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Volumn 1, Issue 2, 2013, Pages 109-127

Proteomic workflows for biomarker identification using mass spectrometry - Technical and statistical considerations during initial discovery

Author keywords

Biomarker discovery; Experimental design; High dimensional data; Randomization; Replication

Indexed keywords


EID: 84969394014     PISSN: None     EISSN: 22277382     Source Type: Journal    
DOI: 10.3390/proteomes1020109     Document Type: Review
Times cited : (17)

References (98)
  • 1
    • 78449244161 scopus 로고    scopus 로고
    • Multicenter validation of the diagnostic accuracy of a blood-based gene expression test for assessing obstructive coronary artery disease in nondiabetic patients
    • Rosenberg, S.; Elashoff, M.R.; Beineke, P.; Daniels, S.E.; Wingrove, J.A.; Tingley, W.G.; Sager, P.T.; Sehnert, A.J.; Yau, M.; Kraus, W.E.; et al. Multicenter validation of the diagnostic accuracy of a blood-based gene expression test for assessing obstructive coronary artery disease in nondiabetic patients. Ann. Int. Med. 2010, 153, 425-434
    • (2010) Ann. Int. Med , vol.153 , pp. 425-434
    • Rosenberg, S.1    Elashoff, M.R.2    Beineke, P.3    Daniels, S.E.4    Wingrove, J.A.5    Tingley, W.G.6    Sager, P.T.7    Sehnert, A.J.8    Yau, M.9    Kraus, W.E.10
  • 3
    • 1542469713 scopus 로고    scopus 로고
    • Measurement of gene expression in archival paraffin-embedded tissues: Development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay
    • Cronin, M.; Pho, M.; Dutta, D.; Stephans, J.C.; Shak, S.; Kiefer, M.C.; Esteban, J.M.; Baker, J.B. Measurement of gene expression in archival paraffin-embedded tissues: Development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am. J. Pathol. 2004, 164, 35-42
    • (2004) Am. J. Pathol , vol.164 , pp. 35-42
    • Cronin, M.1    Pho, M.2    Dutta, D.3    Stephans, J.C.4    Shak, S.5    Kiefer, M.C.6    Esteban, J.M.7    Baker, J.B.8
  • 7
    • 84890021402 scopus 로고    scopus 로고
    • Mass spectrometry-based quantification
    • DeSouza, L.V.; Siu, K.W.M. Mass spectrometry-based quantification. Clin. Biochem. 2013, 46, 421-431
    • (2013) Clin. Biochem , vol.46 , pp. 421-431
    • DeSouza, L.V.1    Siu, K.W.M.2
  • 9
    • 0024438708 scopus 로고
    • Electrospray ionization of large for mass spectrometry biomolecules
    • Fenn, J.B.; Mann, M.; Meng, C.K.; Wong, S.F.; Whitehouse, C.M. Electrospray ionization of large for mass spectrometry biomolecules. Science 1989, 246, 64-71
    • (1989) Science , vol.246 , pp. 64-71
    • Fenn, J.B.1    Mann, M.2    Meng, C.K.3    Wong, S.F.4    Whitehouse, C.M.5
  • 10
    • 0032190378 scopus 로고    scopus 로고
    • Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry
    • Gatlin, C.L.; Kleemann, G.R.; Hays, L.G.; Link, A.J.; Yates, J.R., III. Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry. Anal. Biochem. 1998, 263, 93-101
    • (1998) Anal. Biochem , vol.263 , pp. 93-101
    • Gatlin, C.L.1    Kleemann, G.R.2    Hays, L.G.3    Link, A.J.4    Yates, J.R.5
  • 11
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
    • Gygi, S.P.; Rist, B.; Gerber, S.A.; Turecek, F.; Gelb, M.H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 10, 994-999
    • (1999) Nat. Biotechnol , vol.10 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3    Turecek, F.4    Gelb, M.H.5    Aebersold, R.6
  • 12
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn, M.P.; Wolters, D.; Yates, J.R., III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 3, 242-247
