Colorectal cancer biomarker discovery and validation using LC-MS/MS-based proteomics in blood: truth or dare?

References

• Jemal A, Bray F, Center MM, et al. Global cancer statistics. CA Cancer J Clin 2011;61(2):69-90
   PubMed Web of Science ®Google Scholar
• Gingras D, Beliveau R. Colorectal cancer prevention through dietary and lifestyle modifications. Cancer Microenviron 2011;4(2):133-9
   PubMedGoogle Scholar
• Bogaert J, Prenen H. Molecular genetics of colorectal cancer. Ann Gastroenterol 2014;27:1-6
   PubMedGoogle Scholar
• Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000;100(1):57-70
   PubMed Web of Science ®Google Scholar
• Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011;144(5):646-74
   PubMed Web of Science ®Google Scholar
• Ferlay J, Parkin DM, Steliarova-Foucher E. Estimates of cancer incidence and mortality in Europe in 2008. Eur J Cancer 2010;46(4):765-81
   PubMed Web of Science ®Google Scholar
• Robbins AS, Siegel RL, Jemal A. Racial disparities in stage-specific colorectal cancer mortality rates from 1985 to 2008. J Clin Oncol 2012;30(4):401-5
   PubMed Web of Science ®Google Scholar
• Maroni R. Council Recommendation of 2 December 2003 on Cancer Screening. Volume 2003
   Google Scholar
• Garborg K, Holme Ø, Løberg M, et al. Current status of screening for colorectal cancer. Ann Oncol 2013;24(8):1963-72
   PubMed Web of Science ®Google Scholar
• de Wijkerslooth TR, Bossuyt PM, Dekker E. Strategies in screening for colon carcinoma. Neth J Med 2011;69(3):112-19
   PubMed Web of Science ®Google Scholar
• Ransohoff DF, Sandler RS. Clinical practice. Screening for colorectal cancer. N Engl J Med 2002;346(1):40-4
   PubMed Web of Science ®Google Scholar
• Segnan N, Patnik J, von Karsa L. European guidelines for quality assurance in colorectal cancer screening and diagnosis. Volume 1 Publications Office of the European Union; Luxembourg: 2010
   Google Scholar
• Lohsiriwat V. Colonoscopic perforation: incidence, risk factors, management and outcome. World J. Gastroenterol 2010;16(4):425-30
   PubMed Web of Science ®Google Scholar
• Zavoral M, Suchanek S, Zavada F, et al. Colorectal cancer screening in Europe. World J Gastroenterol 2009;15(47):5907-15
   PubMed Web of Science ®Google Scholar
• Neerincx M, Buffart TE, Mulder CJ, et al. The future of colorectal cancer: implications of screening. Gut 2013;62(10):1387-9
   PubMed Web of Science ®Google Scholar
• Bosch LJ, Oort FA, Neerincx M, et al. DNA methylation of phosphatase and actin regulator 3 detects colorectal cancer in stool and complements FIT. Cancer Prev Res (Phila) 2012;5(3):464-72
   PubMed Web of Science ®Google Scholar
• Di LM, Travaglio E, Altomare DF. New strategies for colorectal cancer screening. World J Gastroenterol 2013;19(12):1855-60
   PubMed Web of Science ®Google Scholar
• Sidransky D. Emerging molecular markers of cancer. Nat Rev Cancer 2002;2(3):210-19
   PubMed Web of Science ®Google Scholar
• Issaq HJ, Waybright TJ, Veenstra TD. Cancer biomarker discovery: opportunities and pitfalls in analytical methods. Electrophoresis 2011;32(9):967-75
   PubMed Web of Science ®Google Scholar
• Cho WC, Cheng CH. Oncoproteomics: current trends and future perspectives. Expert Rev Proteomics 2007;4(3):401-10
   PubMed Web of Science ®Google Scholar
• Diaz JA, Slomka T. State of the art review: colorectal cancer screening. Am J Lifestyle Med 2012;6(3):196-203
   PubMedGoogle Scholar
• Cho WC. Epigenetic alteration of microRNAs in feces of colorectal cancer and its clinical significance. Expert Rev Mol Diagn 2011;11(7):691-4
