메뉴 건너뛰기




Volumn 12, Issue 1, 2014, Pages

The Lottia gigantea shell matrix proteome: Re-analysis including MaxQuant iBAQ quantitation and phosphoproteome analysis

Author keywords

[No Author keywords available]

Indexed keywords

MATRIX PROTEIN; PROTEOME;

EID: 84904216584     PISSN: None     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-12-28     Document Type: Article
Times cited : (57)

References (61)
  • 1
    • 0031408958 scopus 로고    scopus 로고
    • Phosphorylation of the proteins of the extracellular matrix of mineralized tissues by casein kinase-like activity
    • Veis A, Sfeir C, Wu CB. Phosphorylation of the proteins of the extracellular matrix of mineralized tissues by casein kinase-like activity. Crit Rev Oral Biol Med 1997, 8:360-379.
    • (1997) Crit Rev Oral Biol Med , vol.8 , pp. 360-379
    • Veis, A.1    Sfeir, C.2    Wu, C.B.3
  • 2
    • 57349158632 scopus 로고    scopus 로고
    • Phosphorylated proteins and control over apatite nucleation, crystal growth, and inhibition
    • George A, Veis A. Phosphorylated proteins and control over apatite nucleation, crystal growth, and inhibition. Chem Rev 2008, 108:4670-4693.
    • (2008) Chem Rev , vol.108 , pp. 4670-4693
    • George, A.1    Veis, A.2
  • 4
    • 84865021971 scopus 로고    scopus 로고
    • The Raine syndrome protein FAM20C is a Golgi kinase that phosphorylates biomineralization proteins
    • Ishikawa HO, Xu A, Ogura E, Manning G, Irvine KD. The Raine syndrome protein FAM20C is a Golgi kinase that phosphorylates biomineralization proteins. PLoS One 2012, 7:e42988.
    • (2012) PLoS One , vol.7
    • Ishikawa, H.O.1    Xu, A.2    Ogura, E.3    Manning, G.4    Irvine, K.D.5
  • 6
    • 84871504913 scopus 로고    scopus 로고
    • Extracellular phosphorylation and phosphorylated proteins: not just curiosities but physiologically important
    • Yalak G, Vogel V. Extracellular phosphorylation and phosphorylated proteins: not just curiosities but physiologically important. Sci Signal 2012, 5:re7.
    • (2012) Sci Signal , vol.5
    • Yalak, G.1    Vogel, V.2
  • 8
    • 84873523452 scopus 로고    scopus 로고
    • Human osteopontin splicing isoforms: known roles, potential clinical applications and activated signaling pathways
    • Gimba ER, Tilli TM. Human osteopontin splicing isoforms: known roles, potential clinical applications and activated signaling pathways. Cancer Lett 2013, 331:11-17.
    • (2013) Cancer Lett , vol.331 , pp. 11-17
    • Gimba, E.R.1    Tilli, T.M.2
  • 9
    • 84866300463 scopus 로고    scopus 로고
    • The importance of the SIBLING family of proteins on skeletal mineralization and bone remodeling
    • Staines AK, MacRae VE, Farquharson C. The importance of the SIBLING family of proteins on skeletal mineralization and bone remodeling. J Endocrinol 2012, 214:241-255.
    • (2012) J Endocrinol , vol.214 , pp. 241-255
    • Staines, A.K.1    MacRae, V.E.2    Farquharson, C.3
  • 10
    • 0028301910 scopus 로고
    • Modulation of crystal formation by bone phosphoproteins: structural specificity of the osteopontin-mediated inhibition of hydroxyapatite formation
    • Hunter GK, Kyle CL, Goldberg HA. Modulation of crystal formation by bone phosphoproteins: structural specificity of the osteopontin-mediated inhibition of hydroxyapatite formation. Biochem J 1994, 300:723-728.
    • (1994) Biochem J , vol.300 , pp. 723-728
    • Hunter, G.K.1    Kyle, C.L.2    Goldberg, H.A.3
  • 11
    • 0034733562 scopus 로고    scopus 로고
    • Phosphorylation of osteopontin is required for inhibition of vascular smooth muscle cell calcification
    • Jono S, Peinado C, Giachelli CM. Phosphorylation of osteopontin is required for inhibition of vascular smooth muscle cell calcification. J Biol Chem 2000, 275:20197-20203.
