메뉴 건너뛰기




Volumn 11, Issue 6, 2014, Pages 675-684

Biomedical applications of ion mobility-enhanced data-independent acquisition-based label-free quantitative proteomics

Author keywords

biomedical research; data independent acquisition; HDMSE; high definition mass spectrometry; ion mobility separation; label free quantification; MSE; proteomics

Indexed keywords

PROTEOME; STABLE ISOTOPE;

EID: 84910632066     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.2014.971114     Document Type: Article
Times cited : (29)

References (95)
  • 1
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003;422:198-207
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 2
    • 77954464041 scopus 로고    scopus 로고
    • Proteomics: A pragmatic perspective
    • Mallick P, Kuster B. Proteomics: a pragmatic perspective. Nat Biotechnol 2010;28:695-709
    • (2010) Nat Biotechnol , vol.28 , pp. 695-709
    • Mallick, P.1    Kuster, B.2
  • 3
    • 84901611036 scopus 로고    scopus 로고
    • Mass-spectrometry-based draft of the human proteome
    • Wilhelm M, Schlegl J, Hahne H, et al. Mass-spectrometry-based draft of the human proteome. Nature 2014;509:582-7
    • (2014) Nature , vol.509 , pp. 582-587
    • Wilhelm, M.1    Schlegl, J.2    Hahne, H.3
  • 4
    • 84901599553 scopus 로고    scopus 로고
    • A draft map of the human proteome
    • Kim M-S, Pinto SM, Getnet D, et al. A draft map of the human proteome. Nature 2014;509:575-81
    • (2014) Nature , vol.509 , pp. 575-581
    • Kim, M.-S.1    Pinto, S.M.2    Getnet, D.3
  • 5
    • 3242731195 scopus 로고    scopus 로고
    • A model for random sampling and estimation of relative protein abundance in shotgun proteomics
    • Liu H, Sadygov RG, Yates JR. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004;76:4193-201
    • (2004) Anal Chem , vol.76 , pp. 4193-4201
    • Liu, H.1    Sadygov, R.G.2    Yates, J.R.3
  • 6
    • 63049084861 scopus 로고    scopus 로고
    • The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS
    • Geromanos SJ, Vissers JPC, Silva JC, et al. The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics 2009;9: 1683-95
    • (2009) Proteomics , vol.9 , pp. 1683-1695
    • Geromanos, S.J.1    Jpc, V.2    Silva, J.C.3
  • 7
    • 79953719716 scopus 로고    scopus 로고
    • More than 100, 000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS
    • Michalski A, Cox J, Mann M. More than 100, 000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res 2011;10: 1785-93
    • (2011) J Proteome Res , vol.10 , pp. 1785-1793
    • Michalski, A.1    Cox, J.2    Mann, M.3
  • 8
    • 14744293536 scopus 로고    scopus 로고
    • Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
    • Venable JD, Dong M, Wohlschlegel J, et al. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods 2004;1: 39-45
    • (2004) Nat Methods , vol.1 , pp. 39-45
    • Venable, J.D.1    Dong, M.2    Wohlschlegel, J.3
  • 9
    • 77957990113 scopus 로고    scopus 로고
    • Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation
    • Geiger T, Cox J, Mann M. Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol Cell Proteomics 2010;9:2252-61
    • (2010) Mol Cell Proteomics , vol.9 , pp. 2252-2261
    • Geiger, T.1    Cox, J.2    Mann, M.3
  • 10
    • 79954569537 scopus 로고    scopus 로고
    • Faster, quantitative, and accurate precursor acquisition independent from ion count
    • Panchaud A, Jung S, Shaffer Sa, et al. Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem 2011;83:2250-7
    • (2011) Anal Chem , vol.83 , pp. 2250-2257
    • Panchaud, A.1    Jung, S.2    Sa, S.3
  • 11
    • 84861860481 scopus 로고    scopus 로고
    • Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis
    • Gillet LC, Navarro P, Tate S, et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 2012;11:O111.016717
    • (2012) Mol Cell Proteomics , vol.11 , pp. O111-016717
    • Gillet, L.C.1    Navarro, P.2    Tate, S.3
  • 12
    • 20144388265 scopus 로고    scopus 로고
    • Quantitative proteomic analysis by accurate mass retention time pairs
    • Silva JC, Denny R, Dorschel C, et al. Quantitative proteomic analysis by accurate mass retention time pairs. Anal Chem 2005;77:2187-200
    • (2005) Anal Chem , vol.77 , pp. 2187-2200
    • Silva, J.C.1    Denny, R.2    Dorschel, C.3
  • 13
    • 68049114653 scopus 로고    scopus 로고
    • Precursor acquisition independent from ion count: How to dive deeper into the proteomics ocean
    • Panchaud A, Scherl A, Shaffer SA, et al. Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal Chem 2009;81: 6481-8
    • (2009) Anal Chem , vol.81 , pp. 6481-6488
    • Panchaud, A.1    Scherl, A.2    Shaffer, S.A.3
  • 14
    • 0038047154 scopus 로고    scopus 로고
    • Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer
    • Purvine S, Eppel J-T, Yi EC, Goodlett DR. Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 2003;3:847-50
    • (2003) Proteomics , vol.3 , pp. 847-850
    • Purvine, S.1    Eppel, J.-T.2    Yi, E.C.3    Goodlett, D.R.4
  • 15
    • 77951947835 scopus 로고    scopus 로고
    • XDIA: Improving on the label-free data-independent analysis
    • Carvalho PC, Han X, Xu T, et al. XDIA: improving on the label-free data-independent analysis. Bioinformatics 2010;26:847-8
