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2
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0032875697
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Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
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Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17:1999;994-999.
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Gygi, S.P.1
Rist, B.2
Gerber, S.A.3
Turecek, F.4
Gelb, M.H.5
Aebersold, R.6
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3
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0035282172
-
Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer
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The use of MALDI for quantitation was demonstrated with labeled protein standards at approximately 12% for singly charged species. The ability to preserve the separated peptides for repeated analyses and to limit CID to peptides that are potentially more biologically interesting makes this an attractive alternative to ESI-MS approaches.
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Griffin T.J., Gygi S.P., Rist B., Aebersold R., Loboda A., Jilkine A., Ens W., Standing K.G. Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer. Anal. Chem. 73:2001;978-986 The use of MALDI for quantitation was demonstrated with labeled protein standards at approximately 12% for singly charged species. The ability to preserve the separated peptides for repeated analyses and to limit CID to peptides that are potentially more biologically interesting makes this an attractive alternative to ESI-MS approaches.
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Anal. Chem.
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Griffin, T.J.1
Gygi, S.P.2
Rist, B.3
Aebersold, R.4
Loboda, A.5
Jilkine, A.6
Ens, W.7
Standing, K.G.8
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4
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0035563654
-
Toward a high-throughput approach to quantitative proteomic analysis: Expression-dependent protein identification by mass spectrometry
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Griffin T.J., Han D.K., Gygi S.P., Rist B., Lee H., Aebersold R., Parker K.C. Toward a high-throughput approach to quantitative proteomic analysis: expression-dependent protein identification by mass spectrometry. J. Am. Soc. Mass Spectrom. 12:2001;1238-1246.
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J. Am. Soc. Mass Spectrom.
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Griffin, T.J.1
Han, D.K.2
Gygi, S.P.3
Rist, B.4
Lee, H.5
Aebersold, R.6
Parker, K.C.7
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5
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0034789979
-
Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry
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Differentiation of cell-surface proteins of human myeloid leukemia (HL-60) cells induced by phorbol 12-myristate 13-acetate (PMA) was probed using ICAT. Some previously unidentified changes in protein abundance were detected, particularly changes in the various isoforms of PMA activation of protein kinase C, Src protein kinases and protein phosphatases. As the authors state, proteins that lack cysteinyl residues, are in very low abundance or are very hydrophobic, would not be detected by this technique. However, most proteins identified did not exhibit significant changes in relative abundance.
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Han D.K., Eng J., Zhou H., Aebersold R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19:2001;946-951 Differentiation of cell-surface proteins of human myeloid leukemia (HL-60) cells induced by phorbol 12-myristate 13-acetate (PMA) was probed using ICAT. Some previously unidentified changes in protein abundance were detected, particularly changes in the various isoforms of PMA activation of protein kinase C, Src protein kinases and protein phosphatases. As the authors state, proteins that lack cysteinyl residues, are in very low abundance or are very hydrophobic, would not be detected by this technique. However, most proteins identified did not exhibit significant changes in relative abundance.
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Nat. Biotechnol.
, vol.19
, pp. 946-951
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Han, D.K.1
Eng, J.2
Zhou, H.3
Aebersold, R.4
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6
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0036391454
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Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags
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The use of multidimensional chromatography (offline SCX, offline avidin affinity chromatography, and online ESI-μLC-MS/MS) was used to increase the identification and quantification of ICAT-labeled peptides from yeast grown in the presence of either galactose or ethanol as the carbon source. In addition, ICAT labeling and data-dependent MS/MS acquisition methods were evaluated to optimize peptide identification. A total of 986 unique proteins were identified using the three-dimensional approach, a tenfold increase over the one-dimensional μLC separation alone. The increased peak capacity enabled the detection of low abundance proteins.