    • (2001) Nat. Biotechnol , vol.3 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates, J.R.3
  • 13
    • 0036079692 scopus 로고    scopus 로고
    • The SELDI-TOF MS approach to proteomics: Protein profiling and biomarker identification
    • Issaq, H.J.; Veenstra, T.D.; Conrads, T.P.; Felschow, D. The SELDI-TOF MS approach to proteomics: Protein profiling and biomarker identification. Biochem. Biophys. Res. Commun. 2002, 292, 587-592
    • (2002) Biochem. Biophys. Res. Commun , vol.292 , pp. 587-592
    • Issaq, H.J.1    Veenstra, T.D.2    Conrads, T.P.3    Felschow, D.4
  • 14
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong, S.E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D.B.; Steen, H.; Pandey, A.; Mann, M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376-386
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 15
    • 33847174067 scopus 로고    scopus 로고
    • Protein labeling by iTRAQ: A new tool for quantitative mass spectrometry in proteome research
    • Wiese, S.; Reidegeld, K.A.; Meyer, H.E.; Warscheid, B. Protein labeling by iTRAQ: A new tool for quantitative mass spectrometry in proteome research. Proteomics 2007, 7, 340-350
    • (2007) Proteomics , vol.7 , pp. 340-350
    • Wiese, S.1    Reidegeld, K.A.2    Meyer, H.E.3    Warscheid, B.4
  • 17
    • 78650938957 scopus 로고    scopus 로고
    • Identification of candidate IgG biomarkers for Alzheimer's disease via combinatorial library screening
    • Reddy, M.M.; Wilson, R.; Wilson, J.; Connell, S.; Gocke, A.; Hynan, L.; German, D.; Kodadek, T. Identification of candidate IgG biomarkers for Alzheimer's disease via combinatorial library screening. Cell 2011, 144, 132-142
    • (2011) Cell , vol.144 , pp. 132-142
    • Reddy, M.M.1    Wilson, R.2    Wilson, J.3    Connell, S.4    Gocke, A.5    Hynan, L.6    German, D.7    Kodadek, T.8
  • 18
    • 79961054821 scopus 로고    scopus 로고
    • Improving biomarker identification with better designs and reporting
    • Pepe, M.S.; Feng, Z. Improving biomarker identification with better designs and reporting. Clin. Chem. 2011, 57, 1093-1095
    • (2011) Clin. Chem , vol.57 , pp. 1093-1095
    • Pepe, M.S.1    Feng, Z.2
  • 19
    • 16344384887 scopus 로고    scopus 로고
    • The importance of experimental design in proteomic mass spectrometry experiments: Some cautionary tales
    • Hu, J.; Coombes, K.R.; Morris, J.S.; Baggerly, K.A. The importance of experimental design in proteomic mass spectrometry experiments: Some cautionary tales. Brief. Funct. Genomic. Proteomics 2005, 3, 322-331
    • (2005) Brief. Funct. Genomic. Proteomics , vol.3 , pp. 322-331
    • Hu, J.1    Coombes, K.R.2    Morris, J.S.3    Baggerly, K.A.4
  • 20
    • 24144432109 scopus 로고    scopus 로고
    • Influences of blood sample processing on low-molecular-weight proteome identified by surface-enhanced laser desorption/ionization mass spectrometry
    • Banks, R.E.; Stanley, A.J.; Cairns, D.A.; Barrett, J.H.; Clarke, P.; Thompson, D.; Selby, P.J. Influences of blood sample processing on low-molecular-weight proteome identified by surface-enhanced laser desorption/ionization mass spectrometry. Clin. Chem. 2005, 51, 1637-1649
    • (2005) Clin. Chem , vol.51 , pp. 1637-1649
    • Banks, R.E.1    Stanley, A.J.2    Cairns, D.A.3    Barrett, J.H.4    Clarke, P.5    Thompson, D.6    Selby, P.J.7
  • 21
    • 84864395727 scopus 로고    scopus 로고
    • Generalized linear and mixed models for label-free shotgun proteomics
