Summary of Study ST003848

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002406. The data can be accessed directly via it's Project DOI: 10.21228/M8N240 This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST003848
Study TitleOccurrence of white flesh color and refreshing flavor following phytoene synthase 2A gene variation in loquat fruit
Study SummaryThe white fleshed loquat (Eriobotrya japonica) fruit are more preferentially chosen by consumers than the orange fleshed ones. However, the metabolic basis that the white-fleshed loquat are more favorable is not known. The project carried out widely targeted metabolomes on 18 representative cultivars, and identified 1420 metabolites with 223 differentially accumulated metabolites between the two groups. The metabolite comparison in this project demonstrated that low levels of bitter or astringent compounds, such as flavonoids, lignans and coumarins, phenolic acids, nucleotides, alkaloids, and terpenoids, may confer to refreshing flavor of the white fleshed loquats. Furthermore, 18 metabolic biomarkers were identified by machine learning to distinguish loquat flesh colors.
Institute
Fujian Academy of Agricultural Science
DepartmentFruit Research Institute
Last NameSu
First NameWenbing
AddressPudang 104, Jin'an District, Fuzhou, Fujian, 350013, China
Emailsuwenbing13@163.com
Phone86-18459155333
Submit Date2025-02-14
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-04-25
Release Version1
Wenbing Su Wenbing Su
https://dx.doi.org/10.21228/M8N240
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002406
Project DOI:doi: 10.21228/M8N240
Project Title:Occurrence of white flesh color and refreshing flavor following phytoene synthase 2A gene variation in loquat fruit
Project Summary:The white fleshed loquat fruit are more preferentially chosen by consumers than the orange fleshed ones, however, the metabolic basic that the white-fleshed loquat are more favorable is most known. The project carried out widely targeted metabolomes on 18 representative cultivars, and identified 1420 metabolites with 223 differentially accumulated metabolites between the two groups.
Institute:Fujian Academy of Agricultural Science
Department:Fruit Research Institute
Last Name:Su
First Name:Wenbing
Address:Pudang 104, Jin'an District, Fuzhou, Fujian, 350013, China
Email:suwenbing13@163.com
Phone:86-18459155333

Subject:

Subject ID:SU003982
Subject Type:Plant
Subject Species:Loquat (Eriobotrya japonica)
Taxonomy ID:32224
Gender:Not applicable

Factors:

Subject type: Plant; Subject species: Loquat (Eriobotrya japonica) (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA420626JFZ-3-Norange-flesh
SA420627TNK-3-Porange-flesh
SA420628DWX-2-Norange-flesh
SA420629ULLERA-2-Porange-flesh
SA420630ULLERA-3-Porange-flesh
SA420631ULLERA-3-Norange-flesh
SA420632ULLERA-2-Norange-flesh
SA420633ULLERA-1-Norange-flesh
SA420634TNK-3-Norange-flesh
SA420635TNK-2-Norange-flesh
SA420636TNK-1-Norange-flesh
SA420637ZZ-6-1-Porange-flesh
SA420638TNK-1-Porange-flesh
SA420639ZZ-6-2-Porange-flesh
SA420640ZZ-6-3-Porange-flesh
SA420641JFZ-2-Norange-flesh
SA420642JFZ-1-Norange-flesh
SA420643GN-3-Norange-flesh
SA420644GN-2-Norange-flesh
SA420645GN-1-Norange-flesh
SA420646DWX-3-Norange-flesh
SA420647DHP-1-Norange-flesh
SA420648DHP-2-Norange-flesh
SA420649DHP-3-Norange-flesh
SA420650TNK-2-Porange-flesh
SA420651ULLERA-1-Porange-flesh
SA420652DWX-1-Norange-flesh
SA420653DWX-3-Porange-flesh
SA420654DWX-1-Porange-flesh
SA420655DHP-3-Porange-flesh
SA420656DHP-2-Porange-flesh
SA420657DHP-1-Porange-flesh
SA420658GN-1-Porange-flesh
SA420659GN-2-Porange-flesh
SA420660GN-3-Porange-flesh
SA420661JFZ-1-Porange-flesh
SA420662JFZ-2-Porange-flesh
SA420663JFZ-3-Porange-flesh
SA420664ZZ-6-1-Norange-flesh
SA420665ZZ-6-2-Norange-flesh
SA420666ZZ-6-3-Norange-flesh
SA420667DWX-2-Porange-flesh
SA420668GF-1-Nwhite-flesh
SA420669GF-2-Nwhite-flesh
SA420670GF-3-Nwhite-flesh
SA420671ZB-2-Nwhite-flesh
SA420672ZB-1-Nwhite-flesh
SA420673XF-3-Nwhite-flesh
SA420674ZB-3-Nwhite-flesh
SA420675XB-2-2-Nwhite-flesh
SA420676RTBS-1-Nwhite-flesh
SA420677RTBS-2-Nwhite-flesh
SA420678XB-2-1-Nwhite-flesh
SA420679SYB-1-Nwhite-flesh
SA420680SYB-2-Nwhite-flesh
SA420681SYB-3-Nwhite-flesh
SA420682XF-2-Nwhite-flesh
SA420683XF-1-Nwhite-flesh
SA420684XB-8-3-Nwhite-flesh
SA420685XB-1-1-Nwhite-flesh
SA420686XB-1-2-Nwhite-flesh
SA420687XB-8-2-Nwhite-flesh
SA420688XB-8-1-Nwhite-flesh
SA420689XB-2-3-Nwhite-flesh
SA420690XB-1-3-Nwhite-flesh
SA420691RTBS-3-Nwhite-flesh
SA420692BL-1-Pwhite-flesh
SA420693BY-3-Nwhite-flesh
SA420694GF-3-Pwhite-flesh
SA420695XB-1-1-Pwhite-flesh
SA420696SYB-3-Pwhite-flesh
SA420697SYB-2-Pwhite-flesh
SA420698SYB-1-Pwhite-flesh
SA420699RTBS-3-Pwhite-flesh
SA420700RTBS-2-Pwhite-flesh
SA420701RTBS-1-Pwhite-flesh
SA420702GF-2-Pwhite-flesh
SA420703XB-1-3-Pwhite-flesh
SA420704GF-1-Pwhite-flesh
SA420705BY-3-Pwhite-flesh
SA420706BY-2-Pwhite-flesh
SA420707BY-1-Pwhite-flesh
SA420708BXZ-3-Pwhite-flesh
SA420709BXZ-2-Pwhite-flesh
SA420710BXZ-1-Pwhite-flesh
SA420711BL-3-Pwhite-flesh
SA420712XB-1-2-Pwhite-flesh
SA420713XB-2-1-Pwhite-flesh
SA420714BY-2-Nwhite-flesh
SA420715ZB-3-Pwhite-flesh
SA420716BY-1-Nwhite-flesh
SA420717BXZ-3-Nwhite-flesh
SA420718BXZ-2-Nwhite-flesh
SA420719BXZ-1-Nwhite-flesh
SA420720BL-3-Nwhite-flesh
SA420721BL-2-Nwhite-flesh
SA420722BL-2-Pwhite-flesh
SA420723ZB-2-Pwhite-flesh
SA420724XB-2-2-Pwhite-flesh
SA420725ZB-1-Pwhite-flesh
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Collection:

