메뉴 건너뛰기




Volumn 11, Issue 4, 2012, Pages 2103-2113

Statistical considerations of optimal study design for human plasma proteomics and biomarker discovery

Author keywords

biomarkers; mass spectrometry; plasma proteomics; power analysis

Indexed keywords

BIOLOGICAL MARKER; PEROXIREDOXIN 2; PLASMA PROTEIN;

EID: 84859594013     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr200636x     Document Type: Article
Times cited : (54)

References (38)
  • 1
    • 35848929028 scopus 로고    scopus 로고
    • Proteomics from the clinical perspective: Many hopes and much debate
    • Beretta, L. Proteomics from the clinical perspective: many hopes and much debate Nat. Methods 2007, 4, 785-6
    • (2007) Nat. Methods , vol.4 , pp. 785-786
    • Beretta, L.1
  • 2
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross, P. L.; Huang, Y. N.; Marchese, J. N. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents Mol. Cell. Proteomics 2004, 3, 1154-69
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 1154-1169
    • Ross, P.L.1    Huang, Y.N.2    Marchese, J.N.3
  • 3
    • 43849113605 scopus 로고    scopus 로고
    • Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases
    • Pierce, A.; Unwin, R. D.; Evans, C. A. Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases Mol. Cell. Proteomics 2008, 7, 853-63
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 853-863
    • Pierce, A.1    Unwin, R.D.2    Evans, C.A.3
  • 4
    • 33644845960 scopus 로고    scopus 로고
    • Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF
    • Wu, W. W.; Wang, G.; Baek, S. J.; Shen, R. F. Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF J. Proteome Res. 2006, 5, 651-8
    • (2006) J. Proteome Res. , vol.5 , pp. 651-658
    • Wu, W.W.1    Wang, G.2    Baek, S.J.3    Shen, R.F.4
  • 5
    • 34548409217 scopus 로고    scopus 로고
    • Experimental and statistical considerations to avoid false conclusions in proteomics studies using differential in-gel electrophoresis
    • Karp, N. A.; McCormick, P. S.; Russell, M. R.; Lilley, K. S. Experimental and statistical considerations to avoid false conclusions in proteomics studies using differential in-gel electrophoresis Mol. Cell. Proteomics 2007, 6, 1354-64
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 1354-1364
    • Karp, N.A.1    McCormick, P.S.2    Russell, M.R.3    Lilley, K.S.4
  • 6
    • 33747409456 scopus 로고    scopus 로고
    • Detection of biomarkers with a multiplex quantitative proteomic platform in cerebrospinal fluid of patients with neurodegenerative disorders
    • Abdi, F.; Quinn, J. F.; Jankovic, J. Detection of biomarkers with a multiplex quantitative proteomic platform in cerebrospinal fluid of patients with neurodegenerative disorders J. Alzheimers Dis. 2006, 9, 293-348
    • (2006) J. Alzheimers Dis. , vol.9 , pp. 293-348
    • Abdi, F.1    Quinn, J.F.2    Jankovic, J.3
  • 7
    • 34547131803 scopus 로고    scopus 로고
    • Endometrial carcinoma biomarker discovery and verification using differentially tagged clinical samples with multidimensional liquid chromatography and tandem mass spectrometry
    • DeSouza, L. V.; Grigull, J.; Ghanny, S. Endometrial carcinoma biomarker discovery and verification using differentially tagged clinical samples with multidimensional liquid chromatography and tandem mass spectrometry Mol. Cell. Proteomics 2007, 6, 1170-82
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 1170-1182
    • Desouza, L.V.1    Grigull, J.2    Ghanny, S.3
  • 8
    • 39149098117 scopus 로고    scopus 로고
    • Identification of serum biomarkers in brain-injured adults: Potential for predicting elevated intracranial pressure