    • Leitch, M.C.; Mitra, I.; Sadygov, R.G. Generalized linear and mixed models for label-free shotgun proteomics. Stat. Interface 2012, 5, 89-98
    • (2012) Stat. Interface , vol.5 , pp. 89-98
    • Leitch, M.C.1    Mitra, I.2    Sadygov, R.G.3
  • 23
    • 37549029793 scopus 로고    scopus 로고
    • The properties of high-dimensional data spaces: Implications for exploring gene and protein expression data
    • Clarke, R.; Ressom, H.W.; Wang, A.; Xuan, J.; Liu, M.C.; Gehan, E.A.; Wang, Y. The properties of high-dimensional data spaces: Implications for exploring gene and protein expression data. Nat. Rev. Cancer 2008, 8, 37-49
    • (2008) Nat. Rev. Cancer , vol.8 , pp. 37-49
    • Clarke, R.1    Ressom, H.W.2    Wang, A.3    Xuan, J.4    Liu, M.C.5    Gehan, E.A.6    Wang, Y.7
  • 25
    • 0036645099 scopus 로고    scopus 로고
    • Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men
    • Adam, B.L.; Qu, Y.; Davis, J.W.; Ward, M.D.; Clements, M.A.; Cazares, L.H.; Semmes, O.J.; Schellhammer, P.F.; Yasui, Y.; Feng, Z.; 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, 3609-3614
    • (2002) Cancer Res , vol.62 , pp. 3609-3614
    • Adam, B.L.1    Qu, Y.2    Davis, J.W.3    Ward, M.D.4    Clements, M.A.5    Cazares, L.H.6    Semmes, O.J.7    Schellhammer, P.F.8    Yasui, Y.9    Feng, Z.10
  • 28
    • 33747030845 scopus 로고    scopus 로고
    • Protein biomarker discovery and validation: The long and uncertain path to clinical utility
    • Rifai, N.; Gillette, M.A.; Carr, S.A. Protein biomarker discovery and validation: The long and uncertain path to clinical utility. Nat. Biotechnol. 2006, 24, 971-983
    • (2006) Nat. Biotechnol , vol.24 , pp. 971-983
    • Rifai, N.1    Gillette, M.A.2    Carr, S.A.3
  • 29
    • 1942438016 scopus 로고    scopus 로고
    • Rules of evidence for cancer molecular-marker discovery and validation
    • Ransohoff, D.F. Rules of evidence for cancer molecular-marker discovery and validation. Nat. Rev. Cancer 2004, 4, 309-314
    • (2004) Nat. Rev. Cancer , vol.4 , pp. 309-314
    • Ransohoff, D.F.1
  • 33
    • 0036176335 scopus 로고    scopus 로고
    • Use of interphase fluorescence in situ hybridization as a powerful diagnostic tool in cytology
    • Jiang, F.; Katz, R.L. Use of interphase fluorescence in situ hybridization as a powerful diagnostic tool in cytology. Diagn. Mol. Pathol. 2002, 11, 47-57
    • (2002) Diagn. Mol. Pathol , vol.11 , pp. 47-57
    • Jiang, F.1    Katz, R.L.2
  • 34
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena, M.; Shalon, D.; Davis, R.W.; Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270, 467-470
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 36
    • 0001644020 scopus 로고    scopus 로고
    • The human plasma proteome: History, character, and diagnostic prospects
    • Anderson, N.L. The human plasma proteome: History, character, and diagnostic prospects. Mol. Cell. Proteomics 2002, 1, 845-867
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 845-867
    • Anderson, N.L.1
  • 38
    • 39549102648 scopus 로고    scopus 로고
    • Metabolomics in biomarker discovery: Future uses for cancer prevention
    • Kim, Y.S.; Maruvada, P.; Milner, J.A. Metabolomics in biomarker discovery: Future uses for cancer prevention. Future Oncol. 2008, 4, 93-102
    • (2008) Future Oncol , vol.4 , pp. 93-102
    • Kim, Y.S.1    Maruvada, P.2    Milner, J.A.3
  • 40
    • 80053923393 scopus 로고    scopus 로고
    • Proteomic analysis of an immortalized mouse pancreatic stellate cell line identifies differentially-expressed proteins in activated vs. nonproliferating cell states