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Gygi S.P., Rist B., Griffin T.J., Eng J., Aebersold R. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J. Proteome. Res. 1:2002;47-54 The use of multidimensional chromatography (offline SCX, offline avidin affinity chromatography, and online ESI-μLC-MS/MS) was used to increase the identification and quantification of ICAT-labeled peptides from yeast grown in the presence of either galactose or ethanol as the carbon source. In addition, ICAT labeling and data-dependent MS/MS acquisition methods were evaluated to optimize peptide identification. A total of 986 unique proteins were identified using the three-dimensional approach, a tenfold increase over the one-dimensional μLC separation alone. The increased peak capacity enabled the detection of low abundance proteins.
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(2002)
J. Proteome. Res.
, vol.1
, pp. 47-54
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Gygi, S.P.1
Rist, B.2
Griffin, T.J.3
Eng, J.4
Aebersold, R.5
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7
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0036545614
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Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae
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Griffin T.J., Gygi S.P., Ideker T., Rist B., Eng J., Hood L., Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell Proteomics. 1:2002;323-333.
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Mol. Cell Proteomics.
, vol.1
, pp. 323-333
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Griffin, T.J.1
Gygi, S.P.2
Ideker, T.3
Rist, B.4
Eng, J.5
Hood, L.6
Aebersold, R.7
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8
-
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0036303251
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Proteome analysis of camptothecin-treated cortical neurons using isotope-coded affinity tags
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Protein expression in control and camptothecin-treated mouse cortical neurons was probed with ICAT and ESI-μLC-MS using either ion-trap MS or FTICR-MS. In this study, 129 unique proteins were identified with 23% having relative abundance ratios of greater than 1.7 or were unique to either the camptothecin-treated or the control proteome. It was noted that several proteins involved in carbohydrate metabolism (e.g. pyruvate dehydrogenase E1 β-subunit and lactate dehydrogenase 2) were upregulated in the camptothecin-treated cells.
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Yu L.R., Johnson M.D., Conrads T.P., Smith R.D., Morrison R.S., Veenstra T.D. Proteome analysis of camptothecin-treated cortical neurons using isotope-coded affinity tags. Electrophoresis. 23:2002;1591-1598 Protein expression in control and camptothecin-treated mouse cortical neurons was probed with ICAT and ESI-μLC-MS using either ion-trap MS or FTICR-MS. In this study, 129 unique proteins were identified with 23% having relative abundance ratios of greater than 1.7 or were unique to either the camptothecin-treated or the control proteome. It was noted that several proteins involved in carbohydrate metabolism (e.g. pyruvate dehydrogenase E1 β-subunit and lactate dehydrogenase 2) were upregulated in the camptothecin-treated cells.
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(2002)
Electrophoresis
, vol.23
, pp. 1591-1598
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Yu, L.R.1
Johnson, M.D.2
Conrads, T.P.3
Smith, R.D.4
Morrison, R.S.5
Veenstra, T.D.6
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9
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0035477025
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Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis
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Smolka M.B., Zhou H., Purkayastha S., Aebersold R. Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Anal. Biochem. 297:2001;25-31.
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(2001)
Anal. Biochem.
, vol.297
, pp. 25-31
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Smolka, M.B.1
Zhou, H.2
Purkayastha, S.3
Aebersold, R.4
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10
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0036049889
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Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry
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Smolka M., Zhou H., Aebersold R. Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry. Mol. Cell Proteomics. 1:2002;19-29.
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Mol. Cell Proteomics.
, vol.1
, pp. 19-29
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Smolka, M.1
Zhou, H.2
Aebersold, R.3
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11
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0036712835
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Development of a multiplexed microcapillary liquid chromatography system for high-throughput proteome analysis
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Lee H., Griffin T.J., Gygi S.P., Rist B., Aebersold R. Development of a multiplexed microcapillary liquid chromatography system for high-throughput proteome analysis. Anal. Chem. 74:2002;4353-4360.
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(2002)
Anal. Chem.