    • Hergenroeder, G.; Redell, J. B.; Moore, A. N. Identification of serum biomarkers in brain-injured adults: potential for predicting elevated intracranial pressure J. Neurotrauma 2008, 25, 79-93
    • (2008) J. Neurotrauma , vol.25 , pp. 79-93
    • Hergenroeder, G.1    Redell, J.B.2    Moore, A.N.3
  • 9
    • 74049085513 scopus 로고    scopus 로고
    • Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ)
    • Kolla, V.; Jeno, P.; Moes, S. Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ) J. Biomed. Biotechnol. 2010, 952047
    • (2010) J. Biomed. Biotechnol. , pp. 952047
    • Kolla, V.1    Jeno, P.2    Moes, S.3
  • 10
    • 35648936933 scopus 로고    scopus 로고
    • Differential protein expression in male and female human lumbar cerebrospinal fluid using iTRAQ reagents after abundant protein depletion
    • Ogata, Y.; Charlesworth, M. C.; Higgins, L.; Keegan, B. M.; Vernino, S.; Muddiman, D. C. Differential protein expression in male and female human lumbar cerebrospinal fluid using iTRAQ reagents after abundant protein depletion Proteomics 2007, 7, 3726-34
    • (2007) Proteomics , vol.7 , pp. 3726-3734
    • Ogata, Y.1    Charlesworth, M.C.2    Higgins, L.3    Keegan, B.M.4    Vernino, S.5    Muddiman, D.C.6
  • 11
    • 33744926266 scopus 로고    scopus 로고
    • Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells
    • Unwin, R. D.; Smith, D. L.; Blinco, D. Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells Blood 2006, 107, 4687-94
    • (2006) Blood , vol.107 , pp. 4687-4694
    • Unwin, R.D.1    Smith, D.L.2    Blinco, D.3
  • 12
    • 41549147720 scopus 로고    scopus 로고
    • Quantitative proteomics analysis demonstrates post-transcriptional regulation of embryonic stem cell differentiation to hematopoiesis
    • Williamson, A. J.; Smith, D. L.; Blinco, D. Quantitative proteomics analysis demonstrates post-transcriptional regulation of embryonic stem cell differentiation to hematopoiesis Mol. Cell. Proteomics 2008, 7, 459-72
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 459-472
    • Williamson, A.J.1    Smith, D.L.2    Blinco, D.3
  • 13
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias, J. E.; Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat Methods 2007, 4, 207-14
    • (2007) Nat Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 15
    • 38649083118 scopus 로고    scopus 로고
    • Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
    • Käll, L.; Storey, J. D.; MacCoss, M. J.; Noble, W. S. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases J. Proteome Res. 2008, 7, 29-34
    • (2008) J. Proteome Res. , vol.7 , pp. 29-34
    • Käll, L.1    Storey, J.D.2    MacCoss, M.J.3    Noble, W.S.4
  • 16
    • 44449161040 scopus 로고    scopus 로고
    • Mixed-effects statistical model for comparative LC-MS proteomics studies
    • Daly, D. S.; Anderson, K. K.; Panisko, E. A. Mixed-effects statistical model for comparative LC-MS proteomics studies J. Proteome Res. 2008, 7, 1209-17
    • (2008) J. Proteome Res. , vol.7 , pp. 1209-1217
    • Daly, D.S.1    Anderson, K.K.2    Panisko, E.A.3
  • 17
    • 84859626237 scopus 로고    scopus 로고
    • Linear Mixed Model Selection for False Discovery Rate Control in Microarray Data Analysis
    • not supplied
    • Demirkale, C. Y.; Nettleton, D.; Maiti, T. Linear Mixed Model Selection for False Discovery Rate Control in Microarray Data Analysis. Biometrics 2009, not supplied.
    • (2009) Biometrics
    • Demirkale, C.Y.1    Nettleton, D.2    Maiti, T.3
  • 18
    • 33750611947 scopus 로고    scopus 로고