   PubMed Web of Science ®Google Scholar
• Osborne JM, Wilson C, Moore V, et al. Sample preference for colorectal cancer screening tests: Blood or stool? Open J Prev Med 2012;2(3):326-31
   Google Scholar
• Gold P, Freedman SO. Demonstration of tumur-specific antigens in human colonic carcinomata by immunological tolerance and absorption techniques. J Exp Med 1965;121:439-62
   PubMed Web of Science ®Google Scholar
• Zhang Q, Faca V, Hanash S. Mining the plasma proteome for disease applications across seven logs of protein abundance. J Proteome Res 2011;10(1):46-50
   PubMed Web of Science ®Google Scholar
• Duffy MJ, van DA, Haglund C, et al. Tumour markers in colorectal cancer: european Group on Tumour Markers (EGTM) guidelines for clinical use. Eur J Cancer 2007;43(9):1348-60
   PubMed Web of Science ®Google Scholar
• Melle C, Ernst G, Schimmel B, et al. Discovery and identification of alpha-defensins as low abundant, tumor-derived serum markers in colorectal cancer. Gastroenterology 2005;129(1):66-73
   PubMed Web of Science ®Google Scholar
• de Wit M, Fijneman RJ, Verheul HM, et.al. Proteomics in colorectal cancer translational research: biomarker discovery for clinical applications. Clin Biochem 2013;46(6):466-79
   PubMed Web of Science ®Google Scholar
• Pavlou MP, Diamandis EP. The cancer cell secretome: a good source for discovering biomarkers? J Proteomics 2010;73(10):1896-906
   PubMed Web of Science ®Google Scholar
• Makridakis M, Vlahou A. Secretome proteomics for discovery of cancer biomarkers. J Proteomics 2010;73(12):2291-305
   PubMed Web of Science ®Google Scholar
• Shimoda M, Khokha R. Proteolytic factors in exosomes. Proteomics 2013;13(10-11):1624-36
   PubMed Web of Science ®Google Scholar
• Polanski M, Anderson NL. A list of candidate cancer biomarkers for targeted proteomics. Biomark Insights 2007;11-48
   Google Scholar
• Huttenhain R, Soste M, Selevsek N, et al. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci Transl Med 2012;4(142):142ra94
   PubMed Web of Science ®Google Scholar
• Percy AJ, Chambers AG, Yang J, Borchers CH. Multiplexed MRM-based quantitation of candidate cancer biomarker proteins in undepleted and non-enriched human plasma. Proteomics 2013;13(14):2202-15
   PubMed Web of Science ®Google Scholar
• Xie LQ, Zhao C, Cai SJ, et al. Novel proteomic strategy reveal combined alpha1 antitrypsin and cathepsin D as biomarkers for colorectal cancer early screening. J Proteome Res 2010;9(9):4701-9
   PubMed Web of Science ®Google Scholar
• Adkins JN, Varnum SM, Auberry KJ, et al. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol Cell Proteomics 2002;1(12):947-55
   PubMed Web of Science ®Google Scholar
• Zhang H, Liu AY, Loriaux P, et al. Mass spectrometric detection of tissue proteins in plasma. Mol Cell Proteomics 2007;6(1):64-71
   PubMed Web of Science ®Google Scholar
• Choi JW, Liu H, Shin DH, et al. Proteomic and cytokine plasma biomarkers for predicting progression from colorectal adenoma to carcinoma in human patients. Proteomics 2013;13(15):2361-74
   PubMed Web of Science ®Google Scholar
• Issaq HJ, Xiao Z, Veenstra TD. Serum and plasma proteomics. Chem Rev 2007;107(8):3601-20
   PubMed Web of Science ®Google Scholar
• Liumbruno G, D’Alessandro A, Grazzini G, Zolla L. Blood-related proteomics. J Proteomics 2010;73(3):483-507
   PubMed Web of Science ®Google Scholar
• Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. Mass Spectrom Rev 2011;30:685-732
   PubMed Web of Science ®Google Scholar
• Farrah T, Deutsch EW, Omenn GS, et al. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics 2011;10(9):M110.006353
