Measurement of glycolysis reactants by high-throughput solid phase extraction with tandem mass spectrometry: Characterization of pyrophosphate-dependent phosphofructokinase as a case study

Rye, Peter T.; LaMarr, William A.

doi:10.1016/j.ab.2015.03.029

Cited by 35 publications

(12 citation statements)

References 38 publications

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“…Several proteins whose showed a decrease in proteins abundance and exhibited different carbonylation levels were observed which involved in the glycolytic pathway, including phospoglycerate mutase which catalyzes the conversion of 3-phosphoglycerate to 2-phosphoglycerate34, pyruvate decarboxylase (PDC) which catalyses the decarboxylation of pyruvic acid to acetaldehyde and carbon dioxide35, triosephosphate isomerase which catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate D-glyceraldehyde 3-phosphate36, enolase which catalyzes the conversion of 2-phosphoglycerate to phosphoenolpyruvate37, and pyrophosphate-dependent phosphofructokinase which catalyzes the reversible phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate38. Interestingly, PDC gene family was induced in response to environmental stress in plants3940.…”

Section: Discussionmentioning

confidence: 99%

Proteomic and Carbonylation Profile Analysis at the Critical Node of Seed Ageing in Oryza sativa

Yin

Xia

et al. 2017

Sci Rep

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The critical node (CN), which is the transition from the plateau phase to the rapid decreasing phase of seed ageing, is extremely important for seed conservation. Although numerous studies have investigated the oxidative stress during seed ageing, information on the changes in protein abundance at the CN is limited. In this study, we aimed to investigate the abundance and carbonylation patterns of proteins at the CN of seed ageing in rice. The results showed that the germination rate of seeds decreased by less than 20% at the CN; however, the abundance of 112 proteins and the carbonylation levels of 68 proteins markedly changed, indicating oxidative damage. The abundance and activity of mitochondrial, glycolytic, and pentose phosphate pathway proteins were reduced; consequently, this negatively affected energy production and germination. Proteins related to defense, including antioxidant system and heat shock proteins, also reduced in abundance. Overall, energy metabolism was reduced at the CN, leading to a decrease in the antioxidant capacity, whereas seed storage proteins were up-regulated and carbonylated, indicating that the seed had a lower ability to utilize seed storage proteins for germination. Thus, the significant decrease in metabolic activities at the CN might accelerate the loss of seed viability.A notable characteristic of seed viability is the reverse S-shaped survival curve during ageing, which includes a plateau phase (Phase I; P-I), followed by a rapid decreasing phase (Phase II; P-II) and a slow decreasing phase (Phase III; P-III). The transformation from P-I to P-II is defined as the critical node (CN), which is highly important for seed conservation 1 . The average germination of approximately 42,000 diverse accessions stored for 16 to 81 years at the National Center for Genetic Resources Preservation, USA has been decreased by 42% 2 . The average germination rate of peanut (stored for 34 years), soybean (stored for 36 years), wheat (stored for 43.6 years), and barley (stored for 44.4 years) is 6%, 21%, 73%, and 86%, respectively 3 . Similar results have been also reported by the Genebank of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany 4 . Rice is extremely important food crop. One of main aims in genebanks is maintaining the rice seed safe conservation. At the T.T. Chang Genetic Resources Center in International Rice Research Institute, 183 rice accessions stored up to 30 years showed more than 70% germination 5 , and more than 93% of seed lots produced in 1980 still maintained 85% germination after 33 years in storage 6 . Owing to the reduction in seed viability, the regeneration of genetic resources is considered crucial for maintaining genetic integrity. Previous studies have shown that seed regeneration needs to be carried out prior to the CN in order to prevent a large decrease in viability, which can lead to changes in genetic composition 7,8 . Previously, we showed that the mitochondrial ultrastructure of seed at the CN is abnormal owing to the decre...

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Section: Discussionmentioning

confidence: 99%

Proteomic and Carbonylation Profile Analysis at the Critical Node of Seed Ageing in Oryza sativa

Yin

Xia

et al. 2017

Sci Rep

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“…The SPE cartridges can also be packed with different materials, such as C4, C8, C18, graphitic carbon, cyano, phenyl, and HILIC, providing broad extraction for various analytes in complex environmental and biological samples, such as urine and plasma. To date, the Rapidfire SPE system has been applied in several MS studies for ultrafast and high-throughput biological, biomedical, and drug discovery studies (79–86). Recently, this SPE system was coupled with DTIMS, demonstrating the first high-throughput online SPE-DTIMS-MS platform for fast sampling and multidimensional separations (87).…”

Section: Solid-phase Extraction–drift Tube Ion Mobility Spectrometry–mentioning

confidence: 99%

Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses

Zheng

Wojcik

Zhang

et al. 2017

Annual Rev. Anal. Chem.

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Ion mobility spectrometry (IMS) is a widely used analytical technique for rapid molecular separations in the gas phase. Though IMS alone is useful, its coupling with mass spectrometry (MS) and front-end separations is extremely beneficial for increasing measurement sensitivity, peak capacity of complex mixtures, and the scope of molecular information available from biological and environmental sample analyses. In fact, multiple disease screening and environmental evaluations have illustrated that the IMS-based multidimensional separations extract information that cannot be acquired with each technique individually. This review highlights three-dimensional separations using IMS-MS in conjunction with a range of front-end techniques, such as gas chromatography, supercritical fluid chromatography, liquid chromatography, solid-phase extractions, capillary electrophoresis, field asymmetric ion mobility spectrometry, and microfluidic devices. The origination, current state, various applications, and future capabilities of these multidimensional approaches are described in detail to provide insight into their uses and benefits.

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“…The Agilent RapidFireplatform couples SPE sample purification method with FIE-MS in a single automated system, and is capable of throughputs up to 5 s per sample [52]. The RapidFire platform has mostly been used to analyse drug and drug-like molecules in body fluids and in high-throughput enzyme screenings [60,61]. Raterink et al coupled an automated LLE method with DI-MS and applied it to detect drugs and lipids in human plasma [62].…”

Section: Sample Throughput Vsmetabolite Coveragementioning

confidence: 99%

High-throughput platforms for metabolomics

Raad

Fischer

Northen

2016

Current Opinion in Chemical Biology

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Mass spectrometry has become a choice method for broad-spectrum metabolite analysis in both fundamental and applied research. This can range from comprehensive analysis achieved through time-consuming chromatography to the rapid analysis of a few target metabolites without chromatography. In this review article, we highlight current high-throughput MS-based platforms and their potential application in metabolomics. Although current MS platforms can reach throughputs up to 0.5 seconds per sample, the metabolite coverage of these platforms are low compared to low-throughput, separation-based MS methods. High-throughput comes at a cost, as it's a trade-off between sample throughput and metabolite coverage. As we will discuss, promising emerging technologies, including microfluidics and miniaturization of separation techniques, have the potential to achieve both rapid and more comprehensive metabolite analysis.

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Measurement of glycolysis reactants by high-throughput solid phase extraction with tandem mass spectrometry: Characterization of pyrophosphate-dependent phosphofructokinase as a case study

Cited by 35 publications

References 38 publications

Proteomic and Carbonylation Profile Analysis at the Critical Node of Seed Ageing in Oryza sativa

Proteomic and Carbonylation Profile Analysis at the Critical Node of Seed Ageing in Oryza sativa

Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses

High-throughput platforms for metabolomics

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