Highlights on the capacities of "Gel-based" proteomics

Chevalier, François

doi:10.1186/1477-5956-8-23

Cited by 152 publications

(130 citation statements)

References 88 publications

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“…However, proteomic approaches have been employed in only a few studies of developing rice seeds (Lee and Koh 2011;Xu et al 2008;Xu et al 2012). One benefit of gel-based proteomics is that it is simple to determine the amount of proteins and to characterize protein isoforms such as post-translational modifications and spliced forms of the same gene or protein (Chevalier 2010).…”

mentioning

confidence: 99%

Proteomic analysis of stress-related proteins in rice seeds during the desiccation phase of grain filling

Sano

Masaki

Tanabata

et al. 2013

Plant Biotechnology

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During seed maturation, the water content of seeds decreases remarkably. Mature seeds can germinate after imbibition since the embryos are protected by mechanism of desiccation tolerance. To better understand the mechanism of desiccation tolerance in seeds, we analyzed the fluctuation of stress-related proteins in the desiccation phase of rice seeds by a real-time RT-PCR and gel-based proteomic approach. Based on the changes in water content of developing rice seeds, we defined stages from the beginning of dehydration (10 to 20 days after flowering) and the desiccation phase (20 to 40 days after flowering). The proteomic analysis revealed that late embryogenesis abundant proteins, small heat shock proteins and antioxidative proteins accumulate at the beginning of dehydration and remain at a high level in the desiccation phase, suggesting that these proteins are involved in acquisition of desiccation tolerance. The fluctuation in levels of mRNA encoding some stress-related proteins did not precisely reflect the change in levels of these proteins. Therefore, proteomic analysis, which provides an accurate assessment of changes in protein levels, is a more efficient technique than transcriptomics for inferring the role of stress-related proteins in rice seeds.

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mentioning

confidence: 99%

Proteomic analysis of stress-related proteins in rice seeds during the desiccation phase of grain filling

Sano

Masaki

Tanabata

et al. 2013

Plant Biotechnology

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“…As a result, 2-DE may greatly under-represent the whole proteome. In such situations, strategies including the depletion of high abundance proteins, the use of very narrow-range IPG strips (~1 pH unit) or proteome subfractionation (see section below), can be employed to enable the detection of low abundance proteins (Greenough et al, 2004;Chevalier, 2010;Rabilloud et al, 2010).…”

Section: Limitations Of 2-dementioning

confidence: 99%

Two-dimensional gel electrophoresis in bacterial proteomics

et al. 2012

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Two-dimensional gel electrophoresis (2-DE) is a gel-based technique widely used for analyzing the protein composition of biological samples. It is capable of resolving complex mixtures containing more than a thousand protein components into individual protein spots through the coupling of two orthogonal biophysical separation techniques: isoelectric focusing (first dimension) and polyacrylamide gel electrophoresis (second dimension). 2-DE is ideally suited for analyzing the entire expressed protein complement of a bacterial cell: its proteome. Its relative simplicity and good reproducibility have led to 2-DE being widely used for exploring proteomics within a wide range of environmental and medically-relevant bacteria. Here we give a broad overview of the basic principles and historical development of gel-based proteomics, and how this powerful approach can be applied for studying bacterial biology and physiology. We highlight specific 2-DE applications that can be used to analyze when, where and how much proteins are expressed. The links between proteomics, genomics and mass spectrometry are discussed. We explore how proteomics involving tandem mass spectrometry can be used to analyze (post-translational) protein modifications or to identify proteins of unknown origin by de novo peptide sequencing. The use of proteome fractionation techniques and non-gel-based proteomic approaches are also discussed. We highlight how the analysis of proteins secreted by bacterial cells (secretomes or exoproteomes) can be used to study infection processes or the immune response. This review is aimed at non-specialists who wish to gain a concise, comprehensive and contemporary overview of the nature and applications of bacterial proteomics.

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“…A high salt content and a large disproportion between low-and high-abundance proteins are the main factors responsible for the difficulty in fully characterizing the serum/plasma proteome. The wide dynamic range in the abundance of plasma/serum proteins may be greater than 10 orders of magnitude (12)(13)(14). These disproportions are more dramatic in young animals, and especially in neonates.…”

Section: Introductionmentioning

confidence: 99%

“…The aforementioned proteins dominate in the 2D gels and mask the presence of proteins that may have a similar isoelectric point or molecular weight, thereby lowering protein resolution on the gel and limiting the ability to analyze the entire proteome. The remaining 10% are low-abundance proteins, whose concentration is very low and changes markedly in response to regulatory factors (12)(13)(14). Therefore, the most crucial step in the proteomic analysis is proper plasma/ serum sample preparation including depletion of highabundance proteins (13).…”

Section: Introductionmentioning

confidence: 99%

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Impact of the depletion of high-abundance proteins in blood plasma/serum on the proteome of these media in growing farm animals

Lepczyński¹,

Dratwa-Chałupnik²,

Herosimczyk³

et al. 2014

Turk J Vet Anim Sci

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The aim of the study was to use hexapeptide combinatorial libraries to evaluate the influence of high-abundance protein depletion on low-abundance protein enrichment, protein concentration, and 2D gel quality in plasma and serum proteomes of growing piglets and calves. Depleted and nondepleted samples of plasma/serum were resolved using 2D electrophoresis (2DE). Bioinformatic analysis of the 2D gels showed an increased number of detected spots on each gel after depletion of excess high-abundance proteins in calf plasma (+26.46%) and in piglet serum (+49.40%). Relative expression of selected low-abundance protein spots in the blood plasma/ serum samples was higher after high-abundance protein depletion. Both media showed decreased expressions of high-abundance protein spot clusters on 2D gels after treatment. The results of this study confirm both the high efficiency of high-abundance protein depletion and the increase in concentrations of low-abundance proteins on 2D gels after treatment. The method of depletion is reproducible and it may be used as an alternative to immunodepletion for preparing blood plasma/serum samples from young, growing animals for 2DE. Increased content of the low-abundance proteins on the 2D gels enables complete analysis of plasma/serum proteome and thereby allows for the discovery of novel biomarkers that might be useful in veterinary medicine.

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Highlights on the capacities of "Gel-based" proteomics

Cited by 152 publications

References 88 publications

Proteomic analysis of stress-related proteins in rice seeds during the desiccation phase of grain filling

Proteomic analysis of stress-related proteins in rice seeds during the desiccation phase of grain filling

Two-dimensional gel electrophoresis in bacterial proteomics

Impact of the depletion of high-abundance proteins in blood plasma/serum on the proteome of these media in growing farm animals

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