   PubMed Web of Science ®Google Scholar
• Mehta AI, Ross S, Lowenthal MS, et al. Biomarker amplification by serum carrier protein binding. Dis Markers 2003;19(1):1-10
   PubMed Web of Science ®Google Scholar
• Lange T, Dimitrov S, Born J. Effects of sleep and circadian rhythm on the human immune system. Ann N Y Acad Sci 2010;1193:48-59
   PubMed Web of Science ®Google Scholar
• Lee JE, Zamdborg L, Southey BR, et al. Quantitative peptidomics for discovery of circadian-related peptides from the rat suprachiasmatic nucleus. J Proteome Res 2013;12(2):585-93
   PubMed Web of Science ®Google Scholar
• Omenn GS, States DJ, Adamski M, 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(13):3226-45
   PubMed Web of Science ®Google Scholar
• Rai AJ, Gelfand CA, Haywood BC, et al. HUPO plasma proteome project specimen collection and handling:towards the standardization of parameters for plasma proteome samples. Proteomics 2005;5(13):3262-77
   PubMed Web of Science ®Google Scholar
• Tammen H, Schulte I, Hess R, et al. Prerequisites for peptidomic analysis of blood samples: I. Evaluation of blood specimen qualities and determination of technical performance characteristics. Comb Chem High Throughput Screen 2005;8(8):725-33
   PubMed Web of Science ®Google Scholar
• Tammen H, Schulte I, Hess R, et al. Peptidomic analysis of human blood specimens: comparison between plasma specimens and serum by differential peptide display. Proteomics 2005;5(13):3414-22
   PubMed Web of Science ®Google Scholar
• Villanueva J, Shaffer DR, Philip J, et al. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J Clin Invest 2006;116(1):271-84
   PubMed Web of Science ®Google Scholar
• Liotta LA, Petricoin EF. Serum peptidome for cancer detection: spinning biologic trash into diagnostic gold. J Clin Invest 2006;116(1):26-30
   PubMed Web of Science ®Google Scholar
• Liotta LA, Petricoin EF. Mass spectrometry-based protein biomarker discovery: solving the remaining challenges to reach the promise of clinical benefit. Clin Chem 2010;56(10):1641-2
   PubMed Web of Science ®Google Scholar
• Petricoin EF, Belluco C, Araujo RP, Liotta LA. The blood peptidome: a higher dimension of information content for cancer biomarker discovery. Nat Rev Cancer 2006;6(12):961-7
   PubMed Web of Science ®Google Scholar
• Farrah T, Deutsch EW, Aebersold R. Using the Human Plasma PeptideAtlas to study human plasma proteins. Methods Mol Biol 2011;728:349-74
   PubMedGoogle Scholar
• Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 2003;75(17):4646-58
   PubMed Web of Science ®Google Scholar
• Farrah T, Deutsch EW, Omenn GS, et al. State of the human proteome in 2013 as viewed through peptideatlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven human proteome project. J Proteome Res 2014;13(1):60-75
   PubMed Web of Science ®Google Scholar
• Omenn GS, Menon R, Zhang Y. Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. J Proteomics 2013;90:28-37
   PubMed Web of Science ®Google Scholar
• Habermann JK, Roblick UJ, Luke BT, et al. Increased serum levels of complement C3a anaphylatoxin indicate the presence of colorectal tumors. Gastroenterology 2006;131(4):1020-9
   PubMed Web of Science ®Google Scholar
• Albrethsen J, Bøgebo R, Gammeltoft S, et al. Upregulated expression of human neutrophil peptides 1, 2 and 3 (HNP 1-3) in colon cancer serum and tumours: a biomarker study. BMC Cancer 2005;5:8
   PubMed Web of Science ®Google Scholar
• Engwegen JY, Gast MC, Schellens JH, Beijnen JH. Clinical proteomics: SEARCHING for better tumour markers with SELDI-TOF mass spectrometry. Trends Pharmacol Sci 2006;27(5):251-9
