메뉴 건너뛰기




Volumn 12, Issue 1, 2014, Pages 13-19

Super-SILAC: Current trends and future perspectives

Author keywords

biomarkers; cancer; clinical proteomics; mass spectrometry; quantitative proteomics; spike in standard; stable isotope labeling; super SILAC

Indexed keywords

PROTEOME; SECRETOME; UNCLASSIFIED DRUG; AMINO ACID; TUMOR MARKER;

EID: 84921467018     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.2015.982538     Document Type: Article
Times cited : (42)

References (39)
  • 1
    • 84857938446 scopus 로고    scopus 로고
    • Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins
    • M111.014050
    • Geiger T, Wehner A, Schaab C, et al. Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics 2012;11(3):M111.014050
    • (2012) Mol Cell Proteomics , vol.11 , Issue.3
    • Geiger, T.1    Wehner, A.2    Schaab, C.3
  • 2
    • 74049115774 scopus 로고    scopus 로고
    • Mass spectrometry-based label-free quantitative proteomics
    • Zhu W, Smith JW, Huang CM. Mass spectrometry-based label-free quantitative proteomics. J Biomed Biotechnol 2012;2010:840518
    • (2012) J Biomed Biotechnol , vol.2010 , pp. 840518
    • Zhu, W.1    Smith, J.W.2    Huang, C.M.3
  • 3
    • 84907197082 scopus 로고    scopus 로고
    • Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ
    • Cox J, Hein MY, Luber CA, et al. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics 2014;13(9):2513-26
    • (2014) Mol Cell Proteomics , vol.13 , Issue.9 , pp. 2513-2526
    • Cox, J.1    Hein, M.Y.2    Luber, C.A.3
  • 4
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
    • Gygi SP, Rist B, Gerber SA, et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999;17(10):994-9
    • (1999) Nat Biotechnol , vol.17 , Issue.10 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3
  • 5
    • 55849093586 scopus 로고    scopus 로고
    • Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates
    • Boersema PJ, Aye TT, Veen TA, et al. Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates. Proteomics 2008;8(22):4624-32
    • (2008) Proteomics , vol.8 , Issue.22 , pp. 4624-4632
    • Boersema, P.J.1    Aye, T.T.2    Veen, T.A.3
  • 6
    • 0348014635 scopus 로고    scopus 로고
    • Stable-isotope dimethyl labeling for quantitative proteomics
    • Hsu JL, Huang SY, Chow NH, Chen SH. Stable-isotope dimethyl labeling for quantitative proteomics. Anal Chem 2003; 75(24):6843-52
    • (2003) Anal Chem , vol.75 , Issue.24 , pp. 6843-6852
    • Hsu, J.L.1    Huang, S.Y.2    Chow, N.H.3    Chen, S.H.4
  • 7
    • 84883751039 scopus 로고    scopus 로고
    • Comparison of SILAC and mTRAQ quantification for phosphoproteomics on a quadrupole orbitrap mass spectrometer
    • Oppermann FS, Klammer M, Bobe C, et al. Comparison of SILAC and mTRAQ quantification for phosphoproteomics on a quadrupole orbitrap mass spectrometer. J Proteome Res 2013;12(9):4089-100
    • (2013) J Proteome Res , vol.12 , Issue.9 , pp. 4089-4100
    • Oppermann, F.S.1    Klammer, M.2    Bobe, C.3
  • 8
    • 12444345515 scopus 로고    scopus 로고
    • Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS
    • Thompson A, Schafer J, Kuhn K, et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 2003;75(8):1895-904
    • (2003) Anal Chem , vol.75 , Issue.8 , pp. 1895-1904
    • Thompson, A.1    Schafer, J.2    Kuhn, K.3
  • 9
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross PL, Huang YN, Marchese JN, et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004;3(12):1154-69
    • (2004) Mol Cell Proteomics , vol.3 , Issue.12 , pp. 1154-1169
    • Ross, P.L.1    Huang, Y.N.2    Marchese, J.N.3
  • 10
    • 80155124832 scopus 로고    scopus 로고
    • MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics
    • Ting L, Rad R, Gygi SP, Haas W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods 2011;8(11):937-40