    • Paulo, J.A.; Urrutia, R.; Banks, P.A.; Conwell, D.L.; Steen, H. Proteomic analysis of an immortalized mouse pancreatic stellate cell line identifies differentially-expressed proteins in activated vs. nonproliferating cell states. J. Proteome Res. 2011, 10, 4835-4844
    • (2011) J. Proteome Res , vol.10 , pp. 4835-4844
    • Paulo, J.A.1    Urrutia, R.2    Banks, P.A.3    Conwell, D.L.4    Steen, H.5
  • 43
    • 84879012106 scopus 로고    scopus 로고
    • Gene expression analysis of normal and colorectal cancer tissue samples from fresh frozen and matched formalin-fixed, paraffin-embedded (FFPE) specimens after manual and automated RNA isolation
    • Kalmar, A.; Wichmann, B.; Galamb, O.; Spisák, S.; Tóth, K.; Leiszter, K.; Tulassay, Z.; Molnár, B. Gene expression analysis of normal and colorectal cancer tissue samples from fresh frozen and matched formalin-fixed, paraffin-embedded (FFPE) specimens after manual and automated RNA isolation. Methods 2012, 59, S16-S19
    • (2012) Methods , vol.59 , pp. S16-S19
    • Kalmar, A.1    Wichmann, B.2    Galamb, O.3    Spisák, S.4    Tóth, K.5    Leiszter, K.6    Tulassay, Z.7    Molnár, B.8
  • 44
    • 84891713704 scopus 로고    scopus 로고
    • The proteomics of formalin-fixed wax-embedded tissue
    • Vincenti, D.C.; Murray, G.I. The proteomics of formalin-fixed wax-embedded tissue. Clin. Biochem. 2012, 46, 546-551
    • (2012) Clin. Biochem , vol.46 , pp. 546-551
    • Vincenti, D.C.1    Murray, G.I.2
  • 45
    • 78649858218 scopus 로고    scopus 로고
    • Advances in proximal fluid proteomics for disease biomarker discovery
    • Teng, P.; Bateman, N.W.; Hood, B.L.; Conrads, T.P. Advances in proximal fluid proteomics for disease biomarker discovery. J. Proteome Res. 2010, 9, 6091-6100
    • (2010) J. Proteome Res , vol.9 , pp. 6091-6100
    • Teng, P.1    Bateman, N.W.2    Hood, B.L.3    Conrads, T.P.4
  • 46
    • 33645079130 scopus 로고    scopus 로고
    • SELDI-TOF MS of quadruplicate urine and serum samples to evaluate changes related to storage conditions
    • Traum, A.Z.; Wells, M.P.; Aivado, M.; Libermann, T.A.; Ramoni, M.F.; Schachter, A.D. SELDI-TOF MS of quadruplicate urine and serum samples to evaluate changes related to storage conditions. Proteomics 2006, 6, 1676-1680
    • (2006) Proteomics , vol.6 , pp. 1676-1680
    • Traum, A.Z.1    Wells, M.P.2    Aivado, M.3    Libermann, T.A.4    Ramoni, M.F.5    Schachter, A.D.6
  • 47
    • 9244227101 scopus 로고    scopus 로고
    • Potential interferences from blood collection tubes in mass spectrometric analyses of serum polypeptides
    • Drake, S.K.; Bowen, R.A.R.; Remaley, A.T.; Hortin, G.L. Potential interferences from blood collection tubes in mass spectrometric analyses of serum polypeptides. Clin. Chem. 2004, 50, 2398-2401
    • (2004) Clin. Chem , vol.50 , pp. 2398-2401
    • Drake, S.K.1    Bowen, R.A.R.2    Remaley, A.T.3    Hortin, G.L.4
  • 48
    • 33744473319 scopus 로고    scopus 로고
    • Systematical evaluation of the effects of sample collection procedures on low-molecular-weight serum/plasma proteome profiling
    • Hsieh, S.Y.; Chen, R.K.; Pan, Y.H.; Lee, H.L. Systematical evaluation of the effects of sample collection procedures on low-molecular-weight serum/plasma proteome profiling. Proteomics 2006, 6, 3189-3198
    • (2006) Proteomics , vol.6 , pp. 3189-3198
    • Hsieh, S.Y.1    Chen, R.K.2    Pan, Y.H.3    Lee, H.L.4
  • 51
    • 80053238855 scopus 로고    scopus 로고
    • Dynamic range compression: A solution for proteomic biomarker discovery?
