All about DIGE: quantification technology for differential-display 2D-gel proteomics

2D polyacrylamide gel electrophoresis has been the traditional workhorse of proteomics, allowing for the resolution of several thousand proteins in a single gel. Difference gel electrophoresis is an emerging technology that allows for accurate quantification with statistical confidence while controlling for nonbiologic variation, and also increases the dynamic range and sensitivity of traditional 2D polyacrylamide gel electrophoresis. With inclusion of an internal standard formed from equal amounts of every sample in an experiment, difference gel electrophoresis technology also allows for repetitive measurements and multivariable analyses to be quantitatively analyzed in one co-ordinated experiment, yielding statistically-significant changes in protein expression related to many disease states. This technique promises to be an important tool in clinical proteomics and the study of the mechanism of disease, investigating diagnostic biomarkers and pinpointing novel therapeutic targets.

[1]  R. Caprioli,et al.  Proteome analysis of human colon cancer by two‐dimensional difference gel electrophoresis and mass spectrometry , 2004, Proteomics.

[2]  D. Speicher,et al.  Towards global analysis of mammalian proteomes using sample prefractionation prior to narrow pH range two‐dimensional gels and using one‐dimensional gels for insoluble and large proteins , 2001, Electrophoresis.

[3]  Daniel C Liebler,et al.  Quantitative analysis of modified proteins by LC-MS/MS of peptides labeled with phenyl isocyanate. , 2003, Journal of proteome research.

[4]  M. Knowles,et al.  Alterations of stress related proteins in genetically altered mice revealed by two‐dimensional differential in‐gel electrophoresis analysis , 2002, Proteomics.

[5]  A. Görg,et al.  Sample prefractionation with Sephadex isoelectric focusing prior to narrow pH range two‐dimensional gels , 2002, Proteomics.

[6]  R. Wait,et al.  Mass spectrometric analysis of maleimide CyDye labelled model peptides. , 2003, Rapid communications in mass spectrometry : RCM.

[7]  B. Haab.  Methods and applications of antibody microarrays in cancer research , 2003, Proteomics.

[8]  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.

[9]  K. Williams,et al.  Proteome and transcriptome analysis of retinoic acid-induced differentiation of human acute promyelocytic leukemia cells, NB4. , 2004, Journal of proteome research.

[10]  Yu Shyr,et al.  Proteomic patterns of tumour subsets in non-small-cell lung cancer , 2003, The Lancet.

[11]  Stephen O. David,et al.  A novel experimental design for comparative two‐dimensional gel analysis: Two‐dimensional difference gel electrophoresis incorporating a pooled internal standard , 2003, Proteomics.

[12]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[13]  Virginia Espina,et al.  Clinical proteomics: revolutionizing disease detection and patient tailoring therapy. , 2004, Journal of proteome research.

[14]  M. Stoeckli,et al.  Direct profiling of proteins in biological tissue sections by MALDI mass spectrometry. , 1999, Analytical chemistry.

[15]  R. Yolken,et al.  Mitochondrial dysfunction in schizophrenia: evidence for compromised brain metabolism and oxidative stress , 2004, Molecular Psychiatry.

[16]  M. Ünlü,et al.  Difference gel electrophoresis. A single gel method for detecting changes in protein extracts , 1997, Electrophoresis.

[17]  Rainer Cramer,et al.  Evaluation of Two-dimensional Differential Gel Electrophoresis for Proteomic Expression Analysis of a Model Breast Cancer Cell System* , 2002, Molecular & Cellular Proteomics.

[18]  Gang Wang,et al.  Proteome analysis of Saccharomyces cerevisiae under metal stress by two‐dimensional differential gel electrophoresis , 2003, Electrophoresis.

[19]  Jerry Avorn.  Technology , 1929, Nature.

[20]  Tadashi Kondo,et al.  Proteomic signature of human cancer cells , 2004, Proteomics.

[21]  L. Arckens,et al.  Reversed‐phase high‐performance liquid chromatography prefractionation prior to two‐dimensional difference gel electrophoresis and mass spectrometry identifies new differentially expressed proteins between striate cortex of kitten and adult cat , 2003, Electrophoresis.