    • (2011) Nat Methods , vol.8 , Issue.11 , pp. 937-940
    • Ting, L.1    Rad, R.2    Gygi, S.P.3    Haas, W.4
  • 11
    • 80155205237 scopus 로고    scopus 로고
    • Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging
    • Wenger CD, Lee MV, Hebert AS, et al. Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nat Methods 2011;8(11): 933-5
    • (2011) Nat Methods , vol.8 , Issue.11 , pp. 933-935
    • Wenger, C.D.1    Lee, M.V.2    Hebert, A.S.3
  • 12
    • 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 SE, Blagoev B, Kratchmarova I, et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002;1(5):376-86
    • (2002) Mol Cell Proteomics , vol.1 , Issue.5 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3
  • 13
    • 84865595374 scopus 로고    scopus 로고
    • The expanding field of SILAC
    • Ong SE. The expanding field of SILAC. Anal Bioanal Chem 2012;404(4):967-76
    • (2012) Anal Bioanal Chem , vol.404 , Issue.4 , pp. 967-976
    • Ong, S.E.1
  • 14
    • 60849098775 scopus 로고    scopus 로고
    • Temporal profiling of the adipocyte proteome during differentiation using a five-plex SILAC based strategy
    • Molina H, Yang Y, Ruch T, et al. Temporal profiling of the adipocyte proteome during differentiation using a five-plex SILAC based strategy. J Proteome Res 2009;8(1):48-58
    • (2009) J Proteome Res , vol.8 , Issue.1 , pp. 48-58
    • Molina, H.1    Yang, Y.2    Ruch, T.3
  • 15
    • 84885648123 scopus 로고    scopus 로고
    • Development of a 5-plex SILAC method tuned for the quantitation of tyrosine phosphorylation dynamics
    • Tzouros M, Golling S, Avila D, et al. Development of a 5-plex SILAC method tuned for the quantitation of tyrosine phosphorylation dynamics. Mol Cell Proteomics 2013;12(11):3339-49
    • (2013) Mol Cell Proteomics , vol.12 , Issue.11 , pp. 3339-3349
    • Tzouros, M.1    Golling, S.2    Avila, D.3
  • 16
    • 84875716859 scopus 로고    scopus 로고
    • Neutron-encoded mass signatures for multiplexed proteome quantification
    • Hebert AS, Merrill AE, Bailey DJ, et al. Neutron-encoded mass signatures for multiplexed proteome quantification. Nat Methods 2013;10(4):332-4
    • (2013) Nat Methods , vol.10 , Issue.4 , pp. 332-334
    • Hebert, A.S.1    Merrill, A.E.2    Bailey, D.J.3
  • 17
    • 84907221170 scopus 로고    scopus 로고
    • NeuCode labels for relative protein quantification
    • Merrill AE, Hebert AS, MacGilvray ME, et al. NeuCode labels for relative protein quantification. Mol Cell Proteomics 2014; 13(9):2503-12
    • (2014) Mol Cell Proteomics , vol.13 , Issue.9 , pp. 2503-2512
    • Merrill, A.E.1    Hebert, A.S.2    MacGilvray, M.E.3
  • 18
    • 80051569933 scopus 로고    scopus 로고
    • Whole cell proteome regulation by microRNAs captured in a pulsed SILAC mass spectrometry approach
    • Ebner OA, Selbach M. Whole cell proteome regulation by microRNAs captured in a pulsed SILAC mass spectrometry approach. Methods Mol Biol 2011;725:315-31
    • (2011) Methods Mol Biol , vol.725 , pp. 315-331
    • Ebner, O.A.1    Selbach, M.2
  • 19
    • 60849097304 scopus 로고    scopus 로고
    • Turnover of the human proteome: Determination of protein intracellular stability by dynamic SILAC
    • Doherty MK, Hammond DE, Clague MJ, et al. Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC. J Proteome Res 2009;8(1):104-12
    • (2009) J Proteome Res , vol.8 , Issue.1 , pp. 104-112
    • Doherty, M.K.1    Hammond, D.E.2    Clague, M.J.3
  • 20
    • 78049334902 scopus 로고    scopus 로고
    • Trans-SILAC: Sorting out the non-cell-autonomous proteome
    • Rechavi O, Kalman M, Fang Y, et al. Trans-SILAC: sorting out the non-cell-autonomous proteome. Nat Methods 2010;7(11):923-7
    • (2010) Nat Methods , vol.7 , Issue.11 , pp. 923-927
