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Volumn 7, Issue 1, 2003, Pages 70-77

Quantitative proteomics using mass spectrometry

Author keywords

[No Author keywords available]

Indexed keywords

ISOTOPE; PROTEIN; PROTEOME;

EID: 0037304325     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(02)00010-8     Document Type: Review
Times cited : (95)

References (54)
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    • 15N -enriched media and labeling cysteines with an affinity tag for purification of cysteine-containing peptides is described. The cysteine-containing peptides were analysed by LC-FT-ICR MS. They showed that this approach can be used for bacterial cultures as well as mammalian cultures.
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    • 15N -enriched media. These two cultures were mixed and the proteins extracted from the whole cell lysate were digested with trypsin. This complex peptide mixture is first separated by multidimensional LC and then analysed using an LCQ instrument. The identification of more than 800 proteins in a single experiment indicates the great potential of this approach for high-throughput quantitative proteomics.
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    • 15N -enriched media. The advantage of this approach is that the use of isotopically labeled leucine is more suitable to cells of mammalian origin. Although it seems to be of general use for culture cells it could not be applied to body fluids or tissues.
    • 15N -enriched media. The advantage of this approach is that the use of isotopically labeled leucine is more suitable to cells of mammalian origin. Although it seems to be of general use for culture cells it could not be applied to body fluids or tissues.
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    • Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry
    • This study shows that differential labeling with ICAT reagents can be successfully used in a 2D-PAGE experiment. However the affinity purification and therefore the affinity tags are not needed in this kind of experiment and other, simpler procedures would be more suitable.
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    • A method to identify and simultaneously determine the relative quantities of proteins isolated by gel electrophoresis
    • This article further extends the use of deuterated acrylamide to quantitative proteomics. Two complex protein mixtures were separately labeled with acrylamide and deuterated acrylamide before electrophoresis. The ratios between the two isotopic distributions were used for reliably quantification of several proteins present, in ratios from 1:1 to 1:10.
    • Sechi S. A method to identify and simultaneously determine the relative quantities of proteins isolated by gel electrophoresis. Rapid Commun. Mass Spectrom. 16:2002;1416-1424 This article further extends the use of deuterated acrylamide to quantitative proteomics. Two complex protein mixtures were separately labeled with acrylamide and deuterated acrylamide before electrophoresis. The ratios between the two isotopic distributions were used for reliably quantification of several proteins present, in ratios from 1:1 to 1:10.
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    • Quantitative analysis of two-dimensional gel-separated proteins using isotopically marked alkylating agents and matrix-assisted laser desorption/ionization mass spectrometry
    • This study confirms that deuterated acrylamide can be used for quantitation of sample isolated by 2D-PAGE, as previously illustrated.
    • Gehanne S., Cecconi D., Carboni L., Righetti P.G., Domenici E., Hamdan M. Quantitative analysis of two-dimensional gel-separated proteins using isotopically marked alkylating agents and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 16:2002;1692-1698 This study confirms that deuterated acrylamide can be used for quantitation of sample isolated by 2D-PAGE, as previously illustrated.
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    • Gehanne, S.1    Cecconi, D.2    Carboni, L.3    Righetti, P.G.4    Domenici, E.5    Hamdan, M.6
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    • •] is further extended for the comparison of two adenovirus serotypes. Although the use of a high-resolution instrument like an FT-ICR solves the problems related to the overlap of the two isotopic distributions, it seems that the calculation of the relative quantities is still complex.
    • •] is further extended for the comparison of two adenovirus serotypes. Although the use of a high-resolution instrument like an FT-ICR solves the problems related to the overlap of the two isotopic distributions, it seems that the calculation of the relative quantities is still complex.
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    • Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation
    • The relative quantities of proteins are determined by differential labeling of the tryptic digest of two samples with methanol and D3-methanol. This procedure of permethylation has the added benefit of facilitating de novo sequencing.
    • 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 The relative quantities of proteins are determined by differential labeling of the tryptic digest of two samples with methanol and D3-methanol. This procedure of permethylation has the added benefit of facilitating de novo sequencing.