    • (2010) Bioinformatics , vol.26 , pp. 847-848
    • Carvalho, P.C.1    Han, X.2    Xu, T.3
  • 16
    • 84881477986 scopus 로고    scopus 로고
    • Multiplexed MS/MS for improved data-independent acquisition
    • Egertson JD, Kuehn A, Merrihew GE, et al. Multiplexed MS/MS for improved data-independent acquisition. Nat Methods 2013;10:744-6
    • (2013) Nat Methods , vol.10 , pp. 744-746
    • Egertson, J.D.1    Kuehn, A.2    Merrihew, G.E.3
  • 17
    • 84857811076 scopus 로고    scopus 로고
    • Accurate peptide fragment mass analysis: Multiplexed peptide identification and quantification
    • Weisbrod CR, Eng JK, Hoopmann MR, et al. Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification. J Proteome Res 2012;11:1621-32
    • (2012) J Proteome Res , vol.11 , pp. 1621-1632
    • Weisbrod, C.R.1    Eng, J.K.2    Hoopmann, M.R.3
  • 18
    • 33748765574 scopus 로고    scopus 로고
    • Tandem parallel fragmentation of peptides for mass spectrometry
    • Ramos AA, Yang H, Rosen LE, Yao X Tandem parallel fragmentation of peptides for mass spectrometry. Anal Chem 2006;78: 6391-7
    • (2006) Anal Chem , vol.78 , pp. 6391-6397
    • Ramos, A.A.1    Yang, H.2    Rosen, L.E.3    Yao, X.4
  • 19
    • 84887873381 scopus 로고    scopus 로고
    • Recent advances in mass spectrometry: Data independent analysis and hyper reaction monitoring
    • Law KP, Lim YP. Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring. Expert Rev Proteomics 2013;10:551-66
    • (2013) Expert Rev Proteomics , vol.10 , pp. 551-566
    • Law, K.P.1    Lim, Y.P.2
  • 20
    • 84908552210 scopus 로고    scopus 로고
    • Multiplexed and data-independent tandem mass spectrometry for global proteome profiling
    • [Epub ahead of print]
    • Chapman JD, Goodlett DR, Masselon CD. Multiplexed and data-independent tandem mass spectrometry for global proteome profiling. Mass Spectrom Rev 2013. [Epub ahead of print]
    • (2013) Mass Spectrom Rev
    • Chapman, J.D.1    Goodlett, D.R.2    Masselon, C.D.3
  • 21
    • 31644446949 scopus 로고    scopus 로고
    • Absolute quantification of proteins by LCMSE: A virtue of parallel MS acquisition
    • Silva JC, Gorenstein M V, Li G-Z, et al. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol Cell Proteomics 2006;5:144-56
    • (2006) Mol Cell Proteomics , vol.5 , pp. 144-156
    • Silva, J.C.1    Gorenstein, M.V.2    Li, G.-Z.3
  • 22
    • 79551500036 scopus 로고    scopus 로고
    • Less label, more free: Approaches in label-free quantitative mass spectrometry
    • Neilson KA, Ali NA, Muralidharan S, et al. Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 2011;11:535-53
    • (2011) Proteomics , vol.11 , pp. 535-553
    • Neilson, K.A.1    Ali, N.A.2    Muralidharan, S.3
  • 23
    • 83055168515 scopus 로고    scopus 로고
    • Absolute quantification of the glycolytic pathway in yeast: Deployment of a complete QconCAT approach
    • Carroll KM, Simpson DM, Eyers CE, et al. Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach. Mol Cell Proteomics 2011;10:M111.007633
    • (2011) Mol Cell Proteomics , vol.10 , pp. M111-007633
    • Carroll, K.M.1    Simpson, D.M.2    Eyers, C.E.3
  • 24
    • 79956322553 scopus 로고    scopus 로고
    • Global quantification of mammalian gene expression control
    • Schwanhausser B, Busse D, Li N, et al. Global quantification of mammalian gene expression control. Nature 2011;473:337-42
    • (2011) Nature , vol.473 , pp. 337-342
    • Schwanhausser, B.1    Busse, D.2    Li, N.3
  • 25
    • 79959963697 scopus 로고    scopus 로고
    • RIBAR and xRIBAR: Methods for reproducible relative MS/MS-based label-free protein quantification
    • Colaert N, Gevaert K, Martens L. RIBAR and xRIBAR: methods for reproducible relative MS/MS-based label-free protein quantification. J Proteome Res 2011;10: 3183-9
    • (2011) J Proteome Res , vol.10 , pp. 3183-3189
    • Colaert, N.1    Gevaert, K.2    Martens, L.3
  • 26
    • 84865542140 scopus 로고    scopus 로고
    • Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli
    • Arike L, Valgepea K, Peil L, et al. Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli. J Proteomics 2012;75: 5437-48
    • (2012) J Proteomics , vol.75 , pp. 5437-5448
    • Arike, L.1    Valgepea, K.2    Peil, L.3
  • 27
    • 84859256741 scopus 로고    scopus 로고
    • To label or not to label: Applications of quantitative proteomics in neuroscience research
    • Filiou MD, Martins-de-Souza D, Guest PC, et al. To label or not to label: applications of quantitative proteomics in neuroscience research. Proteomics 2012;12:736-47
    • (2012) Proteomics , vol.12 , pp. 736-747
    • Filiou, M.D.1    Martins-De-Souza, D.2    Guest, P.C.3
  • 29
    • 84878011768 scopus 로고    scopus 로고
    • Label-free quantitative proteomics trends for protein-protein interactions
    • Tate S, Larsen B, Bonner R, Gingras A-C. Label-free quantitative proteomics trends for protein-protein interactions. J Proteomics 2013;81:91-101
    • (2013) J Proteomics , vol.81 , pp. 91-101
    • Tate, S.1    Larsen, B.2    Bonner, R.3    Gingras, A.-C.4
  • 30
    • 84865603658 scopus 로고    scopus 로고
    • An insight into iTRAQ: Where do we stand now?