Collection ID:CO003975
Collection Summary:Fruit from eight-year-old loquat trees of 18 cultivars, including seven traditional orange fleshed cultivars and eleven white fleshed cultivars, were collected and immediately frozen in liquid nitrogen, then freeze-dried under vacuum and grounded into fine powder using a mixer mill (MM400, Retsch, China) at 30 Hz for 1.5 mins. Thereafter, the powder samples were stored in -80 °C refrigerator for widely targeted metabolomics analyses.
Sample Type:plant fruit

Treatment:

Treatment ID:TR003991
Treatment Summary:no treatment was carried out on the fruits. The fruits are natural grouped into two classes (the white-fleshed cultivars and the orange-fleshed cultivars), this work focus on identifying metabolites contribute to flavor difference of the two groups.

Sample Preparation:

Sampleprep ID:SP003988
Sampleprep Summary:Weigh 50 mg of sample powder using an electronic balance (MS105DΜ) and add 1200 μL of -20 °C pre-cooled 70% methanolic aqueous internal standard extract (less than 50 mg added at the rate of 1200 μL extractant per 50 mg sample). Vortex once every 30 min for 30 sec, for a total of 6 times. After centrifugation (rotation speed 12000 rpm, 3 min), the supernatant was aspirated, and the sample was filtered through a microporous membrane (0.22 μm pore size) and stored in the injection vial for UPLC-MS/MS analysis.

Combined analysis:

Analysis ID AN006323 AN006324
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1200 Agilent 1200
Column Agilent ZORBAX RRHD SB-C18 (100 x 2.1mm,1.8um) Agilent ZORBAX RRHD SB-C18 (100 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type QTRAP QTRAP
MS instrument name ABI Sciex 6500 QTrap ABI Sciex 6500 QTrap
Ion Mode POSITIVE NEGATIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH004797
Chromatography Summary:Agilent SB-C18 Reversed phase column was used
Instrument Name:Agilent 1200
Column Name:Agilent ZORBAX RRHD SB-C18 (100 x 2.1mm,1.8um)
Column Temperature:40°C
Flow Gradient:95% A, 5%B. Within 9 min, a linear gradient to 5% A, 95% B was programmed, and a composition of 5% A, 95% B was kept for 1 min. Subsequently, a composition of 95% A, 5.0% B was adjusted within 1.1 min and kept for 2.9 min.
Flow Rate:0.35 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS006024
Analysis ID:AN006323
Instrument Name:ABI Sciex 6500 QTrap
Instrument Type:QTRAP
MS Type:ESI
MS Comments:The ESI source operation parameters were as follows: source temperature 500°C; ion spray voltage (IS) 5500 V (positive ion mode)/-4500 V (negative ion mode); ion source gas I (GSI), gas II(GSII), curtain gas (CUR) were set at 50, 60, and 25 psi, respectively; the collision-activated dissociation(CAD) was high. QQQ scans were acquired as MRM experiments with collision gas (nitrogen) set to medium. DP(declustering potential) and CE(collision energy) for individual MRM transitions was done with further DP and CE optimization. A specific set of MRM transitions were monitored for each period according to the metabolites eluted within this period.
Ion Mode:POSITIVE
  
MS ID:MS006025
Analysis ID:AN006324
Instrument Name:ABI Sciex 6500 QTrap
Instrument Type:QTRAP
MS Type:ESI
MS Comments:The ESI source operation parameters were as follows: source temperature 500°C; ion spray voltage (IS) 5500 V (positive ion mode)/-4500 V (negative ion mode); ion source gas I (GSI), gas II(GSII), curtain gas (CUR) were set at 50, 60, and 25 psi, respectively; the collision-activated dissociation(CAD) was high. QQQ scans were acquired as MRM experiments with collision gas (nitrogen) set to medium. DP(declustering potential) and CE(collision energy) for individual MRM transitions was done with further DP and CE optimization. A specific set of MRM transitions were monitored for each period according to the metabolites eluted within this period.
Ion Mode:NEGATIVE
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