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    • Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety
    • Complex protein mixtures were separated by 2D- or 1D-PAGE and the spots to be identified/quantified were selected from two gels (e.g. treated and control). The proteins were succinilated with a heavy (D4) or light (D0) reagent before digestion with Asp/Glu-C. The conditions for succinilation of the lysine were improved and optimized to avoid secondary unwanted reactions. An added benefit of this procedure is that the labeling of the N-terminus facilitates de novo sequencing because the b-ion intensities are greatly increased. Although this approach has several advantages, it does not overcome the issue of reproducibility that is inherent to 2DE.
    • 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 Complex protein mixtures were separated by 2D- or 1D-PAGE and the spots to be identified/quantified were selected from two gels (e.g. treated and control). The proteins were succinilated with a heavy (D4) or light (D0) reagent before digestion with Asp/Glu-C. The conditions for succinilation of the lysine were improved and optimized to avoid secondary unwanted reactions. An added benefit of this procedure is that the labeling of the N-terminus facilitates de novo sequencing because the b-ion intensities are greatly increased. Although this approach has several advantages, it does not overcome the issue of reproducibility that is inherent to 2DE.
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    • Fractionation of isotopically labeled peptides in quantitative proteomics
    • In this study, the elution times between the heavy and the light forms of acetylated peptides are compared with the retention time of peptides modified with ICAT reagents. Acetylated peptides co-elute independently from the label, whereas the light and heavy forms of the ICAT-modified peptides have different retention times.
    • Zhang R., Sioma C.S., Wang S., Regnier F.E. Fractionation of isotopically labeled peptides in quantitative proteomics. Anal. Chem. 73:2001;5142-5149 In this study, the elution times between the heavy and the light forms of acetylated peptides are compared with the retention time of peptides modified with ICAT reagents. Acetylated peptides co-elute independently from the label, whereas the light and heavy forms of the ICAT-modified peptides have different retention times.
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    • Zhang, R.1    Sioma, C.S.2    Wang, S.3    Regnier, F.E.4
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    • Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates
    • The novelty of this procedure is that a purification step for isolating cysteine- and/or histidine-containing peptides is used. The quantification procedure is the same as previously described for succinic anhydride. The approach seems reasonable, although the copper affinity column might not be exclusively selecting for histidine-containing peptides.
    • 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 The novelty of this procedure is that a purification step for isolating cysteine- and/or histidine-containing peptides is used. The quantification procedure is the same as previously described for succinic anhydride. The approach seems reasonable, although the copper affinity column might not be exclusively selecting for histidine-containing peptides.
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    • Wang, S.1    Zhang, X.2    Regnier, F.E.3
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    • An isotope coding strategy for proteomics involving both amine and carboxyl group labeling
    • Liu P., Regnier F.E. An isotope coding strategy for proteomics involving both amine and carboxyl group labeling. J. Proteome Res. 1:2002;443.
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    • Quantifying peptides in isotopically labeled protease digests by ion mobility/time-of-flight mass spectrometry
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    • De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging
    • MCAT is introduced. Lysine guanidination, previously employed to facilitate sequencing by post-source decay (PSD), was used to facilitate sequencing by LC-MS/MS. The comparison of the isotopic distribution of unlabeled peptides with guanidinilated peptides was used for relative quantitation of yeast proteins. Although the average errors are within 25%, some peptides have errors as big as 62%, perhaps due to changes in ionization between lysine and guanidil-lysine.
    • Cagney G., Emili A. De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging. Nat. Biotechnol. 20:2002;163-170 MCAT is introduced. Lysine guanidination, previously employed to facilitate sequencing by post-source decay (PSD), was used to facilitate sequencing by LC-MS/MS. The comparison of the isotopic distribution of unlabeled peptides with guanidinilated peptides was used for relative quantitation of yeast proteins. Although the average errors are within 25%, some peptides have errors as big as 62%, perhaps due to changes in ionization between lysine and guanidil-lysine.