    • Evans C, Noirel J, Ow SY, et al. An insight into iTRAQ: where do we stand now? Anal Bioanal Chem 2012;404:1011-27
    • (2012) Anal Bioanal Chem , vol.404 , pp. 1011-1027
    • Evans, C.1    Noirel, J.2    Ow, S.Y.3
  • 31
    • 84892403340 scopus 로고    scopus 로고
    • Assessment of reproducibility in depletion and enrichment workflows for plasma proteomics using label-free quantitative data-independent LC-MS
    • Hakimi A, Auluck J, Jones GD, et al. Assessment of reproducibility in depletion and enrichment workflows for plasma proteomics using label-free quantitative data-independent LC-MS. Proteomics 2014;14:4-13
    • (2014) Proteomics , vol.14 , pp. 4-13
    • Hakimi, A.1    Auluck, J.2    Jones, G.D.3
  • 32
    • 71649108493 scopus 로고    scopus 로고
    • Isotope coded protein label quantification of serum proteins-comparison with the label-free LC-MS and validation using the MRM approach
    • Turtoi A, Mazzucchelli GD, De Pauw E. Isotope coded protein label quantification of serum proteins-comparison with the label-free LC-MS and validation using the MRM approach. Talanta 2010;80:1487-95
    • (2010) Talanta , vol.80 , pp. 1487-1495
    • Turtoi, A.1    Mazzucchelli, G.D.2    De Pauw, E.3
  • 33
    • 72149119458 scopus 로고    scopus 로고
    • Multidimensional protein fractionation of blood proteins coupled to data-independent nanoLC-MS/MS analysis
    • Levin Y, Jaros JAJ, Schwarz E, Bahn S. Multidimensional protein fractionation of blood proteins coupled to data-independent nanoLC-MS/MS analysis. J Proteomics 2010;73:689-95
    • (2010) J Proteomics , vol.73 , pp. 689-695
    • Levin, Y.1    Jaj, J.2    Schwarz, E.3    Bahn, S.4
  • 34
    • 84884901285 scopus 로고    scopus 로고
    • Differential seminal plasma proteome according to semen retrieval in men with spinal cord injury
    • Da Silva BF, Souza GHMF, lo Turco EG, et al. Differential seminal plasma proteome according to semen retrieval in men with spinal cord injury. Fertil Steril 2013;100: 959-69
    • (2013) Fertil Steril , vol.100 , pp. 959-969
    • Da Silva, B.F.1    Ghmf, S.2    Lo Turco, E.G.3
  • 35
    • 84877128306 scopus 로고    scopus 로고
    • Proteomic analysis of human bronchoalveolar lavage fluid after subsgemental exposure
    • Foster MW, Thompson JW, Que LG, et al. Proteomic analysis of human bronchoalveolar lavage fluid after subsgemental exposure. J Proteome Res 2013;12:2194-205
    • (2013) J Proteome Res , vol.12 , pp. 2194-2205
    • Foster, M.W.1    Thompson, J.W.2    Que, L.G.3
  • 36
    • 78650087650 scopus 로고    scopus 로고
    • Protein markers for insulin-producing beta cells with higher glucose sensitivity
    • Martens GA, Jiang L, Verhaeghen K, et al. Protein markers for insulin-producing beta cells with higher glucose sensitivity. PLoS ONE 2010;5:e14214
    • (2010) PLoS ONE , vol.5 , pp. e14214
    • Martens, G.A.1    Jiang, L.2    Verhaeghen, K.3
  • 37
    • 79959976223 scopus 로고    scopus 로고
    • Label-free protein profiling of adipose-derived human stem cells under hyperosmotic treatment
    • Oswald ES, Brown LM, Bulinski JC, Hung CT. Label-free protein profiling of adipose-derived human stem cells under hyperosmotic treatment. J Proteome Res 2011;10:3050-9
    • (2011) J Proteome Res , vol.10 , pp. 3050-3059
    • Oswald, E.S.1    Brown, L.M.2    Bulinski, J.C.3    Hung, C.T.4
  • 38
    • 84885401478 scopus 로고    scopus 로고
    • Identification of differentially expressed proteins by treatment with PUGNAc in 3T3-L1 adipocytes through analysis of ATP-binding proteome
    • Lee J-E, Park J-H, Moon P-G, Baek M-C. Identification of differentially expressed proteins by treatment with PUGNAc in 3T3-L1 adipocytes through analysis of ATP-binding proteome. Proteomics 2013;13:2998-3012
    • (2013) Proteomics , vol.13 , pp. 2998-3012
    • Lee, J.-E.1    Park, J.-H.2    Moon, P.-G.3    Baek, M.-C.4
  • 39
    • 84870156802 scopus 로고    scopus 로고
    • Analysis of the rat hypothalamus proteome by data-independent label-free LC-MS/MS
    • Stelzhammer V, Amess B, Martins-de-Souza D, et al. Analysis of the rat hypothalamus proteome by data-independent label-free LC-MS/MS. Proteomics 2012;12:3386-92
    • (2012) Proteomics , vol.12 , pp. 3386-3392
    • Stelzhammer, V.1    Amess, B.2    Martins-De-Souza, D.3
  • 40