, vol.74
, pp. 4353-4360
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Lee, H.1
Griffin, T.J.2
Gygi, S.P.3
Rist, B.4
Aebersold, R.5
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12
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0035499083
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Fractionation of isotopically labeled peptides in quantitative proteomics
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Zhang R., Sioma C.S., Wang S., Regnier F.E. Fractionation of isotopically labeled peptides in quantitative proteomics. Anal. Chem. 73:2001;5142-5149.
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Anal. Chem.
, vol.73
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Zhang, R.1
Sioma, C.S.2
Wang, S.3
Regnier, F.E.4
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13
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0036523809
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Minimizing resolution of isotopically coded peptides in comparative proteomics
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Zhang R., Regnier F.E. Minimizing resolution of isotopically coded peptides in comparative proteomics. J. Proteome. Res. 1:2002;139-147.
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J. Proteome. Res.
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Zhang, R.1
Regnier, F.E.2
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14
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0036682618
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Controlling deuterium isotope effects in comparative proteomics
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Zhang R., Sioma C.S., Thompson R.A., Xiong L., Regnier F.E. Controlling deuterium isotope effects in comparative proteomics. Anal. Chem. 74:2002;3662-3669.
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(2002)
Anal. Chem.
, vol.74
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Zhang, R.1
Sioma, C.S.2
Thompson, R.A.3
Xiong, L.4
Regnier, F.E.5
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15
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0037093117
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Low-energy collision-induced dissociation fragmentation analysis of cysteinyl-modified peptides
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3+ peptides searched against databases using SEQUEST. Due to the label, CID at lower amplitude settings resulted in lower SEQUEST scores for labeled peptides when compared with their unmodified counterparts. At a sufficient CID amplitude setting (35%), both labeled and unlabeled peptides were correctly identified by SEQUEST.
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3+ peptides searched against databases using SEQUEST. Due to the label, CID at lower amplitude settings resulted in lower SEQUEST scores for labeled peptides when compared with their unmodified counterparts. At a sufficient CID amplitude setting (35%), both labeled and unlabeled peptides were correctly identified by SEQUEST.
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(2002)
Anal. Chem.
, vol.74
, pp. 2284-2292
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Borisov, O.V.1
Goshe, M.B.2
Conrads, T.P.3
Rakov, V.S.4
Veenstra, T.D.5
Smith, R.D.6
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16
-
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0036246088
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Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry
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13C isotope coding system and employing a non-amino-acid linker to facilitate quantitation and identification.
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13C isotope coding system and employing a non-amino-acid linker to facilitate quantitation and identification.
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(2002)
Nat. Biotechnol.
, vol.20
, pp. 512-515
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Zhou, H.1
Ranish, J.A.2
Watts, J.D.3
Aebersold, R.4
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17
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0036645730
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Quantitation of neuropeptides in Cpe(fat)/Cpe(fat) mice using differential isotopic tags and mass spectrometry
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Che F.Y., Fricker L.D. Quantitation of neuropeptides in Cpe(fat)/Cpe(fat) mice using differential isotopic tags and mass spectrometry. Anal. Chem. 74:2002;3190-3198.
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(2002)
Anal. Chem.
, vol.74
, pp. 3190-3198
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Che, F.Y.1
Fricker, L.D.2
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18
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0034604802
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Strategy for qualitative and quantitative analysis in proteomics based on signature peptides
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Ji J., Chakraborty A., Geng M., Zhang X., Amini A., Bina M., Regnier F. Strategy for qualitative and quantitative analysis in proteomics based on signature peptides. J. Chromatogr. B Biomed. Sci. Appl. 745:2000;197-210.
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J. Chromatogr. B Biomed. Sci. Appl.
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Ji, J.1
Chakraborty, A.2
Geng, M.3
Zhang, X.4
Amini, A.5
Bina, M.6
Regnier, F.7
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19
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0033956669
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Signature-peptide approach to detecting proteins in complex mixtures
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Geng M., Ji J., Regnier F.E. Signature-peptide approach to detecting proteins in complex mixtures. J. Chromatogr. A. 870:2000;295-313.