   PubMed Web of Science ®Google Scholar
• Ward DG, Suggett N, Cheng Y, et al. Identification of serum biomarkers for colon cancer by proteomic analysis. Br J Cancer 2006;94(12):1898-905
   PubMed Web of Science ®Google Scholar
• Fung ET, Yip TT, Lomas L, et al. Classification of cancer types by measuring variants of host response proteins using SELDI serum assays. Int J Cancer 2005;115(5):783-9
   PubMed Web of Science ®Google Scholar
• Liu C, Pan C, Shen J, et al. MALDI-TOF MS combined with magnetic beads for detecting serum protein biomarkers and establishment of boosting decision tree model for diagnosis of colorectal cancer. Int J Med Sci 2011;8(1):39-47
   PubMed Web of Science ®Google Scholar
• Murakoshi Y, Honda K, Sasazuki S, et al. Plasma biomarker discovery and validation for colorectal cancer by quantitative shotgun mass spectrometry and protein microarray. Cancer Sci 2011;102(3):630-8
   PubMed Web of Science ®Google Scholar
• Liu XP, Shen J, Li ZF, et al. A serum proteomic pattern for the detection of colorectal adenocarcinoma using surface enhanced laser desorption and ionization mass spectrometry. Cancer Invest 2006;24(8):747-53
   PubMed Web of Science ®Google Scholar
• Zheng GX, Wang CX, Qu X, et al. Establishment of serum protein pattern for screening colorectal cancer using SELDI-TOF-MS. Exp Oncol 2006;28(4):282-7
   PubMedGoogle Scholar
• Wang Q, Shen J, Li ZF, et al. Limitations in SELDI-TOF MS whole serum proteomic profiling with IMAC surface to specifically detect colorectal cancer. BMC Cancer 2009;9:287
   PubMed Web of Science ®Google Scholar
• Liu M, Li CF, Chen HS, et al. Differential expression of proteomics models of colorectal cancer, colorectal benign disease and healthy controls. Proteome Sci 2010;8:16
   PubMed Web of Science ®Google Scholar
• Huijbers A, Velstra B, Dekker TJ, et al. Proteomic serum biomarkers and their potential application in cancer screening programs. Int J Mol Sci 2010;11(11):4175-93
   PubMed Web of Science ®Google Scholar
• Bunger S, Haug U, Kelly M, et al. A novel multiplex-protein array for serum diagnostics of colon cancer: a case-control study. BMC Cancer 2012;12:393
   PubMed Web of Science ®Google Scholar
• Albrethsen J, Bøgebo R, Møller CH, et al. Candidate biomarker verification: critical examination of a serum protein pattern for human colorectal cancer. Proteomics Clin Appl 2012;6(3-4):182-9
   PubMed Web of Science ®Google Scholar
• Zhang X, Xiao Z, Liu X, et al. The potential role of ORM2 in the development of colorectal cancer. PLoS One 2012;7(2):e31868
   PubMed Web of Science ®Google Scholar
• Ransohoff DF, Martin C, Wiggins WS, et al. Assessment of serum proteomics to detect large colon adenomas. Cancer Epidemiol Biomarkers Prev 2008;17(8):2188-93
   PubMed Web of Science ®Google Scholar
• Jimenez CR, Knol JC, Meijer GA, Fijneman RJ. Proteomics of colorectal cancer: overview of discovery studies and identification of commonly identified cancer-associated proteins and candidate CRC serum markers. J Proteomics 2010;73(10):1873-95
   PubMed Web of Science ®Google Scholar
• Becker JO, Hoofnagle AN. Replacing immunoassays with tryptic digestion-peptide immunoaffinity enrichment and LC-MS/MS. Bioanalysis 2012;4(3):281-90
   PubMed Web of Science ®Google Scholar
• Wild N, Andres H, Rollinger W, et al. A combination of serum markers for the early detection of colorectal cancer. Clin Cancer Res 2010;16(24):6111-21
   PubMed Web of Science ®Google Scholar