    • 84858062262 scopus 로고    scopus 로고
    • Identification of proteomic signatures associated with depression and psychotic depression in post-mortem brains from major depression patients
    • Martins-de-Souza D, Guest PC, Harris LW, et al. Identification of proteomic signatures associated with depression and psychotic depression in post-mortem brains from major depression patients. Transl Psychiatry 2012;2:e87
    • (2012) Transl Psychiatry , vol.2 , pp. e87
    • Martins-De-Souza, D.1    Guest, P.C.2    Harris, L.W.3
  • 41
    • 79251509589 scopus 로고    scopus 로고
    • Analysis of the human pituitary proteome by data independent label-free liquid chromatography tandem mass spectrometry
    • Krishnamurthy D, Levin Y, Harris LW, et al. Analysis of the human pituitary proteome by data independent label-free liquid chromatography tandem mass spectrometry. Proteomics 2011;11:495-500
    • (2011) Proteomics , vol.11 , pp. 495-500
    • Krishnamurthy, D.1    Levin, Y.2    Harris, L.W.3
  • 42
    • 83655212332 scopus 로고    scopus 로고
    • Asymmetric proteome equalization of the skeletal muscle proteome using a combinatorial hexapeptide library
    • Rivers J, Hughes C, McKenna T, et al. Asymmetric proteome equalization of the skeletal muscle proteome using a combinatorial hexapeptide library. PLoS ONE 2011;6:e28902
    • (2011) PLoS ONE , vol.6 , pp. e28902
    • Rivers, J.1    Hughes, C.2    McKenna, T.3
  • 43
    • 84873721021 scopus 로고    scopus 로고
    • A critical role for the cholesterol-associated proteolipids PLP and M6B in myelination of the central nervous system
    • Werner HB, Krämer-Albers E-M, Strenzke N, et al. A critical role for the cholesterol-associated proteolipids PLP and M6B in myelination of the central nervous system. Glia 2013;61:567-86
    • (2013) Glia , vol.61 , pp. 567-586
    • Werner, H.B.1    Krämer-Albers, E.-M.2    Strenzke, N.3
  • 44
    • 80052845560 scopus 로고    scopus 로고
    • Caspase-8 regulates TNF-a-induced epithelial necroptosis and terminal ileitis
    • Günther C, Martini E, Wittkopf N, et al. Caspase-8 regulates TNF-a-induced epithelial necroptosis and terminal ileitis. Nature 2011;477:335-9
    • (2011) Nature , vol.477 , pp. 335-339
    • Günther, C.1    Martini, E.2    Wittkopf, N.3
  • 45
    • 80755127213 scopus 로고    scopus 로고
    • Quantitative and integrative proteome analysis of peripheral nerve myelin identifies novel myelin proteins and candidate neuropathy loci
    • Patzig J, Jahn O, Tenzer S, et al. Quantitative and integrative proteome analysis of peripheral nerve myelin identifies novel myelin proteins and candidate neuropathy loci. J Neurosci 2011;31: 16369-86
    • (2011) J Neurosci , vol.31 , pp. 16369-16386
    • Patzig, J.1    Jahn, O.2    Tenzer, S.3
  • 46
    • 69849114213 scopus 로고    scopus 로고
    • Myelin proteomics: Molecular anatomy of an insulating sheath
    • Jahn O, Tenzer S, Werner HB. Myelin proteomics: molecular anatomy of an insulating sheath. Mol Neurobiol 2009;40: 55-72
    • (2009) Mol Neurobiol , vol.40 , pp. 55-72
    • Jahn, O.1    Tenzer, S.2    Werner, H.B.3
  • 48
    • 84892168084 scopus 로고    scopus 로고
    • Proteomic analyses of human cytomegalovirus strain AD169 derivatives reveal highly conserved patterns of viral and cellular proteins in infected fibroblasts
    • Reyda S, Büscher N, Tenzer S, Plachter B. Proteomic analyses of human cytomegalovirus strain AD169 derivatives reveal highly conserved patterns of viral and cellular proteins in infected fibroblasts. Viruses 2014;6:172-88
    • (2014) Viruses , vol.6 , pp. 172-188
    • Reyda, S.1    Büscher, N.2    Tenzer, S.3    Plachter, B.4
  • 49
    • 84899734394 scopus 로고    scopus 로고
    • Quantitative proteomic analysis of hepatocyte-secreted extracellular vesicles reveals candidate markers for liver toxicity
    • Rodŕiguez-Suárez E, Gonzalez E, Hughes C, et al. Quantitative proteomic analysis of hepatocyte-secreted extracellular vesicles reveals candidate markers for liver toxicity. J Proteomics 2014;103:227-40
    • (2014) J Proteomics , vol.103 , pp. 227-240
    • Rodŕiguez-Suárez, E.1    Gonzalez, E.2    Hughes, C.3
  • 50
    • 38449095118 scopus 로고    scopus 로고
    • Oligodendrocytes secrete exosomes containing major myelin and stress-protective proteins: Trophic support for axons?
