web of Science ®Google Scholar
• Kozak KR, Amneus MW, Pusey SM, Su F, Luong MN, Luong SA, et al. Identification of biomarkers for ovarian cancer using strong anion-exchange ProteinChips: Potential use in diagnosis and prognosis. Proc Natl Acad Sci USA 2003; 100: 12343–8
   PubMed Web of Science ®Google Scholar
• Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM, et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002; 359(9306)572–7
   PubMed Web of Science ®Google Scholar
• Diamandis EP. Analysis of serum proteomic patterns for early cancer diagnosis: Drawing attention to potential problems. J Natl Cancer Inst 2004; 96: 353–6
   PubMed Web of Science ®Google Scholar
• Puente XS, Sanchez LM, Overall CM, Lopez-Otin C, et al. Human and mouse proteases: A comparative genomic approach. Nature Rev Gen 2003; 4: 544–58
   PubMed Web of Science ®Google Scholar
• Kanduc D, Mittelman A, Serpico R, Sinigaglia E, Sinha AA, Natale C, et al. Cell death: Apoptosis versus necrosis (review). Int J Oncol 2002; 21: 165–70
   PubMed Web of Science ®Google Scholar
• Olivieri E, Herbert B, Righetti PG. The effect of protease inhibitors on the two-dimensional electrophoresis pattern of red blood cell membranes. Electrophoresis 2001; 22: 560–5
   PubMed Web of Science ®Google Scholar
• Mykles DL. Proteinase families and their inhibitors. Methods Cell Biol 2001; 66: 247–87
   PubMed Web of Science ®Google Scholar
• Rivard AL, Gallegos RP, Bianco RW, Liao K. The basic science aspect of donor heart preservation: A review. J Extra-Corp Technol 2004;269–74.
   PubMedGoogle Scholar
• Cosi C, Marien M. Decreases in mouse brain NAD+ and ATP induced by 1-methyl-4-phenyl-1, 2,3,6-tetrahydropyridine (MPTP): Prevention by the poly(ADP-ribose) polymerase inhibitor, benzamide. Brain Res 1998; 809: 58–67
   PubMed Web of Science ®Google Scholar
• Ansari KA, Rand A, Hendrickson H, Bentley MD. Qualitative and quantitative studies on human myelin basic protein in situ with respect to time interval between death and autopsy. J Neuropathol Exp Neurol 1976; 35: 180–90
   PubMed Web of Science ®Google Scholar
• Berlet HH, Volk B. Studies of human myelin proteins during old age. Mech Ageing Dev 1980; 14: 211–22
   PubMed Web of Science ®Google Scholar
• Goggins M, Scott JM, Weir DG. Regional differences in protein carboxymethylation in post-mortem human brain. Clin Sci (Lond) 1998; 94: 677–85
   PubMed Web of Science ®Google Scholar
• Naser NA, Naser SA. Clinical Chemistry Laboratory Manual 1998: Mosby Inc.
   Google Scholar
• Ludwig JA, Weinstein JN. Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer 2005; 5: 845–56
   PubMed Web of Science ®Google Scholar
• Mustard JF, Kinlough-Rathbone RL, Packham MA. Isolation of human platelets from plasma by centrifugation and washing. Methods Enzymol 1989; 169: 3–11
   PubMed Web of Science ®Google Scholar
• Lewis MR, Callas PW, Jenny NS, Tracy RP. Longitudinal stability of coagulation, fibrinolysis, and inflammation factors in stored plasma samples. Thromb Haemost 2001; 86: 1495–500
   PubMed Web of Science ®Google Scholar
• Chaurand P, Schwartz SA, Billheimer D, Xu BJ, Crecelius A, Caprioli R. Integrating histology and imaging mass spectrometry. Anal Chem 2004; 76: 1145–55
   PubMed Web of Science ®Google Scholar
• Schwartz SA, Weil RJ, Thompson RC, Shyr Y, Moore JH, Toms SA, et al. Proteomic-based prognosis of brain tumor patients using direct-tissue matrix-assisted laser desorption ionization mass spectrometry. Cancer Res 2005; 65: 7674–81
   PubMed Web of Science ®Google Scholar
• Schwartz SA, Weil RJ, Johnson MD, Toms SA, Caprioli RM. Protein profiling in brain tumors using mass spectrometry: Feasibility of a new technique for the analysis of protein expression. Clin Cancer Res 2004; 10: 981–7
   PubMed Web of Science ®Google Scholar
• Dill KA. Dominant forces in protein folding. Biochemistry 1990; 29: 7133–55
   PubMed Web of Science ®Google Scholar
• Kauzmann W. Some factors in the interpretation of protein denaturation. Adv Protein Chem 1959; 14: 1–63
   PubMedGoogle Scholar
• Scopes RK. Making an extract, in protein purification: Principles and practice. 1987.
   Google Scholar
• Dignam JD. Preparation of extracts from higher eukaryotes. Methods Enzymol 1990; 182: 194–203
   PubMed Web of Science ®Google Scholar
• Bollag DM, Edelstein SJ. Protein Methods. New YorkChichester, Brisbane, Toronto, Singapore: Wiley-Liss; 1991.