• Kanojia D, Garg M, Gupta S, et al. Sperm-associated antigen 9 is a novel biomarker for colorectal cancer and is involved in tumor growth and tumorigenicity. Am J Pathol 2011;178(3):1009-20
   PubMed Web of Science ®Google Scholar
• Liu ZP, Li LM, Liu XL, Zhang DX. Comparative analysis of tumor markers and evaluation of their predictive value in patients with colorectal cancer. Onkologie 2012;35(3):108-13
   PubMedGoogle Scholar
• Kim JT, Song EY, Chung KS, et al. Up-regulation and clinical significance of serine protease kallikrein 6 in colon cancer. Cancer 2011;117(12):2608-19
   PubMed Web of Science ®Google Scholar
• Hurst NG, Stocken DD, Wilson S, et al. Elevated serum matrix metalloproteinase 9 (MMP-9) concentration predicts the presence of colorectal neoplasia in symptomatic patients. Br J Cancer 2007;97(7):971-7
   PubMed Web of Science ®Google Scholar
• Holten-Andersen MN, Christensen IJ, Nielsen HJ, et al. Total levels of tissue inhibitor of metalloproteinases 1 in plasma yield high diagnostic sensitivity and specificity in patients with colon cancer. Clin Cancer Res 2002;8(1):156-64
   PubMed Web of Science ®Google Scholar
• Holten-Andersen MN, Murphy G, Nielsen HJ, et al. Quantitation of TIMP-1 in plasma of healthy blood donors and patients with advanced cancer. Br J Cancer 1999;80(3-4):495-503
   PubMed Web of Science ®Google Scholar
• Fung KY, Priebe I, Purins L, et al. Performance of serum lipocalin 2 as a diagnostic marker for colorectal cancer. Cancer Biomark 2013;13(2):75-9
   PubMed Web of Science ®Google Scholar
• Kolliopoulos C, Bounias D, Bouga H, et al. Hyaluronidases and their inhibitors in the serum of colorectal carcinoma patients. J Pharm Biomed Anal 2013;83:299-304
   PubMed Web of Science ®Google Scholar
• Ramcharan SK, Lip GY, Stonelake PS, Blann AD. Angiogenin outperforms VEGF, EPCs and CECs in predicting Dukes’ and AJCC stage in colorectal cancer. Eur J Clin Invest 2013;43(8):801-8
   PubMed Web of Science ®Google Scholar
• Song M, Wu K, Ogino S, et al. A prospective study of plasma inflammatory markers and risk of colorectal cancer in men. Br J Cancer 2013;108(9):1891-8
   PubMed Web of Science ®Google Scholar
• Damery S, Nichols L, Holder R, et al. Assessing the value of matrix metalloproteinase 9 (MMP9) in improving the appropriateness of referrals for colorectal cancer. Br J Cancer 2013;108(5):1149-56
   PubMed Web of Science ®Google Scholar
• Birgisson H, Jirstrom K, Stenman UH. Serum concentrations of human chorionic gonadotropin beta and its association with survival in patients with colorectal cancer. Cancer Biomark 2012;11(4):173-81
   PubMed Web of Science ®Google Scholar
• Barrow H, Rhodes JM, Yu LG. Simultaneous determination of serum galectin-3 and -4 levels detects metastases in colorectal cancer patients. Cell Oncol (Dordr) 2013;36(1):9-13
   PubMed Web of Science ®Google Scholar
• Gomceli I, Tez M, Bostanci EB, et al. Preoperative serum levels of soluble endoglin for prediction of recurrence in stage III colorectal cancer patients. Acta Med (Hradec Kralove) 2012;55(2):74-7
   PubMedGoogle Scholar
• Tsai MH, Wu CC, Peng PH, et al. Identification of secretory gelsolin as a plasma biomarker associated with distant organ metastasis of colorectal cancer. J Mol Med (Berl) 2012;90(2):187-200
   PubMed Web of Science ®Google Scholar
• Olink bioscience. Available from: www.olink.com
   Google Scholar
• Chen G, Pramanik BN. Application of LC/MS to proteomics studies: current status and future prospects. Drug Discov Today 2009;14(9-10):465-71
   PubMed Web of Science ®Google Scholar
• Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 2008;4:222