    • (2000) J Biol Chem , vol.275 , pp. 20197-20203
    • Jono, S.1    Peinado, C.2    Giachelli, C.M.3
  • 12
    • 25844489058 scopus 로고    scopus 로고
    • Phosphorylation of phosphophoryn is crucial for its function as a mediator of biomineralization
    • He G, Ramachandran A, Dahl T, George S, Schultz D, Cookson D, Veis A, George A. Phosphorylation of phosphophoryn is crucial for its function as a mediator of biomineralization. J Biol Chem 2005, 280:33109-33114.
    • (2005) J Biol Chem , vol.280 , pp. 33109-33114
    • He, G.1    Ramachandran, A.2    Dahl, T.3    George, S.4    Schultz, D.5    Cookson, D.6    Veis, A.7    George, A.8
  • 13
    • 80051514375 scopus 로고    scopus 로고
    • Primary structure and phosphorylation of dentin matrix protein 1 (DMP1) and dentin phosphoryn (DPP) uniquely determine their role in biomineralization
    • Deshpande AS, Fang P-A, Zhang X, Jayaraman T, Sfeir C, Beniash E. Primary structure and phosphorylation of dentin matrix protein 1 (DMP1) and dentin phosphoryn (DPP) uniquely determine their role in biomineralization. Biomacromolecules 2011, 12:2933-2945.
    • (2011) Biomacromolecules , vol.12 , pp. 2933-2945
    • Deshpande, A.S.1    Fang, P.-A.2    Zhang, X.3    Jayaraman, T.4    Sfeir, C.5    Beniash, E.6
  • 14
    • 0037472633 scopus 로고    scopus 로고
    • Phosphorylation ofserine residues is fundamental for the calcium-binding ability of orchestin, a soluble matrix protein from crustacean calcium storage structures
    • Hecker A, Testenière O, Marin F, Luquet G. Phosphorylation ofserine residues is fundamental for the calcium-binding ability of orchestin, a soluble matrix protein from crustacean calcium storage structures. FEBS Lett 2003, 535:49-54.
    • (2003) FEBS Lett , vol.535 , pp. 49-54
    • Hecker, A.1    Testenière, O.2    Marin, F.3    Luquet, G.4
  • 15
    • 33847713391 scopus 로고    scopus 로고
    • Phosphoproteins of the chicken eggshell calcified layer
    • Mann K, Olsen JV, Maček B, Gnad F, Mann M. Phosphoproteins of the chicken eggshell calcified layer. Proteomics 2007, 7:106-115.
    • (2007) Proteomics , vol.7 , pp. 106-115
    • Mann, K.1    Olsen, J.V.2    Maček, B.3    Gnad, F.4    Mann, M.5
  • 16
    • 77649091052 scopus 로고    scopus 로고
    • Phosphoproteomes of Strongylocentrotus purpuratus shell and tooth matrix: identification of a major acidic sea urchin tooth phosphoprotein, phosphodontin
    • Mann K, Poustka AJ, Mann M. Phosphoproteomes of Strongylocentrotus purpuratus shell and tooth matrix: identification of a major acidic sea urchin tooth phosphoprotein, phosphodontin. Proteome Sci 2010, 8:6.
    • (2010) Proteome Sci , vol.8 , pp. 6
    • Mann, K.1    Poustka, A.J.2    Mann, M.3
  • 17
    • 84862198201 scopus 로고    scopus 로고
    • In-depth proteomic analysis of a mollusk shell: acid-soluble and acid-insoluble matrix of the limpet Lottia gigantea
    • Mann K, Edsinger-Gonzales E, Mann M. In-depth proteomic analysis of a mollusk shell: acid-soluble and acid-insoluble matrix of the limpet Lottia gigantea. Proteome Sci 2012, 10:28.
    • (2012) Proteome Sci , vol.10 , pp. 28
    • Mann, K.1    Edsinger-Gonzales, E.2    Mann, M.3
  • 18
    • 84872025590 scopus 로고    scopus 로고
    • The shell-forming proteome of Lottia gigantea reveals both deep conservation and lineage-specific novelties
    • Marie B, Jackson DJ, Ramos-Silva P, Zanella-Cleon I, Guichard N, Marin F. The shell-forming proteome of Lottia gigantea reveals both deep conservation and lineage-specific novelties. FEBS J 2013, 280:214-232.
    • (2013) FEBS J , vol.280 , pp. 214-232
    • Marie, B.1    Jackson, D.J.2    Ramos-Silva, P.3    Zanella-Cleon, I.4    Guichard, N.5    Marin, F.6
  • 20
    • 67349266694 scopus 로고    scopus 로고
    • Universal sample preparation method for proteome analysis
    • Wisniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods 2009, 6:359-362.