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    • Cagney, G.1    Emili, A.2
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    • Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry
    • This study describes a procedure for simultaneous solid-phase enrichment and labeling of cysteinyl peptides. The method described seems to be a significant improvement to the typical ICAT approach.
    • Zhou H., Ranish J.A., Watts J.D., Aebersold R. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat. Biotechnol. 20:2002;512-515 This study describes a procedure for simultaneous solid-phase enrichment and labeling of cysteinyl peptides. The method described seems to be a significant improvement to the typical ICAT approach.
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    • Zhou, H.1    Ranish, J.A.2    Watts, J.D.3    Aebersold, R.4
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    • Quantitative dynamics of site-specific protein phosphorylation determined using liquid chromatography electrospray ionization mass spectrometry
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    • In this article, labeled synthetic peptides were used as internal standards in an LC-MS experiment for quantifying the grade of phosphorylation of separase, a protein involved in chromatid separation during the anaphase.
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    • Phosphoprotein isotope-coded affinity tags: Application to the enrichment and identification of low-abundance phosphoproteins
    • 4 after β-elimination. The proof of principle is done using casein. In theory, this approach could be used for the quantitation of phosphorylation sites on a proteomic scale. However, using the described method, O-glycosylation sites would be also labeled and the procedure for avoiding the labeling of these sites has not been developed.
    • 4 after β-elimination. The proof of principle is done using casein. In theory, this approach could be used for the quantitation of phosphorylation sites on a proteomic scale. However, using the described method, O-glycosylation sites would be also labeled and the procedure for avoiding the labeling of these sites has not been developed.
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    • Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae
    • This study describes a methodology for phosphoproteome characterization. Although it has not been used for quantitation purposes, this enrichment procedure is of general use for phosphopeptides. More than 1000 phosphopeptides were detected and 383 phosphorylation sites identified in one experiment from yeast cell lysate.
    • 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 study describes a methodology for phosphoproteome characterization. Although it has not been used for quantitation purposes, this enrichment procedure is of general use for phosphopeptides. More than 1000 phosphopeptides were detected and 383 phosphorylation sites identified in one experiment from yeast cell lysate.
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    • Ficarro, S.B.1    McCleland, M.L.2    Stukenberg, P.T.3    Burke, D.J.4    Ross, M.M.5    Shabanowitz, J.6    Hunt, D.F.7    White, F.M.8
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    • Analysis of receptor signaling pathways by mass spectrometry: Identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors
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    • Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways
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    • Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry
    • Determination of quantities base only on ion intensities from LC-MS spectra. This seems a preliminary but promising approach.
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    • Imaging mass spectrometry: A new technology for the analysis of protein expression in mammalian tissues
    • This article elegantly describes the use of MS for imaging. The image is generated by MALDI MS, scanning a tissue section imbedded with matrix. Several mouse brain sections are used to illustrate the technology.
    • Stoeckli M., Chaurand P., Hallahan D.E., Caprioli R.M. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nat. Med. 7:2001;493 This article elegantly describes the use of MS for imaging. The image is generated by MALDI MS, scanning a tissue section imbedded with matrix. Several mouse brain sections are used to illustrate the technology.
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    • Stoeckli, M.1    Chaurand, P.2    Hallahan, D.E.3    Caprioli, R.M.4
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    • Current achievements using ProteinChip Array technology
    • This article reviews the use of ProteinChip array for quantitation using surface enhanced laser-desorption (SELDI) protein chips.
    • Weinberger S.R., Dalmasso E.A., Fung E.T. Current achievements using ProteinChip Array technology. Curr. Opin. Chem. Biol. 6:2002;86-91 This article reviews the use of ProteinChip array for quantitation using surface enhanced laser-desorption (SELDI) protein chips.
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    • Weinberger, S.R.1    Dalmasso, E.A.2    Fung, E.T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.