   PubMed Web of Science ®Google Scholar
• Mallick P, Schirle M, Chen SS, et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol 2007;25(1):125-31
   PubMed Web of Science ®Google Scholar
• Mead JA, Bianco L, Ottone V, et al. MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mol Cell Proteomics 2009;8(4):696-705
   PubMed Web of Science ®Google Scholar
• Sherwood CA, Eastham A, Lee LW, et al. MaRiMba: a software application for spectral library-based MRM transition list assembly. J Proteome Res 2009;8(10):4396-405
   PubMed Web of Science ®Google Scholar
• Makawita S, Diamandis EP. The bottleneck in the cancer biomarker pipeline and protein quantification through mass spectrometry-based approaches: current strategies for candidate verification. Clin Chem 2010;56(2):212-22
   PubMed Web of Science ®Google Scholar
• Addona TA, Abbatiello SE, Schilling B, et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol 2009;27(7):633-41
   PubMed Web of Science ®Google Scholar
• Randall SA, McKay MJ, Baker MS, Molloy MP. Evaluation of blood collection tubes using selected reaction monitoring MS: implications for proteomic biomarker studies. Proteomics 2010;10(10):2050-6
   PubMed Web of Science ®Google Scholar
• Tomasini-Johansson BR, Sundberg C, Lindmark G, et al. Vitronectin in colorectal adenocarcinoma--synthesis by stromal cells in culture. Exp Cell Res 1994;214(1):303-12
   PubMed Web of Science ®Google Scholar
• Anderson NL, Jackson A, Smith D, et al. SISCAPA peptide enrichment on magnetic beads using an in-line bead trap device. Mol Cell Proteomics 2009;8(5):995-1005
   PubMed Web of Science ®Google Scholar
• Ahn YH, Lee JY, Lee JY, et al. Quantitative analysis of an aberrant glycoform of TIMP1 from colon cancer serum by L-PHA-enrichment and SISCAPA with MRM mass spectrometry. J Proteome Res 2009;8(9):4216-24
   PubMed Web of Science ®Google Scholar
• Kuhn E, Whiteaker JR, Mani DR, et al. Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol Cell Proteomics 2012;11(6):M111.013854
   PubMed Web of Science ®Google Scholar
• Jaffe JD, Keshishian H, Chang B, et al. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification. Mol Cell Proteomics 2008;7(10):1952-62
   PubMed Web of Science ®Google Scholar
• Abbatiello SE, Mani DR, Schilling B, et al. Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS). Mol Cell Proteomics 2013;12(9):2623-39
   PubMed Web of Science ®Google Scholar
• Keshishian H, Addona T, Burgess M, et al. Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics 2009;8(10):2339-49
   PubMed Web of Science ®Google Scholar
• Peterson AC, Russell JD, Bailey DJ, et al. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol Cell Proteomics 2012;11(11):1475-88
   PubMed Web of Science ®Google Scholar
• Gallien S, Duriez E, Crone C, et al. Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol Cell Proteomics 2012;11(12):1709-23
   PubMed Web of Science ®Google Scholar
• Hanash SM, Pitteri SJ, Faca VM. Mining the plasma proteome for cancer biomarkers. Nature 2008;452(7187):571-9
   PubMed Web of Science ®Google Scholar
• Millioni R, Tolin S, Puricelli L, et al. High abundance proteins depletion vs low abundance proteins enrichment: comparison of methods to reduce the plasma proteome complexity. PLoS One 2011;6(5):e19603
   PubMed Web of Science ®Google Scholar
• Boschetti E, Giorgio RP. Hexapeptide combinatorial ligand libraries: the march for the detection of the low-abundance proteome continues. Biotechniques 2008;44(5):663-5
   PubMed Web of Science ®Google Scholar
