Proteomics:  from Gel Based to Gel Free

Ethier, Martin; Smith, Jeffrey C.; Figeys, Daniel

doi:10.1021/ac050586d

Cited by 106 publications

(83 citation statements)

References 178 publications

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“…In addition, gel-based methods provide more reliable inference of posttranslational modifications (see Supplemental Table 5 online). Moreover, 22 proteins of the GC proteome were exclusively identified by gel-based methods, indicating that gel-free methods cannot completely replace traditional gel-based methods (Lambert et al, 2005). Although we evaluated the 22 proteins for common characteristics (e.g., molecular weight, pI, predicted subcellular localization, and the predicted trypsin-digestion patterns of these protein sequences) that might have enhanced their detection by gel-based over gel-free methods, no such characteristics could be identified.…”

Section: Comparison Of the Three Proteomic Methodsmentioning

confidence: 99%

Functional Proteomics ofArabidopsis thalianaGuard Cells Uncovers New Stomatal Signaling Pathways

et al. 2008

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We isolated a total of 3 3 10 8 guard cell protoplasts from 22,000 Arabidopsis thaliana plants and identified 1734 unique proteins using three complementary proteomic methods: protein spot identification from broad and narrow pH range twodimensional (2D) gels, and 2D liquid chromatography-matrix assisted laser desorption/ionization multidimensional protein identification technology. This extensive single-cell-type proteome includes 336 proteins not previously represented in transcriptome analyses of guard cells and 52 proteins classified as signaling proteins by Gene Ontology analysis, of which only two have been previously assessed in the context of guard cell function. THIOGLUCOSIDE GLUCOHYDROLASE1 (TGG1), a myrosinase that catalyzes the production of toxic isothiocyanates from glucosinolates, showed striking abundance in the guard cell proteome. tgg1 mutants were hyposensitive to abscisic acid (ABA) inhibition of guard cell inward K + channels and stomatal opening, revealing that the glucosinolate-myrosinase system, previously identified as a defense against biotic invaders, is required for key ABA responses of guard cells. Our results also suggest a mechanism whereby exposure to abiotic stresses may enhance plant defense against subsequent biotic stressors and exemplify how enhanced knowledge of the signaling networks of a specific cell type can be gained by proteomics approaches.

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Section: Comparison Of the Three Proteomic Methodsmentioning

confidence: 99%

Functional Proteomics ofArabidopsis thalianaGuard Cells Uncovers New Stomatal Signaling Pathways

et al. 2008

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“…An alternative approach is the gel-free proteomics technology, which is more suitable for the analysis of proteins with low abundance in complex samples. [7,17,24]. Separation of proteins using gel-free techniques revolutionized the study of proteome in the cell [24,25].…”

Section: Fluorescent Two-dimensional "Difference Gel Electrophoresis"mentioning

confidence: 99%

Proteomics: A Successful Approach to Understand the Molecular Mechanism of Plant-Pathogen Interaction

Lodha¹,

Hembram²,

Tep³

2013

AJPS

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In recent years, proteomics has played a key role in identifying changes in protein levels in plant hosts upon infection by pathogenic organisms and in characterizing cellular and extracellular virulence and pathogenicity factors produced by pathogens. Proteomics offers a constantly evolving set of novel techniques to study all aspects of protein structure and function. Proteomics aims to find out the identity and amount of each and every protein present in a cell and actual function mediating specific cellular processes. Structural proteomics elucidates the development and application of experimental approaches to define the primary, secondary and tertiary structures of proteins, while functional proteomics refers to the development and application of global (proteome wide or system-wide) experimental approaches to assess protein function. A detail understanding of plant defense response using successful combination of proteomic techniques and other high throughput techniques of cell biology, biochemistry as well as genomics is needed for practical application to secure and stabilize yield of many crop plants. This review starts with a brief introduction to gel-and non gel-based proteomic techniques followed by the basics of plant-pathogen interaction, the use of proteomics in recent pasts to decipher the mysteries of plant-pathogen interaction, and ends with the future prospects of this technology.

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“…The most successful approach, named "shotgun" or Multidimensional protein identification technology (MudPIT),), employs tryptic digestion of the entire protein mixture and analysis of the peptides with the combination of nanoscale liquid chromatography and electrospray tandem mass spectrometry [16,17]. In the gel-free workflow, several combinations of peptide separation methods can be used prior to LC-MS/MS analysis, including strong cation exchange and reversed phase high-performance liquid chromatography, liquid phase isoelectric focusing, and capillary electrophoresis [18]. As a "hybrid" alternative, a combination of SDS-PAGE, ingel digestion and LC-MS/MS (named GeLC-MS/MS) can be also employed [19].…”

Section: Current Technologies Enabling Qualitative and Quantitative Amentioning

confidence: 99%

High throughput genomic and proteomic technologies in the fight against infectious diseases

Tanca

Deligios

Addis

et al. 2013

J Infect Dev Ctries

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New technologies have shown significant promise in the fight against infectious diseases, with the discovery of novel molecular targets for in vitro diagnostics and the improved design of vaccines. In developing countries, especially in areas of neglected diseases and resources-poor settings, a number of technological innovations are further needed, such as the integration of old and new biomarkers in suitable analysis platforms, the simplification of existing analysis systems, and the improvement of sample preservation and management. However, in these areas, identification of new biomarkers for infectious diseases is still a core issue in the diagnostic quest. Similarly, new technologies will allow scientists to design vaccines with improved immunogenicity, efficacy and safety in the local area, according to the circulating pathogenic strains and the genetic background of the population to be immunized. In this work we review the current omics-based technologies and their potential for accelerating the development of next generation vaccines and the identification of biomarkers suitable for point-of-care (POC) diagnostic applications.

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Proteomics: from Gel Based to Gel Free

Cited by 106 publications

References 178 publications

Functional Proteomics ofArabidopsis thalianaGuard Cells Uncovers New Stomatal Signaling Pathways

Functional Proteomics ofArabidopsis thalianaGuard Cells Uncovers New Stomatal Signaling Pathways

Proteomics: A Successful Approach to Understand the Molecular Mechanism of Plant-Pathogen Interaction

High throughput genomic and proteomic technologies in the fight against infectious diseases

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