    • Griffin, T.J.; Bandhakavi, S. Dynamic range compression: A solution for proteomic biomarker discovery? Bioanalysis 2011, 3, 2053-2056
    • (2011) Bioanalysis , vol.3 , pp. 2053-2056
    • Griffin, T.J.1    Bandhakavi, S.2
  • 54
    • 0016711037 scopus 로고
    • High resolution two-dimensional electrophoresis of proteins
    • O'Farrell, P.H. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 1975, 250, 4007-4021
    • (1975) J. Biol. Chem , vol.250 , pp. 4007-4021
    • O'Farrell, P.H.1
  • 55
    • 34548178909 scopus 로고    scopus 로고
    • In-gel digestion for mass spectrometric characterization of proteins and proteomes
    • Shevchenko, A.; Tomas, H.; Havlis, J.; Olsen, J.V.; Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 2006, 1, 2856-2860
    • (2006) Nat. Protoc , vol.1 , pp. 2856-2860
    • Shevchenko, A.1    Tomas, H.2    Havlis, J.3    Olsen, J.V.4    Mann, M.5
  • 56
    • 26844575524 scopus 로고    scopus 로고
    • Reversed-phase high-performance liquid chromatographic prefractionation of immunodepleted human serum proteins to enhance mass spectrometry identification of lower-abundant proteins
    • Martosella, J.; Zolotarjova, N.; Liu, H.; Nicol, G.; Boyes, B.E. Reversed-phase high-performance liquid chromatographic prefractionation of immunodepleted human serum proteins to enhance mass spectrometry identification of lower-abundant proteins. J. Proteome Res. 2005, 4, 1522-1537
    • (2005) J. Proteome Res , vol.4 , pp. 1522-1537
    • Martosella, J.1    Zolotarjova, N.2    Liu, H.3    Nicol, G.4    Boyes, B.E.5
  • 57
    • 11144356366 scopus 로고    scopus 로고
    • Characterization of the human urinary proteome: A method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots
    • Pieper, R.; Gatlin, C.L.; McGrath, A.M.; Makusky, A.J.; Mondal, M.; Seonarain, M.; Field, E.; Schatz, C.R.; Estock, M.A.; Ahmed, N.; et al. Characterization of the human urinary proteome: A method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots. Proteomics 2004, 4, 1159-1174
    • (2004) Proteomics , vol.4 , pp. 1159-1174
    • Pieper, R.1    Gatlin, C.L.2    McGrath, A.M.3    Makusky, A.J.4    Mondal, M.5    Seonarain, M.6    Field, E.7    Schatz, C.R.8    Estock, M.A.9    Ahmed, N.10
  • 58
    • 79956260679 scopus 로고    scopus 로고
    • A systematic analysis of the effects of increasing degrees of serum immunodepletion in terms of depth of coverage and other key aspects in top-down and bottom-up proteomic analyses
    • Smith, M.P.W.; Wood, S.L.; Zougman, A.; Ho, J.T.C.; Peng, J.; Jackson, D.; Cairns, D.A.; Lewington, A.J.P.; Selby, P.J.; Banks, R.E. A systematic analysis of the effects of increasing degrees of serum immunodepletion in terms of depth of coverage and other key aspects in top-down and bottom-up proteomic analyses. Proteomics 2011, 11, 2222-2235
    • (2011) Proteomics , vol.11 , pp. 2222-2235
    • Smith, M.P.W.1    Wood, S.L.2    Zougman, A.3    Ho, J.T.C.4    Peng, J.5    Jackson, D.6    Cairns, D.A.7    Lewington, A.J.P.8    Selby, P.J.9    Banks, R.E.10
  • 59
    • 31644438577 scopus 로고    scopus 로고
    • Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT)
    • Chen, E.I.; Hewel, J.; Felding-Habermann, B.; Yates, J.R. Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT). Mol. Cell. Proteomics 2006, 5, 53-56
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 53-56
    • Chen, E.I.1    Hewel, J.2    Felding-Habermann, B.3    Yates, J.R.4
  • 60
    • 79952310105 scopus 로고    scopus 로고
    • Statistical issues in quality control of proteomic analyses: Good experimental design and planning
    • Cairns, D.A. Statistical issues in quality control of proteomic analyses: Good experimental design and planning. Proteomics 2011, 11, 1037-1048