• Millioni R, Tolin S, Fadini GP, et al. High confidence and sensitivity four-dimensional fractionation for human plasma proteome analysis. Amino Acids 2012;43(5):2199-202
   PubMed Web of Science ®Google Scholar
• Boichenko AP, Govorukhina N, van der Zee AG, Bischoff R. Multidimensional separation of tryptic peptides from human serum proteins using reversed-phase, strong cation exchange, weak anion exchange, and fused-core fluorinated stationary phases. J Sep Sci 2013;36(21-22):3463-70
   PubMed Web of Science ®Google Scholar
• Bandow JE. Comparison of protein enrichment strategies for proteome analysis of plasma. Proteomics 2010;10(7):1416-25
   PubMed Web of Science ®Google Scholar
• Diamandis EP. Cancer biomarkers: can we turn recent failures into success? J Natl Cancer Inst 2010;102(19):1462-7
   PubMedGoogle Scholar
• Bailly-Chouriberry L, Cormant F, Garcia P, et al. Identification of α-cobratoxin in equine plasma by LC-MS/MS for doping control. Anal Chem 2013;85(10):5219-25
   PubMed Web of Science ®Google Scholar
• Wu L, Candille SI, Choi Y, et al. Variation and genetic control of protein abundance in humans. Nature 2013;499(7456):79-82
   PubMed Web of Science ®Google Scholar
• Maes E, Landuyt B, Mertens I, Schoofs L. Interindividual variation in the proteome of human peripheral blood mononuclear cells. PLoS One 2013;8(4):e61933
   PubMed Web of Science ®Google Scholar
• Molloy MP, Brzezinski EE, Hang J, et al. Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 2003;3(10):1912-19
   PubMed Web of Science ®Google Scholar
• Karp NA, Lilley KS. Investigating sample pooling strategies for DIGE experiments to address biological variability. Proteomics 2009;9(2):388-97
   PubMed Web of Science ®Google Scholar
• Diz AP. Truebano M,Skibinski DO. The consequences of sample pooling in proteomics: an empirical study. Electrophoresis 2009;30(17):2967-75
   PubMed Web of Science ®Google Scholar
• Tuck MK, Chan DW, Chia D, et al. Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group. J Proteome Res 2009;8(1):113-17
   PubMed Web of Science ®Google Scholar
• Delobel J, Rubin O, Prudent M, et al. Biomarker analysis of stored blood products: emphasis on pre-analytical issues. Int J Mol Sci 2010;11(11):4601-17
   PubMed Web of Science ®Google Scholar
• Wildes D, Wells JA. Sampling the N-terminal proteome of human blood. Proc Natl Acad Sci USA 2010;107(10):4561-6
   PubMed Web of Science ®Google Scholar
• Yi J, Liu Z, Craft D, et al. Intrinsic peptidase activity causes a Sequential Multi-Step Reaction (SMSR) in digestion of human plasma peptides. J Proteome Res 2008;7(12):5112-18
   PubMed Web of Science ®Google Scholar
• Yi J, Kim C, Gelfand CA. Inhibition of intrinsic proteolytic activities moderates preanalytical variability and instability of human plasma. J Proteome Res 2007;6(5):1768-81
   PubMed Web of Science ®Google Scholar
• Yi J, Craft D, Gelfand CA. Minimizing preanalytical variation of plasma samples by proper blood collection and handling. Methods Mol Biol 2011;728:137-49
   PubMedGoogle Scholar
• Klingler D, Hardt M. Profiling protease activities by dynamic proteomics workflows. Proteomics 2012;12(4-5):587-96
   PubMed Web of Science ®Google Scholar
• Marshall J, Kupchak P, Zhu W, et al. Processing of serum proteins underlies the mass spectral fingerprinting of myocardial infarction. J Proteome Res 2003;2(4):361-72
   PubMed Web of Science ®Google Scholar
• Findeisen P, Thumfart JO, Costina V, et al. MS-based monitoring of proteolytic decay of synthetic reporter peptides for quality control of plasma and serum specimens. Am J Clin Pathol 2013;140(3):314-23