    • Rechavi, O.1    Kalman, M.2    Fang, Y.3
  • 21
    • 84881475017 scopus 로고    scopus 로고
    • Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments
    • Gauthier NP, Soufi B, Walkowicz WE, et al. Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments. Nat Methods 2013;10(8):768-73
    • (2013) Nat Methods , vol.10 , Issue.8 , pp. 768-773
    • Gauthier, N.P.1    Soufi, B.2    Walkowicz, W.E.3
  • 22
    • 84904106705 scopus 로고    scopus 로고
    • Cell-specific labeling enzymes for analysis of cell-cell communication in continuous co-culture
    • Tape CJ, Norrie IC, Worboys JD, et al. Cell-specific labeling enzymes for analysis of cell-cell communication in continuous co-culture. Mol Cell Proteomics 2014; 13(7):1866-76
    • (2014) Mol Cell Proteomics , vol.13 , Issue.7 , pp. 1866-1876
    • Tape, C.J.1    Norrie, I.C.2    Worboys, J.D.3
  • 23
    • 22844436250 scopus 로고    scopus 로고
    • Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards
    • Ishihama Y, Sato T, Tabata T, et al. Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards. Nat Biotechnol 2005;23(5):617-21
    • (2005) Nat Biotechnol , vol.23 , Issue.5 , pp. 617-621
    • Ishihama, Y.1    Sato, T.2    Tabata, T.3
  • 24
    • 44449162195 scopus 로고    scopus 로고
    • Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level
    • Hanke S, Besir H, Oesterhelt D, Mann M. Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level. J Proteome Res 2008;7(3): 1118-30
    • (2008) J Proteome Res , vol.7 , Issue.3 , pp. 1118-1130
    • Hanke, S.1    Besir, H.2    Oesterhelt, D.3    Mann, M.4
  • 25
    • 80855154135 scopus 로고    scopus 로고
    • A Protein epitope signature tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines
    • Zeiler M, Straube WL, Lundberg E, et al. A Protein epitope signature tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines. Mol Cell Proteomics 2012;11(3): O111-009613
    • (2012) Mol Cell Proteomics , vol.11 , Issue.3 , pp. O111-009613
    • Zeiler, M.1    Straube, W.L.2    Lundberg, E.3
  • 26
    • 47549099572 scopus 로고    scopus 로고
    • SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function
    • Kruger M, Moser M, Ussar S, et al. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 2008;134(2):353-64
    • (2008) Cell , vol.134 , Issue.2 , pp. 353-364
    • Kruger, M.1    Moser, M.2    Ussar, S.3
  • 27
    • 77958018495 scopus 로고    scopus 로고
    • The SILAC fly allows for accurate protein quantification in vivo
    • Sury MD, Chen JX, Selbach M. The SILAC fly allows for accurate protein quantification in vivo. Mol Cell Proteomics 2010;9(10):2173-83
    • (2010) Mol Cell Proteomics , vol.9 , Issue.10 , pp. 2173-2183
    • Sury, M.D.1    Chen, J.X.2    Selbach, M.3
  • 28
    • 80053369492 scopus 로고    scopus 로고
    • Quantitative proteomics by amino acid labeling in C. Elegans
    • Fredens J, Engholm-Keller K, Giessing A, et al. Quantitative proteomics by amino acid labeling in C. elegans. Nat Methods 2011;8(10):845-7
    • (2011) Nat Methods , vol.8 , Issue.10 , pp. 845-847
    • Fredens, J.1    Engholm-Keller, K.2    Giessing, A.3
  • 29
    • 82355185718 scopus 로고    scopus 로고
    • SILAC zebrafish for quantitative analysis of protein turnover and tissue regeneration
    • Westman-Brinkmalm A, Abramsson A, Pannee J, et al. SILAC zebrafish for quantitative analysis of protein turnover and tissue regeneration. J Proteomics 2011; 75(2):425-34
    • (2011) J Proteomics , vol.75 , Issue.2 , pp. 425-434
    • Westman-Brinkmalm, A.1    Abramsson, A.2    Pannee, J.3
  • 30
    • 84878741907 scopus 로고    scopus 로고
    • Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse
    • Geiger T, Velic A, Macek B, et al. Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse. Mol Cell Proteomics 2013;12(6):1709-22