   Google Scholar
• Deutscher MP. Maintaining protein stability. Methods Enzymol 1990; 182: 83–9
   PubMed Web of Science ®Google Scholar
• Nielsen UB, Cardone MH, Sinskey AJ, MacBeath G, Sorger PK. Profiling receptor tyrosine kinase activation by using Ab microarrays. Proc Natl Acad Sci USA 2003; 100: 9330–5
   PubMed Web of Science ®Google Scholar
• Harder A, Wildgruber R, Nawrocki A, Fey SJ, Larsen PM, Gorg A. Comparison of yeast cell protein solubilization procedures for two-dimensional electrophoresis. Electrophoresis 1999; 20: 826–9
   PubMed Web of Science ®Google Scholar
• Newcombe J, Eriksson B, Ottervald J, Yang Y, Franzen B. Extraction and proteomic analysis of proteins from normal and multiple sclerosis postmortem brain. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 815: 191–202
   PubMed Web of Science ®Google Scholar
• Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970; 227(259)680–5
   PubMed Web of Science ®Google Scholar
• Laemmli UK, Favre M. Maturation of the head of bacteriophage T4. I. DNA packaging events. J Mol Biol 1973; 80: 575–99
   PubMed Web of Science ®Google Scholar
• Steinberg TH, Jones LJ, Haugland RP, Singer VL. SYPRO orange and SYPRO red protein gel stains: One-step fluorescent staining of denaturing gels for detection of nanogram levels of protein. Anal Biochem 1996; 239: 223–37
   PubMed Web of Science ®Google Scholar
• Steinberg TH, Haugland RP, Singer VL. Applications of SYPRO orange and SYPRO red protein gel stains. Anal Biochem 1996; 239: 238–45
   PubMed Web of Science ®Google Scholar
• Mackintosh JA, Choi HY, Bae SH, Veal DA, Bell PJ, Ferrari BC, et al. A fluorescent natural product for ultra sensitive detection of proteins in one-dimensional and two-dimensional gel electrophoresis. Proteomics 2003; 3: 2273–88
   PubMed Web of Science ®Google Scholar
• Steinberg TH, Pretty On Top K, Berggren KN, Kemper C, Jones L, Diwu Z, et al. Rapid and simple single nanogram detection of glycoproteins in polyacrylamide gels and on electroblots. Proteomics 2001; 1: 841–55
   PubMed Web of Science ®Google Scholar
• Burnette WN. “Western blotting”: Electrophoretic transfer of proteins from sodium dodecyl sulfate–polyacrylamide gels to unmodified nitrocellulose and radiographic detection with antibody and radioiodinated protein A. Anal Biochem 1981; 112: 195–203
   PubMed Web of Science ®Google Scholar
• Bjellqvist B, Ek K, Righetti PG, Gianazza E, Gorg A, Westermeier R, et al. Isoelectric focusing in immobilized pH gradients: Principle, methodology and some applications. J Biochem Biophys Methods 1982; 6: 317–39
   PubMedGoogle Scholar
• O'Farrell PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975; 250: 4007–21
   PubMed Web of Science ®Google Scholar
• O'Farrell PZ, Goodman HM, O'Farrell PH. High resolution two-dimensional electrophoresis of basic as well as acidic proteins. Cell 1977; 12: 1133–41
   PubMed Web of Science ®Google Scholar
• Sabounchi-Schutt F, Astrom J, Olsson I, Eklund A, Grunewald J, Bjellqvist B. An immobiline DryStrip application method enabling high-capacity two-dimensional gel electrophoresis. Electrophoresis 2000; 21: 3649–56
   PubMed Web of Science ®Google Scholar
• Li J, Zhang Z, Rosenzweig J, Wang YY, Chan DW. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 2002; 48: 1296–304
   PubMed Web of Science ®Google Scholar
• Michaud GA, Salcius M, Zhou F, Bangham R, Bonin J, Guo H, et al. Analyzing antibody specificity with whole proteome microarrays. Nat Biotechnol 2003; 21: 1509–12
   PubMed Web of Science ®Google Scholar
• Chalmers MJ, Quinn JP, Blakney GT, Emmett MR, Mischak H, Gaskell SJ, et al. Liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometric characterization of protein kinase C phosphorylation. J Proteome Res 2003; 2: 373–82
   PubMed Web of Science ®Google Scholar
• Goshe MB, Veenstra TD, Panisko EA, Conrads TP, Angell NH, Smith RD. Phosphoprotein isotope-coded affinity tags: Application to the enrichment and identification of low-abundance phosphoproteins. Anal Chem 2002; 74: 607–16
   PubMed Web of Science ®Google Scholar
• Zhou H, Watts JD, Aebersold R. A systematic approach to the analysis of protein phosphorylation. Nat Biotechnol 2001; 19: 375–8
   PubMed Web of Science ®Google Scholar
• Alban A, David SO, Bjorkesten L, Andersson C, Sloge E, Lewis S, et al. A novel experimental design for comparative two-dimensional gel analysis: Two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 2003; 3: 36–44
   PubMed Web of Science ®Google Scholar
• Andersen JS, Wilkinson CJ, Mayor T, Mortensen P, Nigg EA, Mann M. Proteomic characterization of the human centrosome by protein correlation profiling. Nature 2003; 426(6966)570–4
   PubMed Web of Science ®Google Scholar
• Blagoev B, Kratchmarova I, Ong SE, Nielsen M, Foster LJ, Mann M. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol 2003; 21: 315–8
   PubMed Web of Science ®Google Scholar
• Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999; 17: 994–9
   PubMed Web of Science ®Google Scholar
• Gygi SP, Rist B, Griffin TJ, Eng J, Aebersold R. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J Proteome Res 2002; 1: 47–54
   PubMed Web of Science ®Google Scholar
• Ranish JA, Yi EC, Leslie DM, Purvine SO, Goodlett DR, Eng J, et al. The study of macromolecular complexes by quantitative proteomics. Nat Genet 2003; 33: 349–55
   PubMed Web of Science ®Google Scholar
• Wingren C, Ingvarsson J, Lindstedt M, Borrebaeck CA. Recombinant antibody microarrays–a viable option?. Nat Biotechnol 2003; 21: 223
   PubMed Web of Science ®Google Scholar
• Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 2003; 100: 6940–5
   PubMed Web of Science ®Google Scholar