SE156:/S1/M1/D1

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.
Comment

PubMed

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
Comment

Analytical Method Information

ID	M1
Title	CE-TOF MS
Method Details ID	MS1
Sample Amount
Comment

Analytical Method Details Information

ID	MS1
Title	CE-TOF MS
Instrument	CE:Agilent CE capillary electrophoresis system (Agilent Technologies) TOF-MS:Agilent G3250AA LC/MSD TOF system (Agilent Technologies) CE-MS:Agilent G1603A
Instrument Type
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. Metabolite profiling using CE-TOF MS For the analysis of ionic metabolites, hydrophobic and high molecular weight compounds were removed by the preparative processes of liquid–liquid separation using chloroform and water, and ultrafiltration using a 5 kDa cutoff filter, respectively, prior to the metabolomic analyses. Comprehensive analysis of ionic metabolites using CE-TOF MS was performed as previously reported.
Comment_of_details

PubMed

Data Analysis Information

ID	D1
Title	Data analysis and statistics
Data Analysis Details ID	DS2
Recommended decimal places of m/z
Comment

Data Analysis Details Information

ID	DS2
Title	Data analysis and statistics
Description	Data describing the quantified or relative amounts of metabolites were integrated into one sheet. These data were standardized by subtraction of the averages from each amount and division of the resulting values by the standard deviations. The standardized data were subjected to principal component analysis (PCA) and hierarchical clustering analysis (HCA) using DrDMass (http://kanaya.naist.jp/DrDMASS/) and PermutMatrix (http://www.lirmm.fr/~caraux/PermutMatrix/), respectively. In HCA, Euclidean distance and Ward’s minimum variance were used as a dissimilarity and a linkage rule, respectively.
Comment_of_details