    • (2009) Nat Methods , vol.6 , pp. 359-362
    • Wisniewski, J.R.1    Zougman, A.2    Nagaraj, N.3    Mann, M.4
  • 21
    • 24944519450 scopus 로고    scopus 로고
    • Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns
    • Larsen MR, Thingholm TE, Jensen ON, Roepstorff P, Jorgensen TJD. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomics 2005, 4:873-886.
    • (2005) Mol Cell Proteomics , vol.4 , pp. 873-886
    • Larsen, M.R.1    Thingholm, T.E.2    Jensen, O.N.3    Roepstorff, P.4    Jorgensen, T.J.D.5
  • 23
    • 34548183872 scopus 로고    scopus 로고
    • Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips
    • Rappsilber J, Mann M, Ishihama Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2007, 2:1896-1906.
    • (2007) Nat Protoc , vol.2 , pp. 1896-1906
    • Rappsilber, J.1    Mann, M.2    Ishihama, Y.3
  • 28
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification
    • Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2009, 26:1367-1372.
    • (2009) Nat Biotechnol , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 29
    • 84868336980 scopus 로고    scopus 로고
    • Expert system for computer-assisted annotation of MS/MS spectra
    • Neuhauser N, Michalski A, Cox J, Mann M. Expert system for computer-assisted annotation of MS/MS spectra. Mol Cell Proteom 2012, 11:1500-1509.
    • (2012) Mol Cell Proteom , vol.11 , pp. 1500-1509
    • Neuhauser, N.1    Michalski, A.2    Cox, J.3    Mann, M.4
  • 30
    • 44149105911 scopus 로고    scopus 로고
    • PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation and prediction of phospho sites
    • Gnad F, Ren S, Cox J, Olsen JV, Macek B, Oroshi M, Mann M. PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation and prediction of phospho sites. Genome Biol 2007, 8:R250.
    • (2007) Genome Biol , vol.8
    • Gnad, F.1    Ren, S.2    Cox, J.3    Olsen, J.V.4    Macek, B.5    Oroshi, M.6    Mann, M.7
  • 31
    • 78651277460 scopus 로고    scopus 로고
    • PHOSIDA 2011: the posttranslational modification database
    • Gnad F, Gunawardena J, Mann M. PHOSIDA 2011: the posttranslational modification database. Nuc Acids Res 2011, 39(supplement1):D253-260.
    • (2011) Nuc Acids Res , vol.39 , Issue.SUPPL.1
    • Gnad, F.1    Gunawardena, J.2    Mann, M.3
  • 36
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: discriminating signal peptides from transmembrane regions
    • Petersen TN, Brunak S, von Heinje G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011, 8:785-786.
    • (2011) Nat Methods , vol.8 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    von Heinje, G.3    Nielsen, H.4
  • 38
    • 24044538903 scopus 로고    scopus 로고
    • IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    • Dosztányi Z, Csizmók V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 2005, 21:3433-3434.
    • (2005) Bioinformatics , vol.21 , pp. 3433-3434
    • Dosztányi, Z.1    Csizmók, V.2    Tompa, P.3    Simon, I.4
  • 40
    • 84885949386 scopus 로고    scopus 로고
    • Improved disorder prediction by combination of orthogonal approaches
    • Schlessinger A, Punta M, Yachdav G, Kajan L, Rost B. Improved disorder prediction by combination of orthogonal approaches. PLoS One 2009, 4:e4433-e4433.
    • (2009) PLoS One , vol.4
    • Schlessinger, A.1    Punta, M.2    Yachdav, G.3    Kajan, L.4    Rost, B.5
  • 41
    • 26844559000 scopus 로고    scopus 로고
    • Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    • Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 2005, 4:1265-1272.
    • (2005) Mol Cell Proteomics , vol.4 , pp. 1265-1272
    • Ishihama, Y.1    Oda, Y.2    Tabata, T.3    Sato, T.4    Nagasu, T.5    Rappsilber, J.6    Mann, M.7
  • 42
    • 84883275474 scopus 로고    scopus 로고
    • Critical assessment of proteome-wide label-free absolute abundance estimation strategies
    • Ahrne E, Molzahn L, Glatter T, Schmidt A. Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics 2013, 13:2567-2578.
    • (2013) Proteomics , vol.13 , pp. 2567-2578
    • Ahrne, E.1    Molzahn, L.2    Glatter, T.3    Schmidt, A.4
  • 43
    • 84947543553 scopus 로고
    • Studies on shell formation in molluscs
    • Timmermans LPM. Studies on shell formation in molluscs. Netherlands J Zool 1969, 19:417-523.