   PubMed Web of Science ®Google Scholar
• Drake SK, Bowen RA, Remaley AT, Hortin GL. Potential interferences from blood collection tubes in mass spectrometric analyses of serum polypeptides. Clin Chem 2004;50(12):2398-401
   PubMed Web of Science ®Google Scholar
• Newhall KJ, Diemer GS, Leshinsky N, et al. Evidence for endotoxin contamination in plastic Na+-heparin blood collection tube lots. Clin Chem 2010;56(9):1483-91
   PubMed Web of Science ®Google Scholar
• Pieragostino D, Petrucci F, Del BP, et al. Pre-analytical factors in clinical proteomics investigations: impact of ex vivo protein modifications for multiple sclerosis biomarker discovery. J Proteomics 2010;73(3):579-92
   PubMed Web of Science ®Google Scholar
• Tammen H, Hess R. Collection and handling of blood specimens for peptidomics. Methods Mol Biol 2011;728:151-9
   PubMedGoogle Scholar
• Bossuyt PM, Reitsma JB, Bruns DE, et al. The STARD statement for reporting studies of diagnostic accuracy: explanation and elaboration. Ann Intern Med 2003;138(1):W1-12
   PubMedGoogle Scholar
• Bossuyt PM, Reitsma JB, Bruns DE, et al. The STARD statement for reporting studies of diagnostic accuracy: explanation and elaboration. Clin Chem 2003;49(1):7-18
   PubMed Web of Science ®Google Scholar
• Whiting P, Rutjes AW, Reitsma JB, et al. The development of QUADAS: a tool for the quality assessment of studies of diagnostic accuracy included in systematic reviews. BMC Med Res Methodol 2003;3:25
   PubMedGoogle Scholar
• Lucas NP, Macaskill P, Irwig L, Bogduk N. The development of a quality appraisal tool for studies of diagnostic reliability (QAREL). J Clin Epidemiol 2010;63(8):854-61
   PubMed Web of Science ®Google Scholar
• Moher D, Hopewell S, Schulz KF, et al. CONSORT 2010 Explanation and Elaboration: updated guidelines for reporting parallel group randomised trials. J Clin Epidemiol 2010;63(8):e1-37
   PubMed Web of Science ®Google Scholar
• Schulz KF, Altman DG, Moher D. CONSORT 2010 statement: updated guidelines for reporting parallel group randomised trials. PLoS Med 2010;7(3):e1000251
   PubMed Web of Science ®Google Scholar
• Greystoke A, Mullamitha SA. How many diseases are colorectal cancer? Gastroenterol Res Pract 2012;2012:564741
   PubMed Web of Science ®Google Scholar
• Agard NJ, Mahrus S, Trinidad JC, et al. Global kinetic analysis of proteolysis via quantitative targeted proteomics. Proc Natl Acad Sci USA 2012;109(6):1913-18
   PubMed Web of Science ®Google Scholar
• Leroy G, Dimaggio PA, Chan EY, et al. A quantitative atlas of histone modification signatures from human cancer cells. Epigenetics Chromatin 2013;6(1):20
   PubMed Web of Science ®Google Scholar
• Shi T, Su D, Liu T, et al. Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics. Proteomics 2012;12(8):1074-92
   PubMed Web of Science ®Google Scholar
• Ayache S, Panelli M, Marincola FM, Stroncek DF. Effects of storage time and exogenous protease inhibitors on plasma protein levels. Am J Clin Pathol 2006;126(2):174-84
   PubMed Web of Science ®Google Scholar
• Haab BB, Geierstanger BH, Michailidis G, et al. Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: systematic variation between sample types and calibration of mass spectrometry data. Proteomics 2005;5(13):3278-91
   PubMed Web of Science ®Google Scholar
• White JG, Escolar G. EDTA-induced changes in platelet structure and function: adhesion and spreading. Platelets 2000;11(1):56-61
   PubMed Web of Science ®Google Scholar
• Capila I, Linhardt RJ. Heparin-Protein Interactions. Angew Chem Int Ed Engl 2002;41:390-412
   Web of Science ®Google Scholar