    • (2011) Proteomics , vol.11 , pp. 1037-1048
    • Cairns, D.A.1
  • 62
    • 0036023414 scopus 로고    scopus 로고
    • Normal, benign, preneoplastic, and malignant prostate cells have distinct protein expression profiles resolved by surface enhanced laser desorption/ionization mass spectrometry
    • Cazares, L.H.; Adam, B.L.; Ward, M.D.; Nasim, S.; Schellhammer, P.F.; Semmes, O.J.; Wright, G.L. Normal, benign, preneoplastic, and malignant prostate cells have distinct protein expression profiles resolved by surface enhanced laser desorption/ionization mass spectrometry. Clin. Cancer Res. 2002, 8, 2541-2552
    • (2002) Clin. Cancer Res , vol.8 , pp. 2541-2552
    • Cazares, L.H.1    Adam, B.L.2    Ward, M.D.3    Nasim, S.4    Schellhammer, P.F.5    Semmes, O.J.6    Wright, G.L.7
  • 65
    • 66749171697 scopus 로고    scopus 로고
    • Statistical design of quantitative mass spectrometry-based proteomic experiments
    • Oberg, A.L.; Vitek, O. Statistical design of quantitative mass spectrometry-based proteomic experiments. J. Proteome Res. 2009, 8, 2144-2156
    • (2009) J. Proteome Res , vol.8 , pp. 2144-2156
    • Oberg, A.L.1    Vitek, O.2
  • 66
    • 0347181849 scopus 로고    scopus 로고
    • A data review and re-assessment of ovarian cancer serum proteomic profiling
    • Sorace, J.M.; Zhan, M. A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinform. 2003, 4, e24
    • (2003) BMC Bioinform , vol.4
    • Sorace, J.M.1    Zhan, M.2
  • 67
    • 19544383638 scopus 로고    scopus 로고
    • Sample size determination in microarray experiments for class comparison and prognostic classification
    • Dobbin, K.; Simon, R. Sample size determination in microarray experiments for class comparison and prognostic classification. Biostatistics 2005, 6, 27-38
    • (2005) Biostatistics , vol.6 , pp. 27-38
    • Dobbin, K.1    Simon, R.2
  • 68
    • 33645825183 scopus 로고    scopus 로고
    • Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer
    • Ein-Dor, L.; Zuk, O.; Domany, E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc. Natl. Acad. Sci. USA 2006, 103, 5923-5928
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 5923-5928
    • Ein-Dor, L.1    Zuk, O.2    Domany, E.3
  • 69
    • 0142151385 scopus 로고    scopus 로고
    • Overcoming technical variation and biological variation in quantitative proteomics
    • Molloy, M.P.; Brzezinski, E.E.; Hang, J.; McDowell, M.T.; VanBogelen, R.A. Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 2003, 3, 1912-1919
    • (2003) Proteomics , vol.3 , pp. 1912-1919
    • Molloy, M.P.1    Brzezinski, E.E.2    Hang, J.3    McDowell, M.T.4    VanBogelen, R.A.5
  • 71
    • 70450030926 scopus 로고    scopus 로고
    • The consequences of sample pooling in proteomics: An empirical study
    • Diz, A.P.; Truebano, M.; Skibinski, D.O.F. The consequences of sample pooling in proteomics: An empirical study. Electrophoresis 2009, 30, 2967-2975
    • (2009) Electrophoresis , vol.30 , pp. 2967-2975
    • Diz, A.P.1    Truebano, M.2    Skibinski, D.O.F.3
  • 75
    • 0036791428 scopus 로고    scopus 로고
    • Boosted decision tree analysis of surface-enhanced laser desorption/ ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients
    • Qu, Y.; Adam, B.L.; Yasui, Y.; Ward, M.D.; Cazares, L.H.; Schellhammer, P.F.; Feng, Z.; Semmes, O.J.; Wright, G.L. Boosted decision tree analysis of surface-enhanced laser desorption/ ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients. Clin. Chem. 2002, 48, 1835-1843
    • (2002) Clin. Chem , vol.48 , pp. 1835-1843
    • Qu, Y.1    Adam, B.L.2    Yasui, Y.3    Ward, M.D.4    Cazares, L.H.5    Schellhammer, P.F.6    Feng, Z.7    Semmes, O.J.8    Wright, G.L.9
  • 77
    • 65549116090 scopus 로고    scopus 로고