    • Krämer-Albers E-M, Bretz N, Tenzer S, et al. Oligodendrocytes secrete exosomes containing major myelin and stress-protective proteins: trophic support for axons? Proteomics Clin Appl 2007;1: 1446-61
    • (2007) Proteomics Clin Appl , vol.1 , pp. 1446-1461
    • Krämer-Albers, E.-M.1    Bretz, N.2    Tenzer, S.3
  • 51
    • 84872684824 scopus 로고    scopus 로고
    • Proteomic analysis of endothelial cell secretome: A means of studying the pleiotropic effects of Hmg-CoA reductase inhibitors
    • Brioschi M, Lento S, Tremoli E, Banfi C. Proteomic analysis of endothelial cell secretome: a means of studying the pleiotropic effects of Hmg-CoA reductase inhibitors. J Proteomics 2013;78:346-61
    • (2013) J Proteomics , vol.78 , pp. 346-361
    • Brioschi, M.1    Lento, S.2    Tremoli, E.3    Banfi, C.4
  • 52
    • 80052579106 scopus 로고    scopus 로고
    • Secretome of the preimplantation human embryo by bottom-up label-free proteomics
    • Cortezzi SS, Garcia JS, Ferreira CR, et al. Secretome of the preimplantation human embryo by bottom-up label-free proteomics. Anal Bioanal Chem 2011;401:1331-9
    • (2011) Anal Bioanal Chem , vol.401 , pp. 1331-1339
    • Cortezzi, S.S.1    Garcia, J.S.2    Ferreira, C.R.3
  • 53
    • 84898731970 scopus 로고    scopus 로고
    • Comprehensive absolute quantification of the cytosolic proteome of Bacillus subtilis by data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS(E))
    • Muntel J, Fromion V, Goelzer A, et al. Comprehensive absolute quantification of the cytosolic proteome of Bacillus subtilis by data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS(E)). Mol Cell Proteomics 2014;13: 1008-19
    • (2014) Mol Cell Proteomics , vol.13 , pp. 1008-1019
    • Muntel, J.1    Fromion, V.2    Goelzer, A.3
  • 54
    • 80054097155 scopus 로고    scopus 로고
    • A historical and proteomic analysis of botulinum neurotoxin type/G
    • Terilli RR, Moura H, Woolfitt AR, et al. A historical and proteomic analysis of botulinum neurotoxin type/G. BMC Microbiol 2011;11:232
    • (2011) BMC Microbiol , vol.11 , pp. 232
    • Terilli, R.R.1    Moura, H.2    Woolfitt, A.R.3
  • 55
    • 84899924231 scopus 로고    scopus 로고
    • Proteomic analysis and label-free quantification of the large Clostridium difficile toxins
    • Moura H, Terilli RR, Woolfitt AR, et al. Proteomic analysis and label-free quantification of the large Clostridium difficile toxins. Int J Proteomics 2013;2013:293782
    • (2013) Int J Proteomics , vol.2013 , pp. 293782
    • Moura, H.1    Terilli, R.R.2    Woolfitt, A.R.3
  • 56
    • 79960763879 scopus 로고    scopus 로고
    • Quantification of proteins using data-independent analysis (MSE) in simple andcomplex samples: A systematic evaluation
    • Levin Y, Hradetzky E, Bahn S. Quantification of proteins using data-independent analysis (MSE) in simple andcomplex samples: a systematic evaluation. Proteomics 2011;11:3273-87
    • (2011) Proteomics , vol.11 , pp. 3273-3287
    • Levin, Y.1    Hradetzky, E.2    Bahn, S.3
  • 57
    • 33645725976 scopus 로고    scopus 로고
    • Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: A sweet tale
    • Silva JC, Denny R, Dorschel C, et al. Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale. Mol Cell Proteomics 2006;5: 589-607
    • (2006) Mol Cell Proteomics , vol.5 , pp. 589-607
    • Silva, J.C.1    Denny, R.2    Dorschel, C.3
  • 58
    • 67650351489 scopus 로고    scopus 로고
    • A comparison of labeling and label-free mass spectrometry-based proteomics approaches
    • Patel VJ, Thalassinos K, Slade SE, et al. A comparison of labeling and label-free mass spectrometry-based proteomics approaches. J Proteome Res 2009;8:3752-9
    • (2009) J Proteome Res , vol.8 , pp. 3752-3759
    • Patel, V.J.1    Thalassinos, K.2    Slade, S.E.3
  • 59
    • 84895071750 scopus 로고    scopus 로고
    • Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics
    • Distler U, Kuharev J, Navarro P, et al. Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics. Nat Methods 2014;11:167-70
    • (2014) Nat Methods , vol.11 , pp. 167-170
    • Distler, U.1    Kuharev, J.2    Navarro, P.3
  • 60
    • 84865583665 scopus 로고    scopus 로고
    • Using ion purity scores for enhancing quantitative accuracy and precision in complex proteomics samples
    • Geromanos SJ, Hughes C, Ciavarini S, et al. Using ion purity scores for enhancing quantitative accuracy and precision in complex proteomics samples. Anal Bioanal Chem 2012;404:1127-39
    • (2012) Anal Bioanal Chem , vol.404 , pp. 1127-1139
    • Geromanos, S.J.1    Hughes, C.2    Ciavarini, S.3
  • 61
    • 23744458105 scopus 로고    scopus 로고
    • Developing liquid chromatography ion mobility mass spectometry techniques
    • Valentine SJ, Liu X, Plasencia MD, et al. Developing liquid chromatography ion mobility mass spectometry techniques. Expert Rev Proteomics 2005;2:553-65
