SE156:/S1/M2/D1

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Sample Set Information

ID TSE1312
Title Metabolic Profiling of Developing Pear Fruits Reveals Dynamic Variation in Primary and Secondary Metabolites, Including Plant Hormones.
Description Metabolites in the fruits of edible plants include sweet sugars, visually appealing pigments, various products with human nutritional value, and biologically active plant hormones. Although quantities of these metabolites vary during fruit development and ripening because of cell division and enlargement, there are few reports describing the actual dynamics of these changes. Therefore, we applied multiple metabolomic techniques to identify the changes in metabolite levels during the development and ripening of pear fruits (Pyrus communis L. ‘La France’). We quantified and classified over 250 metabolites into six groups depending on their specific patterns of variation during development and ripening. Approximately half the total number of metabolites, including histidine and malate, accumulated transiently around the blooming period, during which cells are actively dividing, and then decreased either rapidly or slowly. Furthermore, the amounts of sulfur-containing amino acids also increased in pear fruits around 3–4 months after the blooming period, when fruit cells are enlarging, but virtually disappeared from ripened fruits. Some metabolites, including the plant hormone abscisic acid, accumulated particularly in the receptacle prior to blooming and/or fruit ripening. Our results show several patterns of variation in metabolite levels in developing and ripening pear fruits, and provide fundamental metabolomic data that is useful for understanding pear fruit physiology and enhancing the nutritional traits of new cultivars.
Authors Oikawa A, Otsuka T, Nakabayashi R, Jikumaru Y, Isuzugawa K, Murayama H, Saito K, Shiratake K.
Reference PLoS One. 2015 Jul 13;10(7):e0131408. doi: 10.1371/journal.pone.0131408. eCollection 2015.
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Sample Information

ID S1
Title Pear fruits (Pyrus communis L. ‘La France’)
Organism - Scientific Name Pyrus communis L.
Organism - ID NCBI taxonomy:23211
Compound - ID
Compound - Source
Preparation Pear fruits (Pyrus communis L. ‘La France’) were harvested from a private orchard in Yamagata Prefecture, Japan (lat. 38°11ʹN and long. 140°28ʹE) in 2010 and 2011 with the permission of the owner. Receptacles were removed at 2 weeks before blooming (2WBB), 1 week before blooming (1WBB), the time of blooming (B), and 2 weeks after blooming (2WAB). Furthermore, peeled and deseeded fruits were collected at 1 month after blooming (1MAB), 2 months after blooming (2MAB), 3 months after blooming (3MAB), 4 months after blooming (4MAB), and the time of harvesting (H; 5 months after blooming) and 1 month after harvesting (1MAH; ripened fruits) and used for subsequent metabolomic analyses. These samples were transferred from the orchard to the laboratory as quickly as possible and were then frozen in liquid nitrogen. The frozen samples were weighed and then crushed using a homogenizer. The crushed pear fruits were placed in conical tubes and stored at –80°C until extraction. At least three biological replicates were prepared for each sample.
Sample Preparation Details ID
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Analytical Method Information

ID M2
Title LC-QTOF-MS
Method Details ID MS2
Sample Amount
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Analytical Method Details Information

ID MS2
Title LC-QTOF-MS
Instrument LC, Waters Acquity UPLC system; MS, Waters Xevo G2 Q-Tof
Instrument Type UPLC-QTOF-MS
Ionization ESI
Ion Mode positive and negative
Description Sample extraction

Crushed and frozen samples (10 g) were resuspended in 50 mL of MeOH, including internal standards for standardization of peak areas, and centrifuged (16,000 × g, 3 min, 4°C). Supernatants were dispensed for each analysis as follows: 0.5 mL for ionic metabolites, 1 mL for neutral metabolites, 1 mL for sugars, and 47.5 mL for plant hormones. Because of the small amounts of pear fruit samples obtained in the early periods (2WBB, 1WBB, and B), the initial amounts of these samples were 1 g, extracted in 20 mL of MeOH, and were separately used for each analysis as described above. The residues were subsequently used for starch analysis.

Untargeted metabolome analysis by LC-QTOF-MS
Extracts (1 mL) containing the internal positive and negative standards 2.5 μM lidocaine and 10-camphorsulfonic acid, respectively, were analyzed using LC-QTOF-MS (LC, Waters Acquity UPLC system; MS, Waters Xevo G2 Q-Tof). Analytical conditions were as follows: LC column, Acquity bridged ethyl hybrid (BEH) C18 (1.7 μm, 2.1 mm × 100 mm, Waters); solvent system, solvent A (water containing 0.1% formic acid) and solvent B (acetonitrile containing 0.1% formic acid); gradient program, 99.5%A/0.5%B at 0 min, 99.5%A/0.5%B at 0.1 min, 20%A/80%B at 10 min, 0.5%A/99.5%B at 10.1 min, 0.5%A/99.5%B at 12.0 min, 99.5%A/0.5%B at 12.1 min and 99.5%A/0.5%B at 15.0 min; flow rate, 0.3 mL/min; column temperature, 40°C; MS detection: capillary voltage, +3.0 keV, cone voltage, 25.0 V, source temperature, 120°C, desolvation temperature, 450°C, cone gas flow, 50 L/h; desolvation gas flow, 800 L/h; collision energy, 6 V; mass range, m/z 100‒1500; scan duration, 0.1 s; interscan delay, 0.014 s; mode, centroid; polarity, positive; Lockspray (leucine enkephalin): scan duration, 1.0 s; interscan delay, 0.1 s.

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Data Analysis Information

ID D1
Title Data Processing
Data Analysis Details ID DS1
Recommended decimal places of m/z
Comment


Data Analysis Details Information

ID DS1
Title Data processing (LC-QTOF-MS)
Description The data matrix was aligned with MassLynx version 4.1 (Waters). After alignment, deisotoping, and cutoff of low-intensity peaks (fewer than 500 counts), intensity values of the remaining peaks were divided by those of lidocaine ([M+H]+, m/z 235.1804) and 10-camphorsulfonic acid ([M-H]-, m/z 231.06910) for normalization. MS/MS data were acquired in ramp mode under the following analytical conditions: (1) MS: mass range, m/z 50–1500; scan duration, 0.1 s; interscan delay, 0.014 s; and (2) MS/MS: mass range, m/z 50–1500; scan duration, 0.02 s; interscan delay, 0.014 s; data acquisition, centroid mode; collision energy, ramped from 10 to 50 V. In this mode, MS/MS spectra of the top 10 ions (>1000 counts) in an MS scan were automatically obtained. When the ion intensity was less than 1000, MS/MS data acquisition was not performed. The secondary metabolites were chemically assigned by deciphering MS/MS spectra.
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