[22]  F. Cross,et al.  Accurate quantitation of protein expression and site-specific phosphorylation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Hanno Steen,et al.  Protein Profiling with Cleavable Isotope-coded Affinity Tag (cICAT) Reagents , 2003, Molecular & Cellular Proteomics.

[24]  Jeroen Krijgsveld,et al.  Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics , 2003, Nature Biotechnology.

[25]  S. Hirohashi,et al.  Proteomic signature corresponding to alpha fetoprotein expression in liver cancer cells , 2004, Hepatology.

[26]  K. Parker,et al.  Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.

[27]  S. Hunt,et al.  Multiplex proteomic analysis by two‐dimensional differential in‐gel electrophoresis , 2003, Proteomics.

[28]  M. Stoeckli,et al.  Imaging mass spectrometry: A new technology for the analysis of protein expression in mammalian tissues , 2001, Nature Medicine.

[29]  W. Labeikovsky,et al.  Changes in the mitochondrial proteome from mouse hearts deficient in creatine kinase. , 2001, Physiological genomics.

[30]  Kathryn S Lilley,et al.  Two-dimensional gel electrophoresis: recent advances in sample preparation, detection and quantitation. , 2002, Current opinion in chemical biology.

[31]  Jonathan S. Minden,et al.  Drosophila ventral furrow morphogenesis: a proteomic analysis , 2004, Development.

[32]  M. Kanaoka,et al.  Proteomic analysis of rat heart in ischemia and ischemia‐reperfusion using fluorescence two‐dimensional difference gel electrophoresis , 2003, Proteomics.

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

[34]  Robert Tonge,et al.  Evaluation of saturation labelling two‐dimensional difference gel electrophoresis fluorescent dyes , 2003, Proteomics.

[35]  Kai Stühler,et al.  Genetic analysis of the mouse brain proteome , 2002, Nature Genetics.

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

[37]  A. Link,et al.  Yeast Asc1p and Mammalian RACK1 Are Functionally Orthologous Core 40S Ribosomal Proteins That Repress Gene Expression , 2004, Molecular and Cellular Biology.

[38]  Ruedi Aebersold,et al.  Quantitative Proteome Analysis by Solid-phase Isotope Tagging and Mass Spectrometry Beads Photocleavable Linker Isotope Tag Reactive Group , 2022 .

[39]  R. Leimgruber,et al.  Practical aspects of fluorescent staining for proteomic applications , 2001, Electrophoresis.

[40]  Mahlon D. Johnson,et al.  Protein Profiling in Brain Tumors Using Mass Spectrometry , 2004, Clinical Cancer Research.

[41]  Walter A. Korfmacher,et al.  Direct analysis of drug candidates in tissue by matrix-assisted laser desorption/ionization mass spectrometry. , 2003, Journal of mass spectrometry : JMS.

[42]  Tadashi Kondo,et al.  Application of sensitive fluorescent dyes in linkage of laser microdissection and two‐dimensional gel electrophoresis as a cancer proteomic study tool , 2003, Proteomics.

[43]  Matthew Davison,et al.  Validation and development of fluorescence two‐dimensional differential gel electrophoresis proteomics technology , 2001, Proteomics.

[44]  R. Rabus,et al.  Evaluation of Two-Dimensional Difference Gel Electrophoresis for Protein Profiling , 2003, Journal of Molecular Microbiology and Biotechnology.

[45]  B. Svensson,et al.  Cy5 maleimide labelling for sensitive detection of free thiols in native protein extracts: identification of seed proteins targeted by barley thioredoxin h isoforms. , 2004, The Biochemical journal.

[46]  D. Friedman,et al.  The Drosophila fragile X-related gene regulates axoneme differentiation during spermatogenesis. , 2004, Developmental biology.

[47]  D. Figeys,et al.  18O labeling: a tool for proteomics. , 2001, Rapid communications in mass spectrometry : RCM.