One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation

Journal of Proteomics - Tập 154 - Trang 13-21 - 2017
Dominik A. Megger1, Juliet Padden1, Kristin Rosowski1, Julian Uszkoreit1, Thilo Bracht1, Martin Eisenacher1, Christian Gerges2, Horst Neuhaus2, Brigitte Schumacher3, Jörg. F. Schlaak4, Barbara Sitek1
1Medizinisches Proteom-Center, Ruhr-Universität Bochum, Germany
2Department of Internal Medicine, Evangelisches Krankenhaus, Düsseldorf, Germany
3Klinik für Innere Medizin und Gastroenterologie, Elisabeth Krankenhaus Essen, Essen, Germany
4Department of Internal Medicine, Evangelisches Krankenhaus Duisburg-Nord, Duisburg, Germany

Tài liệu tham khảo

Farina, 2014, Proximal fluid proteomics for the discovery of digestive cancer biomarkers, Biochim. Biophys. Acta, 1844, 988, 10.1016/j.bbapap.2013.10.011 Farina, 2014, Bile proteome in health and disease, Compr. Physiol., 4, 91, 10.1002/cphy.c130016 Yamazaki, 1988, Biliary proteins: assessment of quantitative techniques and comparison in gallstone and nongallstone subjects, J. Lipid Res., 29, 1055, 10.1016/S0022-2275(20)38469-8 Farina, 2009, Proteomic analysis of human bile and potential applications for cancer diagnosis, Expert Rev. Proteomics, 6, 285, 10.1586/epr.09.12 Farina, 2011, A step further in the analysis of human bile proteome, J. Proteome Res., 10, 2047, 10.1021/pr200011b Farid, 2011, Shotgun proteomics of human bile in hilar cholangiocarcinoma, Proteomics, 11, 2134, 10.1002/pmic.201000653 Barbhuiya, 2011, Comprehensive proteomic analysis of human bile, Proteomics, 11, 4443, 10.1002/pmic.201100197 Megger, 2013, Label-free quantification in clinical proteomics, Biochim. Biophys. Acta, 1834, 1581, 10.1016/j.bbapap.2013.04.001 Megger, 2013, Proteomic differences between hepatocellular carcinoma and nontumorous liver tissue investigated by a combined gel-based and label-free quantitative proteomics study, Mol. Cell. Proteomics, 12, 2006, 10.1074/mcp.M113.028027 Reis, 2015, A structured proteomic approach identifies 14-3-3Sigma as a novel and reliable protein biomarker in panel based differential diagnostics of liver tumors, Biochim. Biophys. Acta, 1854, 641, 10.1016/j.bbapap.2014.10.024 Padden, 2014, Identification of novel biomarker candidates for the immunohistochemical diagnosis of cholangiocellular carcinoma, Mol. Cell. Proteomics, 13, 2661, 10.1074/mcp.M113.034942 Megger, 2014, Comparison of label-free and label-based strategies for proteome analysis of hepatoma cell lines, Biochim. Biophys. Acta, 1844, 967, 10.1016/j.bbapap.2013.07.017 Berthold, 2008, KNIME: The Konstanz Information Miner, 319 Martens, 2011, mzML--a community standard for mass spectrometry data, Mol. Cell. Proteomics, 10, 10.1074/mcp.R110.000133 Kessner, 2008, ProteoWizard: open source software for rapid proteomics tools development, Bioinformatics, 24, 2534, 10.1093/bioinformatics/btn323 Weisser, 2013, An automated pipeline for high-throughput label-free quantitative proteomics, J. Proteome Res., 12, 1628, 10.1021/pr300992u Mayer, 2015, ProCon - PROteomics CONversion tool, J. Proteomics, 129, 56, 10.1016/j.jprot.2015.06.015 Huang da, 2009, Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists, Nucleic Acids Res., 37, 1, 10.1093/nar/gkn923 Huang da, 2009, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat. Protoc., 4, 44, 10.1038/nprot.2008.211 Shevchenko, 2006, In-gel digestion for mass spectrometric characterization of proteins and proteomes, Nat. Protoc., 1, 2856, 10.1038/nprot.2006.468 Fang, 2015, Matrix effects break the LC behavior rule for analytes in LC-MS/MS analysis of biological samples, Exp. Biol. Med. (Maywood), 240, 488, 10.1177/1535370214554545 Van Eeckhaut, 2009, Validation of bioanalytical LC-MS/MS assays: evaluation of matrix effects, J. Chromatogr. B Anal. Technol. Biomed. Life Sci., 877, 2198, 10.1016/j.jchromb.2009.01.003 Bantscheff, 2007, Quantitative mass spectrometry in proteomics: a critical review, Anal. Bioanal. Chem., 389, 1017, 10.1007/s00216-007-1486-6 Neilson, 2011, Less label, more free: approaches in label-free quantitative mass spectrometry, Proteomics, 11, 535, 10.1002/pmic.201000553 Bantscheff, 2012, Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present, Anal. Bioanal. Chem., 404, 939, 10.1007/s00216-012-6203-4 Sandra, 2008, Highly efficient peptide separations in proteomics Part 1. Unidimensional high performance liquid chromatography, J. Chromatogr. B Anal. Technol. Biomed. Life Sci., 866, 48, 10.1016/j.jchromb.2007.10.034 Sandra, 2009, Highly efficient peptide separations in proteomics. Part 2: bi- and multidimensional liquid-based separation techniques, J. Chromatogr. B Anal. Technol. Biomed. Life Sci., 877, 1019, 10.1016/j.jchromb.2009.02.050 Naboulsi, 2016, Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma, J. Proteome Res., 15, 38, 10.1021/acs.jproteome.5b00420 Bracht, 2015, Analysis of disease-associated protein expression using quantitative proteomics-fibulin-5 is expressed in association with hepatic fibrosis, J. Proteome Res., 14, 2278, 10.1021/acs.jproteome.5b00053 Chambers, 2015, Multiple Reaction Monitoring Enables Precise Quantification of 97 Proteins in Dried Blood Spots, Mol. Cell. Proteomics, 14, 3094, 10.1074/mcp.O115.049957 Percy, 2014, Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation, J. Proteome Res., 10.1021/pr500317d Chambers, 2014, MRM for the verification of cancer biomarker proteins: recent applications to human plasma and serum, Expert Rev. Proteomics, 11, 137, 10.1586/14789450.2014.877346 Voigtlander, 2015, Endoscopic diagnosis of cholangiocarcinoma: From endoscopic retrograde cholangiography to bile proteomics, Best Pract. Res. Clin. Gastroenterol., 29, 267, 10.1016/j.bpg.2015.02.005 Lankisch, 2011, Bile proteomic profiles differentiate cholangiocarcinoma from primary sclerosing cholangitis and choledocholithiasis, Hepatology, 53, 875, 10.1002/hep.24103