Mapping and comparative proteomic analysis of the starch biosynthetic pathway in rice by 2D PAGE/MS.

KEY MESSAGE: Our results not only provide a comprehensive overview of the starch biosynthetic pathway in the developing endosperm but also reveal some important protein markers that regulate the synthesis of starch. In human diets, rice (Oryza sativa L.) is an important source of starch, a substantial amount of which is accumulated in developing endosperm. A better understanding of the complicated pathways involved in starch biosynthesis is needed to improve the yield and quality of rice and other cereal crops through breeding. One pure line rice mutant, SA0419, was induced from a wild-type rice, TNG67, by sodium azide mutagenesis; therefore, TNG67 and SA0419 share the same genetic background. SA0419 is, however, a unique glutinous rice with a lower amylose content (8%) than that of TNG67 (20%), and the grains of SA0419 develop earlier and faster than those of TNG67. In this study, we used a comparative proteomic analysis to identify the differentially expressed proteins that may explain the differences in starch biosynthesis and the characteristics of TNG67 and SA0419. A gel-based proteomic approach was applied to profile the expressed proteome in the developing endosperm of these two rice varieties by nano-LC/MS/MS. Several over-expressed proteins were found in SA0419, such as plastidial ADP-glucose pyrophosphorylase (AGPase), phosphoglucomutase (PGM), pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP), 6-phosphofructokinase (PFK), pyruvate phosphate dikinase (PPDK), starch branching enzymes (SBE) and starch debranching enzyme (SDBE), with those proteins mainly being involved in the pathways of starch metabolism and PPDK-mediated gluconeogenesis. Those over-expressed enzymes may contribute to the relatively early development, similar starch accumulation and rapid grain filling of SA0419 as compared with TNG67. This study provides a detailed biochemical description of starch biosynthesis and related information regarding a unique starch mutant that may assist future research efforts to improve the yield and quality of grain and starch in rice through breeding.

2-DE combined with two-layer feature selection accurately establishes the origin of oolong tea.

Taiwan is known for its high quality oolong tea. Because of high consumer demand, some tea manufactures mix lower quality leaves with genuine Taiwan oolong tea in order to increase profits. Robust scientific methods are, therefore, needed to verify the origin and quality of tea leaves. In this study, we investigated whether two-dimensional gel electrophoresis (2-DE) and nanoscale liquid chromatography/tandem mass spectroscopy (nano-LC/MS/MS) coupled with a two-layer feature selection mechanism comprising information gain attribute evaluation (IGAE) and support vector machine feature selection (SVM-FS) are useful in identifying characteristic proteins that can be used as markers of the original source of oolong tea. Samples in this study included oolong tea leaves from 23 different sources. We found that our method had an accuracy of 95.5% in correctly identifying the origin of the leaves. Overall, our method is a novel approach for determining the origin of oolong tea leaves.

Analysis of flavonoids by graphene-based surface-assisted laser desorption/ionization time-of-flight mass spectrometry.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a simple and fast technique for the analysis of large biomolecules but is not suitable for the detection of low molecular weight molecules and compounds, such as flavonoids and phenylpropanoids, mainly due to the lack of an appropriate matrix. Flavonoids and phenylpropanoids, such as coumarin and its derivatives, have attracted much attention recently because of their pharmacological activities and putative therapeutic benefits. In this study, we developed a quick and simple LDI-TOF MS method for the detection of flavonoids and the derivatives of coumarin. Analytes were spotted onto a matrix of graphene-based nanoparticles and then analyzed by LDI-TOF MS in the negative ion mode. Analysis of the sensitivity and effect of different graphene-based nanoparticles including graphene, graphene oxide, and reduced graphene oxide on desorption/ionization of analytes showed that graphene oxide was the most suitable matrix. Moreover, we found that graphene oxide sheets of larger lateral size resulted in better desorption/ionization efficiency. Overall, we show that graphene oxide is a useful matrix for the analysis of flavonoids and the derivatives of coumarin by LDI-TOF MS in the negative ion mode.

Magnetic iron oxide nanoparticle enrichment of phosphopeptides on a radiate microstructure MALDI chip.

Several methods can be used to improve the enrichment of phosphorylated proteins. In this paper, phosphopeptides were enriched using magnetic iron(II,III) oxide (magnetite, Fe(3)O(4)) nanoparticles (NPs) on a radiate microstructure silicon chip and then analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) without further purification processes. We have developed a radiate microstructure chip on which samples can be concentrated for analysis by MALDI-TOFMS. The phosphoprotein digests and magnetic iron oxide NPs aqueous solution were deposited onto the central zone of the radiate microstructure silicon chip and enabled the on-chip enrichment of phosphopeptides. Microscopic analysis confirmed that the applied samples were confined to the central zone. Sample spots focused on the chip were much smaller than those on an unmodified plate with the same total volume. Different additives were used and optimized processes were performed to minimize non-phosphopeptides interference. These data collectively demonstrate that our on-chip phosphopeptide enrichment protocol is a rapid and easy-to-use method for phosphoproteome analysis.

Quantum dot enhancement of peptide detection by matrix-assisted laser desorption/ionization mass spectrometry.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is a rapid and sensitive tool for characterizing a wide variety of biomolecules. However, invisible "sweet spots" that form during heterogeneous cocrystallization minimize the analytical throughput and affect the reproducibility of MALDI analysis. In this study, visible "sweet spots" were generated on a metallic sample plate by quantum dots (QDs)-assisted MALDI analysis. To the best of our knowledge, this is the first report to demonstrate that "sweet spots" can be observed directly without using a microscope. The proper proportion of matrix to QDs that results in optimal crystallization was also examined. The signals of standard peptides and phosphopeptides obtained by QD-assisted MALDI analysis were 5- and 3-fold higher, respectively, than those obtained by conventional MALDI analysis. For peptide mixtures, the QD-assisted MALDI analysis not only resulted in more intense peptide signals but also resulted in a greater number of peaks, thereby allowing for better detection of individual peptides in peptide mixtures. Moreover, we demonstrated that application of QDs to a radiate microstructure chip followed by MALDI analysis enhanced the detection of peptide signals. Overall, we show that this method is a simple, sensitive, and high-throughput technique for peptide detection.