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J. Chromatogr. A
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Geng, M.1
Ji, J.2
Regnier, F.E.3
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20
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0034282457
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Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety
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Munchbach M., Quadroni M., Miotto G., James P. Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety. Anal. Chem. 72:2000;4047-4057.
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Anal. Chem.
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Munchbach, M.1
Quadroni, M.2
Miotto, G.3
James, P.4
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21
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0035801716
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Synthesis of D-labeled N-alkylmaleimides and application to quantitative peptide analysis by isotope differential mass spectrometry
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Niwayama S., Kurono S., Matsumoto H. Synthesis of D-labeled N-alkylmaleimides and application to quantitative peptide analysis by isotope differential mass spectrometry. Bioorg. Med. Chem. Lett. 11:2001;2257-2261.
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Bioorg. Med. Chem. Lett.
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Niwayama, S.1
Kurono, S.2
Matsumoto, H.3
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22
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0036463388
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Selective detection of membrane proteins without antibodies: A mass spectrometric version of the western blot
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Arnott D., Kishiyama A., Luis E.A., Ludlum S.G., Marsters J.C. Jr., Stults J.T. Selective detection of membrane proteins without antibodies: a mass spectrometric version of the western blot. Mol. Cell Proteomics. 1:2002;148-156.
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Mol. Cell Proteomics.
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Arnott, D.1
Kishiyama, A.2
Luis, E.A.3
Ludlum, S.G.4
Marsters J.C., Jr.5
Stults, J.T.6
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23
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0035543071
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A novel multifunctional labeling reagent for enhanced protein characterization with mass spectrometry
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Peters E.C., Horn D.M., Tully D.C., Brock A. A novel multifunctional labeling reagent for enhanced protein characterization with mass spectrometry. Rapid. Commun. Mass Spectrom. 15:2001;2387-2392.
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(2001)
Rapid. Commun. Mass Spectrom.
, vol.15
, pp. 2387-2392
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Peters, E.C.1
Horn, D.M.2
Tully, D.C.3
Brock, A.4
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24
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0035958567
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Proteomics based on selecting and quantifying cysteine-containing peptides by covalent chromatography
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Wang S., Regnier F.E. Proteomics based on selecting and quantifying cysteine-containing peptides by covalent chromatography. J. Chromatogr. A. 924:2001;345-357.
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(2001)
J. Chromatogr. A
, vol.924
, pp. 345-357
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Wang, S.1
Regnier, F.E.2
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25
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0037040565
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Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates
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This paper describes a method to select for Cys- and His-containing peptides after differential labeling using perproteo- and perdeutero-succinic anhydride. The approach was demonstrated by quantifying isopropyl-β-D-thiogalactopyranoside-induced changes in plasmid-bearing E. coli. However, it also provides several immobilized affinity and chemical derivation techniques that can be applied to other applications or fractionations to increase proteome coverage using some of the more advanced ESI-μLC-MS-based approaches.
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Wang S., Zhang X., Regnier F.E. Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates. J. Chromatogr. A. 949:2002;153-162 This paper describes a method to select for Cys- and His-containing peptides after differential labeling using perproteo- and perdeutero-succinic anhydride. The approach was demonstrated by quantifying isopropyl-β-D-thiogalactopyranoside-induced changes in plasmid-bearing E. coli. However, it also provides several immobilized affinity and chemical derivation techniques that can be applied to other applications or fractionations to increase proteome coverage using some of the more advanced ESI-μLC-MS-based approaches.
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(2002)
J. Chromatogr. A
, vol.949
, pp. 153-162
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Wang, S.1
Zhang, X.2
Regnier, F.E.3
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26
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0037040607
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Global internal standard technology for comparative proteomics
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Chakraborty A., Regnier F.E. Global internal standard technology for comparative proteomics. J. Chromatogr. A. 949:2002;173-184.