    • (1969) Netherlands J Zool , vol.19 , pp. 417-523
    • Timmermans, L.P.M.1
  • 44
    • 0017763910 scopus 로고
    • Evidence for the mode of sclerotization in a molluscan periostracum
    • Waite JH. Evidence for the mode of sclerotization in a molluscan periostracum. Comp Biochem Physiol 1977, 58B:157-162.
    • (1977) Comp Biochem Physiol , vol.58 B , pp. 157-162
    • Waite, J.H.1
  • 45
    • 0346328276 scopus 로고    scopus 로고
    • A light- and electron microscopic study of enzymes in the embryonic shell-forming tissue of the freshwater snail, Biophalaria glabrata
    • Marxen JC, Witten PE, Fincke D, Reelsen O, Rezgaoui M, Becker W. A light- and electron microscopic study of enzymes in the embryonic shell-forming tissue of the freshwater snail, Biophalaria glabrata. Invertebrate Biol 2003, 122:313-325.
    • (2003) Invertebrate Biol , vol.122 , pp. 313-325
    • Marxen, J.C.1    Witten, P.E.2    Fincke, D.3    Reelsen, O.4    Rezgaoui, M.5    Becker, W.6
  • 46
    • 84880032001 scopus 로고    scopus 로고
    • An ancient process in a modern mollusc: early development of the shell in Lymnea stagnalis
    • Hohagen J, Jackson DJ. An ancient process in a modern mollusc: early development of the shell in Lymnea stagnalis. BMC Dev Biol 2013, 13:27.
    • (2013) BMC Dev Biol , vol.13 , pp. 27
    • Hohagen, J.1    Jackson, D.J.2
  • 47
    • 84865113552 scopus 로고    scopus 로고
    • Unusually Acidic Proteins In Biomineralization
    • Weinheim: Wiley-VCH Verlag, Bäuerlein E, volume 1
    • Marin F, Luquet G. Unusually Acidic Proteins In Biomineralization. Handbook of Biomineralization 2007, 273-290. Weinheim: Wiley-VCH Verlag, Bäuerlein E, volume 1.
    • (2007) Handbook of Biomineralization , pp. 273-290
    • Marin, F.1    Luquet, G.2
  • 48
    • 84870838761 scopus 로고    scopus 로고
    • Aragonite-associated biomineralization proteins are disordered and contain interactive motifs
    • Evans JS. Aragonite-associated biomineralization proteins are disordered and contain interactive motifs. Bioinformatics 2012, 28:3182-3185.
    • (2012) Bioinformatics , vol.28 , pp. 3182-3185
    • Evans, J.S.1
  • 49
    • 84865146912 scopus 로고    scopus 로고
    • Intrinsically Disordered Proteins in Biomineralization
    • Intech, Jong S, Chapter 1
    • Wojtas M, Dobryszycki P, Ozyhar A. Intrinsically Disordered Proteins in Biomineralization. Advanced Topics in Biomineralization 2012, Intech, Jong S, Chapter 1 (http://www.intechopen.com/books/advanced-topics-in-biomineralization).
    • (2012) Advanced Topics in Biomineralization
    • Wojtas, M.1    Dobryszycki, P.2    Ozyhar, A.3
  • 51
    • 77953573499 scopus 로고    scopus 로고
    • Proteomic analysis of sea urchin (Strongylocentrotus purpuratus) spicule matrix
    • Mann K, Wilt FH, Poustka AJ. Proteomic analysis of sea urchin (Strongylocentrotus purpuratus) spicule matrix. Proteome Sci 2010, 8:33.
    • (2010) Proteome Sci , vol.8 , pp. 33
    • Mann, K.1    Wilt, F.H.2    Poustka, A.J.3
  • 52
    • 79953741938 scopus 로고    scopus 로고
    • P58-A and P58-B: novel proteins that mediate skeletogenesis in the sea urchin embryo
    • Adomako-Ankomah A, Ettensohn CA. P58-A and P58-B: novel proteins that mediate skeletogenesis in the sea urchin embryo. Dev Biol 2011, 353:81-93.
    • (2011) Dev Biol , vol.353 , pp. 81-93
    • Adomako-Ankomah, A.1    Ettensohn, C.A.2
  • 53
    • 77952014394 scopus 로고    scopus 로고
    • CXC chemokine receptor 4 is a cell surface receptor for extracellular ubiquitin
    • Saini V, Marchese A, Majetschak M. CXC chemokine receptor 4 is a cell surface receptor for extracellular ubiquitin. J Biol Chem 2010, 285:15566-15576.
