Resources - Selected Papers



Resources - Selected Papers

This document presents selected citations of the proteomics literature, emphasizing papers that introduced ways of applying mass spectrometry and proteomics to biology.

General Proteomics Reviews

Focus on mass spectrometry in proteomics

Various Authors. Nature Methods - 4, 781-833 (2007)

A collection of review articles on proteomics and biological mass spectrometry. Includes Glossary.

General Proteome Profiling

Linking genome and proteome by mass spectrometry: Large-scale identification of yeast proteins from two dimensional gels

Shevchenko et al. Proc. Natl. Acad. Sci. USA Vol. 93, pp. 14440-14445, December 1996

Described the basic proteomics technique of separating proteins on a two-dimensional gel followed by protein identification by mass spectrometry.

Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry.

Wilm, M. et al. Nature. 1996 Feb 1;379(6564):466-9.

Original description of the process of identifying proteins from gels by electrospray-ionization mass spectrometry.

Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels.

Shevchenko, A. et al. Anal Chem. 1996 Mar 1;68(5):850-8.

A citation classic for the technique of in-gel digest and subsequent protein identification.

Characterization of the human heart mitochondrial proteome

Taylor, S.W. et al. Nature Biotechnology 21, 281 - 286 (2003)

Profiling Core Proteomes of Human Cell Lines by One-dimensional PAGE and Liquid Chromatography-Tandem Mass Spectrometry Schirle, M. et al. Molecular & Cellular Proteomics 2:1297-1305 (2003)

These two papers were amongst the first to describe sequential use of 1-D gels and LC-MS to identify large numbers of proteins from cells or organelles.

Quantitative Proteomics

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.

Gygi, S.P. et al. Nat Biotechnol. 1999 Oct;17(10):994-9.

Original description of the ICAT technique for simultaneous identification and quantification of proteins in complex mixtures.

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.

Ong, S.E. et al. Mol Cell Proteomics. 2002 May;1(5):376-86.

This paper introduced SILAC, a technique for quantitative proteomic analysis of proteins from cell culture.

Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) for Studying Dynamics of Protein Abundance and Posttranslational Modifications

Amanchy, R. Sci. STKE, 18 January 2005 Vol. 2005, Issue 267, p. pl2

A review of SILAC and its application to the study of protein complexes and post-translational modifications.

Protein Complexes

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

Ho, Y. et al. Nature 415, 180-183 (10 January 2002)

Large-scale profiling of protein complexes in yeast.

Proteomic analysis of the mammalian nuclear pore complex

Cronshaw, J.M. et al. The Journal of Cell Biology, Volume 158, Number 5, September 2, 2002 915-927

A widely cited study showing focused analysis of a protein complex of interest.

Mass spectrometry–based functional proteomics: from molecular machines to protein networks

Köcher, T and Superti-Furga, G. Nature Methods - 4, 807 - 815 (2007)

A review of the study of protein complexes and protein-protein interactions by mass spectrometry.

Using stable isotope tagging and MS to characterize protein complexes and to detect changes in their composition.

J.A Ranish, M. Brand and R. Aebersold. In: Methods in Molecular Biology: Quantitative proteomics by mass spectrometry, Vol 359 (Clifton, N.J., Totowa, N.J.: Humana Press), 2007

A methodology for characterizing the composition of protein complexes and their dynamic changes in composition by combining affinity purification approaches with stable isotope tagging and mass spectrometry.

Phosphoproteins and Phosphopeptides

Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography.

Andersson and Porath. Anal. Biochem. 1986. Apr;154(1):250-4.

One of several 1986 papers describing immobilized metal affinity chromatography (IMAC) for the purification of phosphoproteins.

Immobilized Fe3+ affinity chromatographic isolation of phosphopeptides

Scanff, P. J Chromatogr. 1991 Feb 22;539(2):425-32.

The first of many papers employing immobilized metal affinity chromatography (IMAC) to selectively purify phosphorylated peptides.

Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae

Ficarro, S. et al. Nat Biotechnol. 2002 Mar;20(3):301-5.

This paper introduced modifications to the IMAC technique that allowed large-scale screening for phosphorylated peptides.

Immunoaffinity profiling of tyrosine phosphorylation in cancer cells

Rush, J. et al. Nature Biotechnology 23, 94 - 101 (2004)

Introduced the technique of peptide immunoprecipitation, using specific antibodies against phosphorylated sequence motifs to isolate peptides for subsequent identification by mass spectrometry.

Differential phosphoproteome profiling by affinity capture and tandem matrix-assisted laser desorption/ionization mass spectrometry. Metodiev et al. 2004. Proteomics 4: 1433.

Comparative analysis of phosphoprotein-enriched myocyte proteomes reveals widespread alterations during differentiation. Puente LG, Carriere JF, Kelly JF, Megeney LA. FEBS 574:138-44, 2004

These two papers describe a simple method for phosphoprotein isolation using commercially available kits and 1-D or 2-D gels.

Kinases

Kinomics: Methods for deciphering the kinome.

Johnson, S.A. and Hunter, T. Nature Methods 2, 17 - 25 (2005)

A review of different methods for discovering protein kinase substrates.

Cell Surface and Membrane Proteins

Global Profiling of the Cell Surface Proteome of Cancer Cells Uncovers an Abundance of Proteins with Chaperone Function

Shin, B.K. et al. J. Biol. Chem., Vol. 278, Issue 9, 7607-7616, February 28, 2003

Described the combination of cell-impermeable protein biotinylation, 2-D gels, and mass spectrometry to profile the surface proteome of eukaryotic cells.

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