    • (2005) Expert Rev Proteomics , vol.2 , pp. 553-565
    • Valentine, S.J.1    Liu, X.2    Plasencia, M.D.3
  • 62
    • 84856614421 scopus 로고    scopus 로고
    • Ion mobility-mass spectrometry for structural proteomics
    • Zhong Y, Hyung S-J, Ruotolo BT. Ion mobility-mass spectrometry for structural proteomics. Expert Rev Proteomics 2012;9: 47-58
    • (2012) Expert Rev Proteomics , vol.9 , pp. 47-58
    • Zhong, Y.1    Hyung, S.-J.2    Ruotolo, B.T.3
  • 63
    • 84860464109 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics: Existing capabilities and future directions
    • Angel TE, Aryal UK, Hengel SM, et al. Mass spectrometry-based proteomics: existing capabilities and future directions. Chem Soc Rev 2012;41:3912-28
    • (2012) Chem Soc Rev , vol.41 , pp. 3912-3928
    • Angel, T.E.1    Aryal, U.K.2    Hengel, S.M.3
  • 64
    • 82755197587 scopus 로고    scopus 로고
    • Extracted Fragment Ion Mobility Distributions: A New Method for Complex Mixture Analysis
    • Lee S, Li Z, Valentine SJ, et al. Extracted Fragment Ion Mobility Distributions: a New Method for Complex Mixture Analysis. Int J Mass Spectrom 2012;309: 154-60
    • (2012) Int J Mass Spectrom , vol.309 , pp. 154-160
    • Lee, S.1    Li, Z.2    Valentine, S.J.3
  • 65
    • 79955870883 scopus 로고    scopus 로고
    • Using ion mobility data to improve peptide identification: Intrinsic amino acid size parameters
    • Valentine SJ, Ewing MA, Dilger JM, et al. Using ion mobility data to improve peptide identification: intrinsic amino acid size parameters. J Proteome Res 2011;10:2318-29
    • (2011) J Proteome Res , vol.10 , pp. 2318-2329
    • Valentine, S.J.1    Ewing, M.A.2    Dilger, J.M.3
  • 66
    • 84879391561 scopus 로고    scopus 로고
    • Improving qualitative and quantitative performance for MS(E)-based label-free proteomics
    • Bond NJ, Shliaha P V, Lilley KS, Gatto L. Improving qualitative and quantitative performance for MS(E)-based label-free proteomics. J Proteome Res 2013;12: 2340-53
    • (2013) J Proteome Res , vol.12 , pp. 2340-2353
    • Bond, N.J.1    Shliaha, P.V.2    Lilley, K.S.3    Gatto, L.4
  • 67
    • 33750988179 scopus 로고    scopus 로고
    • Toward plasma proteome profiling with ion mobility-mass spectrometry
    • Valentine SJ, Plasencia MD, Liu X, et al. Toward plasma proteome profiling with ion mobility-mass spectrometry. J Proteome Res 2006;5:2977-84
    • (2006) J Proteome Res , vol.5 , pp. 2977-2984
    • Valentine, S.J.1    Plasencia, M.D.2    Liu, X.3
  • 68
    • 76149102921 scopus 로고    scopus 로고
    • An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies
    • Baker ES, Livesay EA, Orton DJ, et al. An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies. J Proteome Res 2010;9: 997-1006
    • (2010) J Proteome Res , vol.9 , pp. 997-1006
    • Baker, E.S.1    Livesay, E.A.2    Orton, D.J.3
  • 69
    • 84894259618 scopus 로고    scopus 로고
    • Qualitative and quantitative characterization of plasma proteins when incorporating traveling wave ion mobility into a liquid chromatography-mass spectrometry workflow for biomarker discovery: Use of product ion quantitation as an alternative data analysi
    • Daly CE, Ng LL, Hakimi A, et al. Qualitative and quantitative characterization of plasma proteins when incorporating traveling wave ion mobility into a liquid chromatography-mass spectrometry workflow for biomarker discovery: use of product ion quantitation as an alternative data analysi. Anal Chem 2014;86:1972-9
    • (2014) Anal Chem , vol.86 , pp. 1972-1979
    • Daly, C.E.1    Ng, L.L.2    Hakimi, A.3
  • 70
    • 84867481985 scopus 로고    scopus 로고
    • Proteomic classification of acute leukemias by alignment-based quantitation of LC-MS/MS data sets
    • Foss EJ, Radulovic D, Stirewalt DL, et al. Proteomic classification of acute leukemias by alignment-based quantitation of LC-MS/MS data sets. J Proteome Res 2012;11: 5005-10
    • (2012) J Proteome Res , vol.11 , pp. 5005-5010
    • Foss, E.J.1    Radulovic, D.2    Stirewalt, D.L.3
  • 71
    • 84907197082 scopus 로고    scopus 로고
    • MaxLFQ allows accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction
    • Cox J, Hein MY, Luber CA, et al. MaxLFQ allows accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction. 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
  • 72
    • 84871259414 scopus 로고    scopus 로고
    • LFQuant: A label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data
    • Zhang W, Zhang J, Xu C, et al. LFQuant: a label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data. Proteomics 2012;12:3475-84
    • (2012) Proteomics , vol.12 , pp. 3475-3484
    • Zhang, W.1    Zhang, J.2    Xu, C.3
  • 73
    • 84890276007 scopus 로고    scopus 로고
    • A flexible statistical model for alignment of label-free proteomics data-incorporating ion mobility and product ion information