    • (2010) J Biol Chem , vol.285 , pp. 15566-15576
    • Saini, V.1    Marchese, A.2    Majetschak, M.3
  • 54
    • 84866151569 scopus 로고    scopus 로고
    • Ubiquitylation functions in the calcium carbonate biomineralization in the extracellular matrix
    • Fang D, Pan C, Lin H, Lin Y, Xu G, Zhang G, Wang H, Xie L, Zhang R. Ubiquitylation functions in the calcium carbonate biomineralization in the extracellular matrix. Plos One 2012, 7:e35715.
    • (2012) Plos One , vol.7
    • Fang, D.1    Pan, C.2    Lin, H.3    Lin, Y.4    Xu, G.5    Zhang, G.6    Wang, H.7    Xie, L.8    Zhang, R.9
  • 55
    • 84879217848 scopus 로고    scopus 로고
    • Oyster shell proteins originate from multiple organs and their probable transport pathway to the shell formation front
    • Wang X, Li L, Zhu Y, Du Y, Song X, Chen Y, Huang R, Que H, Zhang G. Oyster shell proteins originate from multiple organs and their probable transport pathway to the shell formation front. PLoS One 2013, 8:e66522.
    • (2013) PLoS One , vol.8
    • Wang, X.1    Li, L.2    Zhu, Y.3    Du, Y.4    Song, X.5    Chen, Y.6    Huang, R.7    Que, H.8    Zhang, G.9
  • 56
    • 78649849874 scopus 로고    scopus 로고
    • Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation
    • Nagaraj N, D'Souza RCJ, Cox J, Olsen JV, Mann M. Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. J Proteome Res 2010, 9:6786-6794.
    • (2010) J Proteome Res , vol.9 , pp. 6786-6794
    • Nagaraj, N.1    D'Souza, R.C.J.2    Cox, J.3    Olsen, J.V.4    Mann, M.5
  • 57
    • 84861805250 scopus 로고    scopus 로고
    • Correction to feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation
    • Nagaraj N, D'Souza RCJ, Cox J, Olsen JV, Mann M. Correction to feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. J Proteome Res 2012, 11:3506-3508.
    • (2012) J Proteome Res , vol.11 , pp. 3506-3508
    • Nagaraj, N.1    D'Souza, R.C.J.2    Cox, J.3    Olsen, J.V.4    Mann, M.5
  • 58
    • 65249137629 scopus 로고    scopus 로고
    • Global and site-specific quantitative phosphoproteomics: princples and applications
    • Maček B, Mann M, Olsen JV. Global and site-specific quantitative phosphoproteomics: princples and applications. Annu Rev Pharmacol Toxicol 2009, 49:199-221.
    • (2009) Annu Rev Pharmacol Toxicol , vol.49 , pp. 199-221
    • Maček, B.1    Mann, M.2    Olsen, J.V.3
  • 59
    • 84878994835 scopus 로고    scopus 로고
    • Biomineralization toolkit: the importance of sample cleaning prior to the characterization of biomineral proteomes
    • Ramos-Silva P, Marin F, Kaandorp J, Marie B. Biomineralization toolkit: the importance of sample cleaning prior to the characterization of biomineral proteomes. Proc Natl Acad Sci U S A 2013, 110:E2144-E2146.
    • (2013) Proc Natl Acad Sci U S A , vol.110
    • Ramos-Silva, P.1    Marin, F.2    Kaandorp, J.3    Marie, B.4
  • 60
    • 84883079738 scopus 로고    scopus 로고
    • The proteome of the calcified layer organic matrix of turkey (Meleagris gallopavo) eggshell
    • Mann K, Mann M. The proteome of the calcified layer organic matrix of turkey (Meleagris gallopavo) eggshell. Proteome Sci 2013, 11:40.
    • (2013) Proteome Sci , vol.11 , pp. 40
    • Mann, K.1    Mann, M.2
  • 61
    • 84887127717 scopus 로고    scopus 로고
    • Proteomics of CaCO3 biomineral-associated proteins: how to properly address their analysis
    • Marie B, Ramos-Silva P, Marin F, Marie A. Proteomics of CaCO3 biomineral-associated proteins: how to properly address their analysis. Proteomics 2013, 13:3109-3116.
    • (2013) Proteomics , vol.13 , pp. 3109-3116
    • Marie, B.1    Ramos-Silva, P.2    Marin, F.3    Marie, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.