    • A qualitative proteome investigation of the sediment portion of human urine: Implications in the biomarker discovery process
    • Mataija-Botelho, D.; Murphy, P.; Pinto, D.M.; Maclellan, D.L.; Langlois, C.; Doucette, A. A qualitative proteome investigation of the sediment portion of human urine: Implications in the biomarker discovery process. Proteomics Clin. Appl. 2009, 3, 95-105
    • (2009) Proteomics Clin. Appl , vol.3 , pp. 95-105
    • Mataija-Botelho, D.1    Murphy, P.2    Pinto, D.M.3    Maclellan, D.L.4    Langlois, C.5    Doucette, A.6
  • 78
    • 0037076322 scopus 로고    scopus 로고
    • Selection bias in gene extraction on the basis of microarray gene-expression data
    • Ambroise, C.; McLachlan, G.J. Selection bias in gene extraction on the basis of microarray gene-expression data. Proc. Natl. Acad. Sci. USA 2002, 99, 6562-6566
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 6562-6566
    • Ambroise, C.1    McLachlan, G.J.2
  • 79
    • 0141855279 scopus 로고    scopus 로고
    • A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples
    • Baggerly, K.A.; Morris, J.S.; Wang, J.; Gold, D.; Xiao, L.C.; Coombes, K.R. A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples. Proteomics 2003, 3, 1667-1672
    • (2003) Proteomics , vol.3 , pp. 1667-1672
    • Baggerly, K.A.1    Morris, J.S.2    Wang, J.3    Gold, D.4    Xiao, L.C.5    Coombes, K.R.6
  • 80
    • 80052262099 scopus 로고    scopus 로고
    • Implications of partial tryptic digestion in organic-aqueous solvent systems for bottom-up proteome analysis
    • Wall, M.J.; Crowell, A.M.J.; Simms, G.A.; Liu, F.; Doucette, A.A. Implications of partial tryptic digestion in organic-aqueous solvent systems for bottom-up proteome analysis. Anal. Chim. Acta 2011, 703, 194-203
    • (2011) Anal. Chim. Acta , vol.703 , pp. 194-203
    • Wall, M.J.1    Crowell, A.M.J.2    Simms, G.A.3    Liu, F.4    Doucette, A.A.5
  • 81
    • 0032986763 scopus 로고    scopus 로고
    • Removal of sodium dodecyl sulfate from protein samples prior to matrix-assisted laser desorption/ionization mass spectrometry
    • Puchades, M.; Westman, A.; Blennow, K.; Davidsson, P. Removal of sodium dodecyl sulfate from protein samples prior to matrix-assisted laser desorption/ionization mass spectrometry. Rapid. Commun. Mass. Spectrom. 1999, 13, 344-349
    • (1999) Rapid. Commun. Mass. Spectrom , vol.13 , pp. 344-349
    • Puchades, M.1    Westman, A.2    Blennow, K.3    Davidsson, P.4
  • 82
    • 61449184562 scopus 로고    scopus 로고
    • Off-line two-dimensional liquid chromatography with maximized sample loading to reversed-phase liquid chromatography-electrospray ionization tandem mass spectrometry for shotgun proteome analysis
    • Wang, N.; Xie, C.; Young, J.B.; Li, L. Off-line two-dimensional liquid chromatography with maximized sample loading to reversed-phase liquid chromatography-electrospray ionization tandem mass spectrometry for shotgun proteome analysis. Anal. Chem. 2009, 81, 1049-1060
    • (2009) Anal. Chem , vol.81 , pp. 1049-1060
    • Wang, N.1    Xie, C.2    Young, J.B.3    Li, L.4
  • 83
    • 77954578929 scopus 로고    scopus 로고
    • Top-down and bottom-up proteomics of SDS-containing solutions following mass-based separation
    • Botelho, D.; Wall, M.J.; Vieira, D.B.; Fitzsimmons, S.; Liu, F.; Doucette, A. Top-down and bottom-up proteomics of SDS-containing solutions following mass-based separation. J. Proteome Res. 2010, 9, 2863-2870
    • (2010) J. Proteome Res , vol.9 , pp. 2863-2870
    • Botelho, D.1    Wall, M.J.2    Vieira, D.B.3    Fitzsimmons, S.4    Liu, F.5    Doucette, A.6
  • 84
    • 78751575766 scopus 로고    scopus 로고
    • High-abundance proteins depletion for serum proteomic analysis: Concomitant removal of non-targeted proteins