    • Benjamin AM, Thompson JW, Soderblom EJ, et al. A flexible statistical model for alignment of label-free proteomics data-incorporating ion mobility and product ion information. BMC Bioinformatics 2013;14:364
    • (2013) BMC Bioinformatics , vol.14 , pp. 364
    • Benjamin, A.M.1    Thompson, J.W.2    Soderblom, E.J.3
  • 74
    • 84879367507 scopus 로고    scopus 로고
    • Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies
    • Shliaha P V, Bond NJ, Gatto L, Lilley KS. Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies. J Proteome Res 2013;12:2323-39
    • (2013) J Proteome Res , vol.12 , pp. 2323-2339
    • Shliaha, P.V.1    Bond, N.J.2    Gatto, L.3    Lilley, K.S.4
  • 75
    • 84871424161 scopus 로고    scopus 로고
    • High-capacity peptide-centric platform to decode the proteomic response to brain injury
    • Cortes DF, Landis MK, Ottens AK High-capacity peptide-centric platform to decode the proteomic response to brain injury. Electrophoresis 2012;33:3712-19
    • (2012) Electrophoresis , vol.33 , pp. 3712-3719
    • Cortes, D.F.1    Landis, M.K.2    Ottens, A.K.3
  • 76
    • 84885192215 scopus 로고    scopus 로고
    • Longitudinal study of differential protein expression in an Alzheimer's mouse model lacking inducible nitric oxide synthase
    • Hoos MD, Richardson BM, Foster MW, et al. Longitudinal study of differential protein expression in an Alzheimer's mouse model lacking inducible nitric oxide synthase. J Proteome Res 2013;12:4462-77
    • (2013) J Proteome Res , vol.12 , pp. 4462-4477
    • Hoos, M.D.1    Richardson, B.M.2    Foster, M.W.3
  • 77
    • 84897469182 scopus 로고    scopus 로고
    • Post-acute brain injury urinary signature: A new resource for molecular diagnostics
    • Ottens AK, Stafflinger JE, Griffin HE, et al. Post-acute brain injury urinary signature: a new resource for molecular diagnostics. J Neurotrauma 2014;31:782-8
    • (2014) J Neurotrauma , vol.31 , pp. 782-788
    • Ottens, A.K.1    Stafflinger, J.E.2    Griffin, H.E.3
  • 78
    • 84878089252 scopus 로고    scopus 로고
    • Mast cell-deficient Kit(W-sh) "sash" mutant mice display aberrant myelopoiesis leading to the accumulation of splenocytes that act as myeloid-derived suppressor cells
    • Michel A, Schuler A, Friedrich P, et al. Mast cell-deficient Kit(W-sh) "Sash" mutant mice display aberrant myelopoiesis leading to the accumulation of splenocytes that act as myeloid-derived suppressor cells. J Immunol 2013;190:5534-44
    • (2013) J Immunol , vol.190 , pp. 5534-5544
    • Michel, A.1    Schuler, A.2    Friedrich, P.3
  • 79
    • 84895769547 scopus 로고    scopus 로고
    • Growth factor priming differentially modulates components of the extracellular matrix proteome in chondrocytes and synovium-derived stem cells
    • Alegre-Aguaron E, Sampat SR, Xiong JC, et al. Growth factor priming differentially modulates components of the extracellular matrix proteome in chondrocytes and synovium-derived stem cells. PLoS One 2014;9:e88053
    • (2014) PLoS One , vol.9 , pp. e88053
    • Alegre-Aguaron, E.1    Sampat, S.R.2    Xiong, J.C.3
  • 80
    • 84880875215 scopus 로고    scopus 로고
    • Label-free mass spectrometry proteome quantification of human embryonic kidney cells following 24 hours of sialic acid overproduction
    • Parviainen VI, Joenväära S, Tohmola N, Renkonen R. Label-free mass spectrometry proteome quantification of human embryonic kidney cells following 24 hours of sialic acid overproduction. Proteome Sci 2013;11:38
    • (2013) Proteome Sci , vol.11 , pp. 38
    • Parviainen, V.I.1    Joenväära, S.2    Tohmola, N.3    Renkonen, R.4
  • 81
    • 84879360770 scopus 로고    scopus 로고
    • Proteome-wide characterization of the RNA-binding protein RALY-interactome using the in vivo-biotinylation-pulldown-quant (iBioPQ) approach
    • Tenzer S, Moro A, Kuharev J, et al. Proteome-wide characterization of the RNA-binding protein RALY-interactome using the in vivo-biotinylation-pulldown-quant (iBioPQ) approach. J Proteome Res 2013;12:2869-84
    • (2013) J Proteome Res , vol.12 , pp. 2869-2884
    • Tenzer, S.1    Moro, A.2    Kuharev, J.3
  • 82
    • 84892685001 scopus 로고    scopus 로고
    • Regulation of ferroptotic cancer cell death by GPX4
    • Yang WS, SriRamaratnam R, Welsch ME, et al. Regulation of ferroptotic cancer cell death by GPX4. Cell 2014;156:317-31
    • (2014) Cell , vol.156 , pp. 317-331
    • Yang, W.S.1    Sriramaratnam, R.2    Welsch, M.E.3
  • 83
    • 84885483569 scopus 로고    scopus 로고
    • Rapid formation of plasma protein corona critically affects nanoparticle pathophysiology
    • Tenzer S, Docter D, Kuharev J, et al. Rapid formation of plasma protein corona critically affects nanoparticle pathophysiology. Nat Nanotechnol 2013;8: 772-81
    • (2013) Nat Nanotechnol , vol.8 , pp. 772-781
    • Tenzer, S.1    Docter, D.2    Kuharev, J.3
  • 84
    • 84892537410 scopus 로고    scopus 로고