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(2002)
J. Chromatogr. A
, vol.949
, pp. 173-184
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Chakraborty, A.1
Regnier, F.E.2
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27
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0034921817
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Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation
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Goodlett D.R., Keller A., Watts J.D., Newitt R., Yi E.C., Purvine S., Eng J.K., von Haller P., Aebersold R., Kolker E. Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation. Rapid Commun. Mass Spectrom. 15:2001;1214-1221.
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(2001)
Rapid Commun. Mass Spectrom.
, vol.15
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Goodlett, D.R.1
Keller, A.2
Watts, J.D.3
Newitt, R.4
Yi, E.C.5
Purvine, S.6
Eng, J.K.7
Von Haller, P.8
Aebersold, R.9
Kolker, E.10
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28
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0036789268
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Acid-labile isotope-coded extractants: A class of reagents for quantitative mass spectrometric analysis of complex protein mixtures
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The ALICE method uses chemically modified resins for enhanced Cys-peptide capture. A mixture of eight test proteins using ALICE exhibited an accuracy of 5% with an average precision of approximately 10%. However, ALICE was not used on a proteome sample.
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Qiu Y., Sousa E.A., Hewick R.M., Wang J.H. Acid-labile isotope-coded extractants: a class of reagents for quantitative mass spectrometric analysis of complex protein mixtures. Anal. Chem. 74:2002;4969-4979 The ALICE method uses chemically modified resins for enhanced Cys-peptide capture. A mixture of eight test proteins using ALICE exhibited an accuracy of 5% with an average precision of approximately 10%. However, ALICE was not used on a proteome sample.
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(2002)
Anal. Chem.
, vol.74
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Qiu, Y.1
Sousa, E.A.2
Hewick, R.M.3
Wang, J.H.4
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29
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0034582298
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Proteome analysis using selective incorporation of isotopically labeled amino acids
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Veenstra T.D., Martinovic S., Anderson G.A., Pasa-Tolic L., Smith R.D. Proteome analysis using selective incorporation of isotopically labeled amino acids. J. Am. Soc. Mass Spectrom. 11:2000;78-82.
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J. Am. Soc. Mass Spectrom.
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Veenstra, T.D.1
Martinovic, S.2
Anderson, G.A.3
Pasa-Tolic, L.4
Smith, R.D.5
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30
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0034654593
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Site-specific mass tagging with stable isotopes in proteins for accurate and efficient protein identification
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Chen X., Smith L.M., Bradbury E.M. Site-specific mass tagging with stable isotopes in proteins for accurate and efficient protein identification. Anal. Chem. 72:2000;1134-1143.
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Anal. Chem.
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Chen, X.1
Smith, L.M.2
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0035886986
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Peptide mass mapping constrained with stable isotope-tagged peptides for identification of protein mixtures
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Hunter T.C., Yang L., Zhu H., Majidi V., Bradbury E.M., Chen X. Peptide mass mapping constrained with stable isotope-tagged peptides for identification of protein mixtures. Anal. Chem. 73:2001;4891-4902.
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Anal. Chem.
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Hunter, T.C.1
Yang, L.2
Zhu, H.3
Majidi, V.4
Bradbury, E.M.5
Chen, X.6
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32
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0036164157
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Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome-wide level
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Martinovic S., Veenstra T.D., Anderson G.A., Pasa-Tolic L., Smith R.D. Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome-wide level. J. Mass Spectrom. 37:2002;99-107.
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J. Mass Spectrom.
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Martinovic, S.1
Veenstra, T.D.2
Anderson, G.A.3
Pasa-Tolic, L.4
Smith, R.D.5
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33
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0036535518
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Residue-specific mass signatures for the efficient detection of protein modifications by mass spectrometry
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Zhu H., Hunter T.C., Pan S., Yau P.M., Bradbury E.M., Chen X. Residue-specific mass signatures for the efficient detection of protein modifications by mass spectrometry. Anal. Chem. 74:2002;1687-1694.
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Anal. Chem.