    • Urinary biomarker profiling in transitional cell carcinoma
    • Munro, N. P.; Cairns, D. A.; Clarke, P. Urinary biomarker profiling in transitional cell carcinoma Int. J. Cancer 2006, 119, 2642-50
    • (2006) Int. J. Cancer , vol.119 , pp. 2642-2650
    • Munro, N.P.1    Cairns, D.A.2    Clarke, P.3
  • 19
    • 23844491490 scopus 로고    scopus 로고
    • Maximising sensitivity for detecting changes in protein expression: Experimental design using minimal CyDyes
    • Karp, N. A.; Lilley, K. S. Maximising sensitivity for detecting changes in protein expression: experimental design using minimal CyDyes Proteomics 2005, 5, 3105-15
    • (2005) Proteomics , vol.5 , pp. 3105-3115
    • Karp, N.A.1    Lilley, K.S.2
  • 20
    • 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
  • 22
    • 0038351087 scopus 로고    scopus 로고
    • Relationship between circulating serum soluble interleukin-6 receptor and the angiogenic cytokines basic fibroblast growth factor and vascular endothelial growth factor in multiple myeloma
    • Alexandrakis, M. G.; Passam, F. H.; Boula, A. Relationship between circulating serum soluble interleukin-6 receptor and the angiogenic cytokines basic fibroblast growth factor and vascular endothelial growth factor in multiple myeloma Ann. Hematol. 2003, 82, 19-23
    • (2003) Ann. Hematol. , vol.82 , pp. 19-23
    • Alexandrakis, M.G.1    Passam, F.H.2    Boula, A.3
  • 23
    • 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, 971-83
    • (2006) Nat. Biotechnol. , vol.24 , pp. 971-983
    • Rifai, N.1    Gillette, M.A.2    Carr, S.A.3
  • 24
    • 79958198057 scopus 로고    scopus 로고
    • General statistical modeling of data from protein relative expression isobaric tags
    • Breitwieser, F. P.; Muller, A.; Dayon, L. General statistical modeling of data from protein relative expression isobaric tags J. Proteome Res. 2011, 10, 2758-66
    • (2011) J. Proteome Res. , vol.10 , pp. 2758-2766
    • Breitwieser, F.P.1    Muller, A.2    Dayon, L.3
  • 25
    • 33847340190 scopus 로고    scopus 로고
    • Wright PC. Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ)
    • Gan, C. S.; Chong, P. K.; Pham, T. K. Wright PC. Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ) J. Proteome Res. 2007, 6, 821-7
    • (2007) J. Proteome Res. , vol.6 , pp. 821-827
    • Gan, C.S.1    Chong, P.K.2    Pham, T.K.3
  • 26
    • 0036319960 scopus 로고    scopus 로고
    • Design issues for cDNA microarray experiments
    • Yang, Y. H.; Speed, T. Design issues for cDNA microarray experiments Nat. Rev. Genet. 2002, 3, 579-88
    • (2002) Nat. Rev. Genet. , vol.3 , pp. 579-588
    • Yang, Y.H.1    Speed, T.2
  • 27
    • 74049118091 scopus 로고    scopus 로고
    • A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation
    • Ernoult, E.; Bourreau, A.; Gamelin, E.; Guette, C. A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation J. Biomed. Biotechnol. 2010, 927917
    • (2010) J. Biomed. Biotechnol. , pp. 927917
    • Ernoult, E.1    Bourreau, A.2    Gamelin, E.3    Guette, C.4
  • 28
    • 74049085513 scopus 로고    scopus 로고
    • Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ)
    • Kolla, V.; Jenö, P.; Moes, S. Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ) J. Biomed. Biotechnol. 2010, 2010, 952047
    • (2010) J. Biomed. Biotechnol. , vol.2010 , pp. 952047
    • Kolla, V.1    Jenö, P.2    Moes, S.3
  • 29
    • 70449558565 scopus 로고    scopus 로고
    • A technically detailed and pragmatic protocol for quantitative serum proteomics using iTRAQ
    • not supplied
    • Tonack, S.; MA-O, D.; Jenkins, R. E. A technically detailed and pragmatic protocol for quantitative serum proteomics using iTRAQ. J. Proteomics 2009, not supplied.