    • (2013) Mol Cell Proteomics , vol.12 , Issue.6 , pp. 1709-1722
    • Geiger, T.1    Velic, A.2    MacEk, B.3
  • 31
    • 77952226764 scopus 로고    scopus 로고
    • Super-SILAC mix for quantitative proteomics of human tumor tissue
    • Geiger T, Cox J, Ostasiewicz P, et al. Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods 2010;7(5):383-5
    • (2010) Nat Methods , vol.7 , Issue.5 , pp. 383-385
    • Geiger, T.1    Cox, J.2    Ostasiewicz, P.3
  • 32
    • 79551663189 scopus 로고    scopus 로고
    • Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics
    • Geiger T, Wisniewski JR, Cox J, et al. Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics. Nat Protoc 2011; 6(2):147-57
    • (2011) Nat Protoc , vol.6 , Issue.2 , pp. 147-157
    • Geiger, T.1    Wisniewski, J.R.2    Cox, J.3
  • 33
    • 84888367069 scopus 로고    scopus 로고
    • SILAC surrogates: Rescue of quantitative information for orphan analytes in spike-in SILAC experiments
    • Gilmore JM, Milloy JA, Gerber SA. SILAC surrogates: rescue of quantitative information for orphan analytes in spike-in SILAC experiments. Anal Chem 2013; 85(22):10812-19
    • (2013) Anal Chem , vol.85 , Issue.22 , pp. 10812-10819
    • Gilmore, J.M.1    Milloy, J.A.2    Gerber, S.A.3
  • 34
    • 84925883970 scopus 로고    scopus 로고
    • Design and application of super-SILAC for proteome quantification
    • Pozniak Y, Geiger T. Design and application of super-SILAC for proteome quantification. Methods Mol Biol 2014;1188:281-91
    • (2014) Methods Mol Biol , vol.1188 , pp. 281-291
    • Pozniak, Y.1    Geiger, T.2
  • 35
    • 84861157792 scopus 로고    scopus 로고
    • Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles
    • Deeb SJ, D'Souza RC, Cox J, et al. Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles. Mol Cell Proteomics 2012;11(5):77-89
    • (2012) Mol Cell Proteomics , vol.11 , Issue.5 , pp. 77-89
    • Deeb, S.J.1    D'Souza, R.C.2    Cox, J.3
  • 36
    • 84864017230 scopus 로고    scopus 로고
    • Quantitative proteomics of primary tumors with varying metastatic capabilities using stable isotope-labeled proteins of multiple histogenic origins
    • Lund RR, Terp MG, Laenkholm AV, et al. Quantitative proteomics of primary tumors with varying metastatic capabilities using stable isotope-labeled proteins of multiple histogenic origins. Proteomics 2012;12(13): 2139-48
    • (2012) Proteomics , vol.12 , Issue.13 , pp. 2139-2148
    • Lund, R.R.1    Terp, M.G.2    Laenkholm, A.V.3
  • 37
    • 70349490370 scopus 로고    scopus 로고
    • Proteome differences between brown and white fat mitochondria reveal specialized metabolic functions
    • Forner F, Kumar C, Luber CA, et al. Proteome differences between brown and white fat mitochondria reveal specialized metabolic functions. Cell Metab 2009; 10(4):324-35
    • (2009) Cell Metab , vol.10 , Issue.4 , pp. 324-335
    • Forner, F.1    Kumar, C.2    Luber, C.A.3
  • 38
    • 79961014854 scopus 로고    scopus 로고
    • Large-scale phosphosite quantification in tissues by a spike-in SILAC method
    • Monetti M, Nagaraj N, Sharma K, Mann M. Large-scale phosphosite quantification in tissues by a spike-in SILAC method. Nat Methods 2011;8(8):655-8
    • (2011) Nat Methods , vol.8 , Issue.8 , pp. 655-658
    • Monetti, M.1    Nagaraj, N.2    Sharma, K.3    Mann, M.4
  • 39
    • 84871860708 scopus 로고    scopus 로고
    • Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples
    • Boersema PJ, Geiger T, Wisniewski JR, Mann M. Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples. Mol Cell Proteomics 2013;12(1):158-71
    • (2013) Mol Cell Proteomics , vol.12 , Issue.1 , pp. 158-171
    • Boersema, P.J.1    Geiger, T.2    Wisniewski, J.R.3    Mann, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.