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Zhu, H.1
Hunter, T.C.2
Pan, S.3
Yau, P.M.4
Bradbury, E.M.5
Chen, X.6
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34
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0036583926
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Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
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3 were used to perform relative quantitation of changes in protein expression during muscle cell differentiation. Glyceraldehyde-3-phosphate dehydrogenase, pyruvate kinase M2, and fibronectin were observed to be upregulated. It was also noted that quantitation was sometimes complicated by the complexity of the MS spectrum, but this would be alleviated if μLC were used. The error of quantitation between different peptides of the same protein was estimated to be ≤25%.
-
3 were used to perform relative quantitation of changes in protein expression during muscle cell differentiation. Glyceraldehyde-3-phosphate dehydrogenase, pyruvate kinase M2, and fibronectin were observed to be upregulated. It was also noted that quantitation was sometimes complicated by the complexity of the MS spectrum, but this would be alleviated if μLC were used. The error of quantitation between different peptides of the same protein was estimated to be ≤25%.
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Mol. Cell Proteomics.
, vol.1
, pp. 376-386
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Ong, S.E.1
Blagoev, B.2
Kratchmarova, I.3
Kristensen, D.B.4
Steen, H.5
Pandey, A.6
Mann, M.7
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35
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0036665484
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Quantitative analysis of the yeast proteome by incorporation of isotopically labeled leucine
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Jiang H., English A.M. Quantitative analysis of the yeast proteome by incorporation of isotopically labeled leucine. J. Proteome. Res. 1:2002;345-350.
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J. Proteome. Res.
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Jiang, H.1
English, A.M.2
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36
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0036787711
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High-throughput global peptide proteomic analysis by combining stable isotope amino acid labeling and data-dependent multiplexed-MS/MS
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Berger S.J., Lee S.-W., Anderson G.A., Pasa-Tolic L., Tolic N., Shen Y., Zhao R., Smith R.D. High-throughput global peptide proteomic analysis by combining stable isotope amino acid labeling and data-dependent multiplexed-MS/MS. Anal. Chem. 74:2002;4994-5000.
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Anal. Chem.
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Berger, S.J.1
Lee, S.-W.2
Anderson, G.A.3
Pasa-Tolic, L.4
Tolic, N.5
Shen, Y.6
Zhao, R.7
Smith, R.D.8
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37
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0035983404
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A method to evaluate tryptic digestion efficiency for high-throughput proteome analyses
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Wierenga S.K., Zocher M.J., Mirus M.M., Conrads T.P., Goshe M.B., Veenstra T.D. A method to evaluate tryptic digestion efficiency for high-throughput proteome analyses. Rapid Commun. Mass Spectrom. 16:2002;1404-1408.
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Rapid Commun. Mass Spectrom.
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Wierenga, S.K.1
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Mirus, M.M.3
Conrads, T.P.4
Goshe, M.B.5
Veenstra, T.D.6
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38
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Accurate quantitation of protein expression and site-specific phosphorylation
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Oda Y., Huang K., Cross F.R., Cowburn D., Chait B.T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. U.S.A. 96:1999;6591-6596.
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15N ratio was made on the same peptide pairs observed in all three analyses and indicated that any protein abundance changes greater than 30% covering one order of magnitude can be confidently measured using ion trap-MS. The variation between labeled samples revealed the need for inverse isotope labeling to verify changes in protein abundance.
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15N ratio was made on the same peptide pairs observed in all three analyses and indicated that any protein abundance changes greater than 30% covering one order of magnitude can be confidently measured using ion trap-MS. The variation between labeled samples revealed the need for inverse isotope labeling to verify changes in protein abundance.
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15N -metabolic labeling
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15N -metabolic labeling and cysteinyl affinity tags was presented as an alternative to ICAT quantitation of proteomes and is the first reported use of metabolic labeling applied to a mammalian cell line.
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15N -metabolic labeling and cysteinyl affinity tags was presented as an alternative to ICAT quantitation of proteomes and is the first reported use of metabolic labeling applied to a mammalian cell line.
