Quantitative mass spectrometry in proteomics: a critical review View Full Text


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Article Info

DATE

2007-08-01

AUTHORS

Marcus Bantscheff, Markus Schirle, Gavain Sweetman, Jens Rick, Bernhard Kuster

ABSTRACT

The quantification of differences between two or more physiological states of a biological system is among the most important but also most challenging technical tasks in proteomics. In addition to the classical methods of differential protein gel or blot staining by dyes and fluorophores, mass-spectrometry-based quantification methods have gained increasing popularity over the past five years. Most of these methods employ differential stable isotope labeling to create a specific mass tag that can be recognized by a mass spectrometer and at the same time provide the basis for quantification. These mass tags can be introduced into proteins or peptides (i) metabolically, (ii) by chemical means, (iii) enzymatically, or (iv) provided by spiked synthetic peptide standards. In contrast, label-free quantification approaches aim to correlate the mass spectrometric signal of intact proteolytic peptides or the number of peptide sequencing events with the relative or absolute protein quantity directly. In this review, we critically examine the more commonly used quantitative mass spectrometry methods for their individual merits and discuss challenges in arriving at meaningful interpretations of quantitative proteomic data.FigureCommon quantitative mass spectrometry workflows. Boxes in blue and yellow represent two experimental conditions. Horizontal lines indicate when samples are combined. Dashed lines indicate points at which experimental variation and thus quantification errors can occur. (adapted with permission from [11]) More... »

PAGES

1017-1031

References to SciGraph publications

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  • 2004-08-15. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics in NATURE BIOTECHNOLOGY
  • 2006-12-31. Computational prediction of proteotypic peptides for quantitative proteomics in NATURE BIOTECHNOLOGY
  • 2006-03-01. Detecting multiple associations in genome-wide studies in HUMAN GENOMICS
  • 2003-09-01. Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 2003-07-13. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics in NATURE BIOTECHNOLOGY
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  • 2002-07-01. A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight (Q-TOF) mass spectrometer for studying protein phosphorylation in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 2007-02-25. An integrated mass spectrometric and computational framework for the analysis of protein interaction networks in NATURE BIOTECHNOLOGY
  • 2005-09-20. Mass spectrometry–based proteomics turns quantitative in NATURE CHEMICAL BIOLOGY
  • 2004-04-01. A method for calculating 16o/18o peptide ion ratios for the relative quantification of proteomes in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 2005-07-22. Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data in BMC BIOINFORMATICS
  • 2005-07-21. Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry in NATURE METHODS
  • 2003-03. Mass spectrometry-based proteomics in NATURE
  • 2005-07-21. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides in NATURE METHODS
  • 2001-03. Large-scale analysis of the yeast proteome by multidimensional protein identification technology in NATURE BIOTECHNOLOGY
  • 1999-10. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags in NATURE BIOTECHNOLOGY
  • 2006-12-24. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation in NATURE BIOTECHNOLOGY
  • 2003-05-18. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry in NATURE BIOTECHNOLOGY
  • Journal

    TITLE

    Analytical and Bioanalytical Chemistry

    ISSUE

    4

    VOLUME

    389

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s00216-007-1486-6

    DOI

    http://dx.doi.org/10.1007/s00216-007-1486-6

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1001825252

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/17668192


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    35 schema:description The quantification of differences between two or more physiological states of a biological system is among the most important but also most challenging technical tasks in proteomics. In addition to the classical methods of differential protein gel or blot staining by dyes and fluorophores, mass-spectrometry-based quantification methods have gained increasing popularity over the past five years. Most of these methods employ differential stable isotope labeling to create a specific mass tag that can be recognized by a mass spectrometer and at the same time provide the basis for quantification. These mass tags can be introduced into proteins or peptides (i) metabolically, (ii) by chemical means, (iii) enzymatically, or (iv) provided by spiked synthetic peptide standards. In contrast, label-free quantification approaches aim to correlate the mass spectrometric signal of intact proteolytic peptides or the number of peptide sequencing events with the relative or absolute protein quantity directly. In this review, we critically examine the more commonly used quantitative mass spectrometry methods for their individual merits and discuss challenges in arriving at meaningful interpretations of quantitative proteomic data.FigureCommon quantitative mass spectrometry workflows. Boxes in blue and yellow represent two experimental conditions. Horizontal lines indicate when samples are combined. Dashed lines indicate points at which experimental variation and thus quantification errors can occur. (adapted with permission from [11])
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