Shotgun proteomics: tools for the analysis of complex biological systems.

Recent interest in proteomics has been fueled by the completion of multiple genome projects and ignited by the common need of biologists to rapidly and comprehensively evaluate complex samples of proteins on a global level. 'Shotgun proteomics' refers to the direct analysis of complex protein mixtures to rapidly generate a global profile of the protein complement within the mixture. This approach has been facilitated by the use of multidimensional protein identification technology (MudPIT), which incorporates multidimensional high-pressure liquid chromatography (LC/LC), tandem mass spectrometry (MS/MS) and database-searching algorithms. This review will focus on the most recent advances in methodologies for shotgun proteomics and address the limitations of the application of each to real biological samples.

[1]  J. Yates,et al.  Probability-based validation of protein identifications using a modified SEQUEST algorithm. , 2002, Analytical chemistry.

[2]  John I. Clark,et al.  Shotgun identification of protein modifications from protein complexes and lens tissue , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[3]  E. Check.  NIH ponders issues of scale in protein push , 2002, Nature.

[4]  P. Cohen,et al.  The origins of protein phosphorylation , 2002, Nature Cell Biology.

[5]  Ruedi Aebersold,et al.  Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry , 2002, Nature Biotechnology.

[6]  Rovshan G Sadygov,et al.  Code developments to improve the efficiency of automated MS/MS spectra interpretation. , 2002, Journal of proteome research.

[7]  John R Yates,et al.  Analysis of quantitative proteomic data generated via multidimensional protein identification technology. , 2002, Analytical chemistry.

[8]  J. Shabanowitz,et al.  Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae , 2002, Nature Biotechnology.

[9]  F. Regnier,et al.  Minimizing resolution of isotopically coded peptides in comparative proteomics. , 2002, Journal of proteome research.

[10]  Andrew Emili,et al.  De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging , 2002, Nature Biotechnology.

[11]  J. Yates,et al.  DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. , 2002, Journal of proteome research.

[12]  J. Yates,et al.  Proteomic analysis of Golgi membrane proteins , 2002 .

[13]  J. Yates,et al.  An automated multidimensional protein identification technology for shotgun proteomics. , 2001, Analytical chemistry.

[14]  F. Regnier,et al.  Fractionation of isotopically labeled peptides in quantitative proteomics. , 2001, Analytical chemistry.

[15]  R. Aebersold,et al.  Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry , 2001, Nature Biotechnology.

[16]  Richard D. Smith,et al.  Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. , 2001, Analytical chemistry.

[17]  R. Aebersold,et al.  A systematic approach to the analysis of protein phosphorylation , 2001, Nature Biotechnology.

[18]  B. Chait,et al.  Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome , 2001, Nature Biotechnology.

[19]  T. Veenstra,et al.  Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling. , 2001, Analytical chemistry.

[20]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[21]  S. Gygi,et al.  Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[22]  T. Stevens,et al.  Do more complex organisms have a greater proportion of membrane proteins in their genomes? , 2000, Proteins.

[23]  D. Hochstrasser,et al.  The dynamic range of protein expression: A challenge for proteomic research , 2000, Electrophoresis.

[24]  M. Molloy,et al.  Membrane proteins and proteomics: Un amour impossible? , 2000, Electrophoresis.

[25]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[26]  J. Yates,et al.  Direct analysis of protein complexes using mass spectrometry , 1999, Nature Biotechnology.

[27]  S. Gygi,et al.  Correlation between Protein and mRNA Abundance in Yeast , 1999, Molecular and Cellular Biology.

[28]  D. Volkin,et al.  Degradative covalent reactions important to protein stability , 1997, Molecular biotechnology.

[29]  R. Krishna,et al.  Post-translational modification of proteins. , 1993, Advances in enzymology and related areas of molecular biology.