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Lipton M.S., Pasa-Tolic L., Anderson G.A., Anderson D.J., Auberry D.L., Battista J.R., Daly M.J., Fredrickson J., Hixson K.K., Kostandarithes H.et al. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc. Natl. Acad. Sci. U.S.A. 99:2002;11049-11054.
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Pasa-Tolic L., Harkewicz R., Anderson G.A., Tolic N., Shen Y., Zhao R., Thrall B., Masselon C., Smith R.D. Increased proteome coverage for quantitative peptide abundance measurements based upon high performance separations and DREAMS FTICR mass spectrometry. J. Am. Soc. Mass Spectrom. 13:2002;954-963.
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Kosaka T., Takazawa T., Nakamura T. Identification and C-terminal characterization of proteins from two-dimensional polyacrylamide gels by a combination of isotopic labeling and nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 72:2000;1179-1185.
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18O labeling was also introduced.
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18O labeling was also introduced.
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15N -metabolic labeling/mass spectrometry for comparative proteomics and rapid identification of protein markers/targets Rapid Commun. Mass Spectrom. 16:2002;1389-1397.
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This paper describes the first experimental report of an isotope-coding approach in conjunction with an affinity tag to enrich and quantify phosphoproteins. A PhIAT reagent, containing a nucleophilic sulfhydryl and an isotopic label covalently linked to a biotin moiety, was synthesized and could be used to reduce the pSer and pThr derivatization into a one step process.
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Goshe M.B., Conrads T.P., Panisko E.A., Angell N.H., Veenstra T.D., Smith R.D. Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. Anal. Chem. 73:2001;2578-2586 This paper describes the first experimental report of an isotope-coding approach in conjunction with an affinity tag to enrich and quantify phosphoproteins. A PhIAT reagent, containing a nucleophilic sulfhydryl and an isotopic label covalently linked to a biotin moiety, was synthesized and could be used to reduce the pSer and pThr derivatization into a one step process.
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Goshe, M.B.1
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55
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This work extended the PhIAT approach to using μLC-MS/MS to sequence phosphopeptides and identify the sites(s) of phosphorylation for low-level phosphoproteins. Details involving the quantitation of phosphorylation state using PhIAT were also discussed.
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Goshe M.B., Veenstra T.D., Panisko E.A., Conrads T.P., Angell N.H., Smith R.D. Phosphoprotein isotope-coded affinity tags: application to the enrichment and identification of low-abundance phosphoproteins. Anal. Chem. 74:2002;607-616 This work extended the PhIAT approach to using μLC-MS/MS to sequence phosphopeptides and identify the sites(s) of phosphorylation for low-level phosphoproteins. Details involving the quantitation of phosphorylation state using PhIAT were also discussed.
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Anal. Chem.
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Oda Y., Nagasu T., Chait B.T. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat. Biotechnol. 19:2001;379-382.
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0035072715
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A systematic approach to the analysis of protein phosphorylation
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2H atoms would enable differences in relative phosphopeptide abundance to be quantified.
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2H atoms would enable differences in relative phosphopeptide abundance to be quantified.
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Nat. Biotechnol.
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Zhou, H.1
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Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae
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This article describes an elegant method of 'phosphoprofiling' using esterification of the carboxylate groups of peptides and IMAC to enhance detection and identification of phosphopeptides when coupled to μLC-MS/MS. Although not experimentally demonstrated, the authors mention that comparative proteomics could be performed by differentially esterifying the carboxylic acid groups using methanol (control) and deuterated methanol (experimental).
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Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20:2002;301-305 This article describes an elegant method of 'phosphoprofiling' using esterification of the carboxylate groups of peptides and IMAC to enhance detection and identification of phosphopeptides when coupled to μLC-MS/MS. Although not experimentally demonstrated, the authors mention that comparative proteomics could be performed by differentially esterifying the carboxylic acid groups using methanol (control) and deuterated methanol (experimental).
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Nat. Biotechnol.
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Ficarro, S.B.1
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Hunt, D.F.7
White, F.M.8
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