    • Bellei, E.; Bergamini, S.; Monari, E.; Fantoni, L.I.; Cuoghi, A.; Ozben, T.; Tomasi, A. High-abundance proteins depletion for serum proteomic analysis: Concomitant removal of non-targeted proteins. Amino Acids 2011, 40, 145-156
    • (2011) Amino Acids , vol.40 , pp. 145-156
    • Bellei, E.1    Bergamini, S.2    Monari, E.3    Fantoni, L.I.4    Cuoghi, A.5    Ozben, T.6    Tomasi, A.7
  • 87
    • 85054232705 scopus 로고    scopus 로고
    • A Probabilistic Spell for the Curse of Dimensionality
    • Chavez, E.; Navarro, G. A Probabilistic Spell for the Curse of Dimensionality. Algorithm Eng. Exp. 2001, 2453, 147-160
    • (2001) Algorithm Eng. Exp , vol.2453 , pp. 147-160
    • Chavez, E.1    Navarro, G.2
  • 90
    • 58149299336 scopus 로고    scopus 로고
    • Significance analysis of spectral count data in label-free shotgun proteomics
    • Choi, H.; Fermin, D.; Nesvizhskii, A.I. Significance analysis of spectral count data in label-free shotgun proteomics. Mol. Cell. Proteomics 2008, 7, 2373-2385
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 2373-2385
    • Choi, H.1    Fermin, D.2    Nesvizhskii, A.I.3
  • 91
    • 0032638628 scopus 로고    scopus 로고
    • Least squares support vector machine classifiers
    • Suykens, J.A.K.; Vandewalle, J. Least squares support vector machine classifiers. Neural Process. Lett. 1999, 9, 293-300
    • (1999) Neural Process. Lett , vol.9 , pp. 293-300
    • Suykens, J.A.K.1    Vandewalle, J.2
  • 92
    • 0032301582 scopus 로고    scopus 로고
    • Data mapping by probabilistic modular networks and information-theoretic criteria
    • Wang, Y.; Lin, S.; Li, H.; Kung, S. Data mapping by probabilistic modular networks and information-theoretic criteria. IEEE Trans. Signal Process. 1998, 46, 3378-3397
    • (1998) IEEE Trans. Signal Process , vol.46 , pp. 3378-3397
    • Wang, Y.1    Lin, S.2    Li, H.3    Kung, S.4
  • 93
    • 21244444543 scopus 로고    scopus 로고
    • Gene selection for microarray data analysis using principal component analysis
    • Wang, A.; Gehan, E. Gene selection for microarray data analysis using principal component analysis. Stat. Med. 2005, 24, 2069-2087
    • (2005) Stat. Med , vol.24 , pp. 2069-2087
    • Wang, A.1    Gehan, E.2
  • 94
    • 0002457803 scopus 로고
    • Selection of variables to preserve multivariate data structure using principal components
    • Krzanowski, W.J. Selection of variables to preserve multivariate data structure using principal components. J. Roy. Statist. Soc. Ser. C 1987, 36, 22-33
    • (1987) J. Roy. Statist. Soc. Ser. C , vol.36 , pp. 22-33
    • Krzanowski, W.J.1
  • 95
    • 0037441446 scopus 로고    scopus 로고
    • A statistical perspective on gene expression data analysis
    • Satagopan, J.M.; Panageas, K.S. A statistical perspective on gene expression data analysis. Stat. Med. 2003, 22, 481-499
    • (2003) Stat. Med , vol.22 , pp. 481-499
    • Satagopan, J.M.1    Panageas, K.S.2
  • 96
    • 29244448340 scopus 로고    scopus 로고
    • Microarray data analysis: From disarray to consolidation and consensus
    • Allison, D.B.; Cui, X.; Page, G.P.; Sabripour, M. Microarray data analysis: From disarray to consolidation and consensus. Nat. Rev. Genet. 2006, 7, 55-65
    • (2006) Nat. Rev. Genet , vol.7 , pp. 55-65
    • Allison, D.B.1    Cui, X.2    Page, G.P.3    Sabripour, M.4
  • 98
    • 33847172327 scopus 로고    scopus 로고
    • Clustering by passing messages between data points
    • Frey, B.J.; Dueck, D. Clustering by passing messages between data points. Science 2007, 315, 972-976
    • (2007) Science , vol.315 , pp. 972-976
    • Frey, B.J.1    Dueck, D.2


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