    • Protein identification and quantification by data-independent acquisition and multi-parallel collision-induced dissociation mass spectrometry (MS(E)) in the chloroplast stroma proteome
    • Helm S, Dobritzsch D, Rodiger A, et al. Protein identification and quantification by data-independent acquisition and multi-parallel collision-induced dissociation mass spectrometry (MS(E)) in the chloroplast stroma proteome. J Proteomics 2014;98:79-89
    • (2014) J Proteomics , vol.98 , pp. 79-89
    • Helm, S.1    Dobritzsch, D.2    Rodiger, A.3
  • 85
    • 84873334559 scopus 로고    scopus 로고
    • Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes
    • Fan Y, Thompson JW, Dubois LG, et al. Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes. J Proteome Res 2013;12:704-18
    • (2013) J Proteome Res , vol.12 , pp. 704-718
    • Fan, Y.1    Thompson, J.W.2    Dubois, L.G.3
  • 86
    • 84899827838 scopus 로고    scopus 로고
    • Multiple enzymatic digestions and ion mobility separation improve quantification of bacterial ribosomal proteins by data independent acquisition liquid chromatography-mass spectrometry
    • Dator RP, Gaston KW, Limbach PA. Multiple enzymatic digestions and ion mobility separation improve quantification of bacterial ribosomal proteins by data independent acquisition liquid chromatography-mass spectrometry. Anal Chem 2014;86:4264-70
    • (2014) Anal Chem , vol.86 , pp. 4264-4270
    • Dator, R.P.1    Gaston, K.W.2    Limbach, P.A.3
  • 87
    • 84887195879 scopus 로고    scopus 로고
    • Data-independent acquisition (MSE) with ion mobility provides a systematic method for analysis of a bacteriophage structural proteome
    • Moran D, Cross T, Brown LM, et al. Data-independent acquisition (MSE) with ion mobility provides a systematic method for analysis of a bacteriophage structural proteome. J Virol Methods 2014;195:9-17
    • (2014) J Virol Methods , vol.195 , pp. 9-17
    • Moran, D.1    Cross, T.2    Brown, L.M.3
  • 88
    • 84877905853 scopus 로고    scopus 로고
    • Quantitative label-free proteomics for discovery of biomarkers in cerebrospinal fluid: Assessment of technical and inter-individual variation
    • Perrin RJ, Payton JE, Malone JP, et al. Quantitative label-free proteomics for discovery of biomarkers in cerebrospinal fluid: assessment of technical and inter-individual variation. PLoS One 2013;8:e64314
    • (2013) PLoS One , vol.8 , pp. e64314
    • Perrin, R.J.1    Payton, J.E.2    Malone, J.P.3
  • 89
    • 84877133620 scopus 로고    scopus 로고
    • Sources of technical variability in quantitative LC-MS proteomics: Human brain tissue sample analysis
    • Piehowski PD, Petyuk VA, Orton DJ, et al. Sources of technical variability in quantitative LC-MS proteomics: human brain tissue sample analysis. J Proteome Res 2013;12:2128-37
    • (2013) J Proteome Res , vol.12 , pp. 2128-2137
    • Piehowski, P.D.1    Petyuk, V.A.2    Orton, D.J.3
  • 90
    • 84890571201 scopus 로고    scopus 로고
    • Data processing methods and quality control strategies for label-free LC-MS protein quantification
    • Sandin M, Teleman J, Malmström J, Levander F. Data processing methods and quality control strategies for label-free LC-MS protein quantification. Biochim Biophys Acta 2014;1844:29-41
    • (2014) Biochim Biophys Acta , vol.1844 , pp. 29-41
    • Sandin, M.1    Teleman, J.2    Malmström, J.3    Levander, F.4
  • 91
    • 84909960220 scopus 로고    scopus 로고
    • Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics
    • [Epub ahead of print]
    • Helm D, Vissers JP, Hughes CJ, et al. Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics. Mol Cell Proteomics 2014; [Epub ahead of print]
    • (2014) Mol Cell Proteomics
    • Helm, D.1    Vissers, J.P.2    Hughes, C.J.3
  • 92
    • 84902841439 scopus 로고    scopus 로고
    • High resolution trapped ion mobility spectrometery of peptides
    • Silveira JA, Ridgeway ME, Park MA. High resolution trapped ion mobility spectrometery of peptides. Anal Chem 2014;86:5624-7
    • (2014) Anal Chem , vol.86 , pp. 5624-5627
    • Silveira, J.A.1    Ridgeway, M.E.2    Park, M.A.3
  • 93
    • 84898665956 scopus 로고    scopus 로고
    • OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data
    • Rost HL, Rosenberger G, Navarro P, et al. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol 2014;32:219-23
    • (2014) Nat Biotechnol , vol.32 , pp. 219-223
    • Rost, H.L.1    Rosenberger, G.2    Navarro, P.3
  • 94
    • 84892877597 scopus 로고    scopus 로고
    • E)-based label-free proteomics and HRMS quantitation of small molecules
    • Liu S, Chen X, Yan Z, et al. E)-based label-free proteomics and HRMS quantitation of small molecules. Proteomics 2014;14:169-80
    • (2014) Proteomics , vol.14 , pp. 169-180
    • Liu, S.1    Chen, X.2    Yan, Z.3
  • 95
    • 84910594793 scopus 로고    scopus 로고
    • Pubmed
    • Pubmed. Available from: ncbi.nlm.nih.gov/entrez/query.fcgi


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.