    • (2009) J. Proteomics
    • Tonack, S.1    Ma-O, D.2    Jenkins, R.E.3
  • 30
    • 51649090933 scopus 로고    scopus 로고
    • ITRAQ experimental design for plasma biomarker discovery
    • Song, X.; Bandow, J.; Sherman, J. iTRAQ experimental design for plasma biomarker discovery J. Proteome Res. 2008, 7, 2952-8
    • (2008) J. Proteome Res. , vol.7 , pp. 2952-2958
    • Song, X.1    Bandow, J.2    Sherman, J.3
  • 31
    • 33847340190 scopus 로고    scopus 로고
    • Wright PC. Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ)
    • Gan, C. S.; Chong, P. K.; Pham, T. K. Wright PC. Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ) J. Proteome Res. 2007, 6, 821-7
    • (2007) J. Proteome Res. , vol.6 , pp. 821-827
    • Gan, C.S.1    Chong, P.K.2    Pham, T.K.3
  • 32
    • 85128759053 scopus 로고    scopus 로고
    • A list of candidate cancer biomarkers for targeted proteomics
    • Polanski, M.; Anderson, N. L. A list of candidate cancer biomarkers for targeted proteomics Biomark. Insights 2007, 1, 1-48
    • (2007) Biomark. Insights , vol.1 , pp. 1-48
    • Polanski, M.1    Anderson, N.L.2
  • 33
    • 34249676802 scopus 로고    scopus 로고
    • Proteomic analysis of pancreatic endocrine tumor cell lines treated with the histone deacetylase inhibitor trichostatin A
    • Cecconi, D.; Donadelli, M.; Rinalducci, S. Proteomic analysis of pancreatic endocrine tumor cell lines treated with the histone deacetylase inhibitor trichostatin A Proteomics 2007, 7, 1644-53
    • (2007) Proteomics , vol.7 , pp. 1644-1653
    • Cecconi, D.1    Donadelli, M.2    Rinalducci, S.3
  • 34
    • 79961166826 scopus 로고    scopus 로고
    • Proteomic analysis of pancreatic juice for the identification of biomarkers of pancreatic cancer
    • Park, J. Y.; Kim, S. A.; Chung, J. W. Proteomic analysis of pancreatic juice for the identification of biomarkers of pancreatic cancer J. Cancer Res. Clin. Oncol. 2011, 137, 1229-38
    • (2011) J. Cancer Res. Clin. Oncol. , vol.137 , pp. 1229-1238
    • Park, J.Y.1    Kim, S.A.2    Chung, J.W.3
  • 35
    • 79953711417 scopus 로고    scopus 로고
    • Differential expression of peroxiredoxins in prostate cancer: Consistent upregulation of PRDX3 and PRDX4
    • Basu, A.; Banerjee, H.; Rojas, H. Differential expression of peroxiredoxins in prostate cancer: consistent upregulation of PRDX3 and PRDX4 Prostate 2011, 71, 755-65
    • (2011) Prostate , vol.71 , pp. 755-765
    • Basu, A.1    Banerjee, H.2    Rojas, H.3
  • 36
    • 80052276754 scopus 로고    scopus 로고
    • Expression of thioredoxin system and related peroxiredoxin proteins is associated with clinical outcome in radiotherapy treated early stage breast cancer
    • Woolston, C. M.; Storr, S. J.; Ellis, I. O.; Morgan, D. A.; Martin, S. G. Expression of thioredoxin system and related peroxiredoxin proteins is associated with clinical outcome in radiotherapy treated early stage breast cancer Radiother. Oncol. 2011, 100, 308-13
    • (2011) Radiother. Oncol. , vol.100 , pp. 308-313
    • Woolston, C.M.1    Storr, S.J.2    Ellis, I.O.3    Morgan, D.A.4    Martin, S.G.5
  • 37
  • 38
    • 70349912263 scopus 로고    scopus 로고
    • False discovery rates of protein identifications: A strike against the two-peptide rule
    • Gupta, N.; Pevzner, P. A. False discovery rates of protein identifications: a strike against the two-peptide rule J. Proteome Res. 2009, 8, 4173-81
    • (2009) J. Proteome Res. , vol.8 , pp. 4173-4181
    • Gupta, N.1    Pevzner, P.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.