Summary of Study ST002169

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 PR001380. The data can be accessed directly via it's Project DOI: 10.21228/M8BH86 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 IDST002169
Study TitleIdentifying putative key metabolites from fingerprinting metabolomics for the authentication of rice origin: A case study of Sengcu rice
Study TypeMS Untargeted analysis
Study SummaryThe expanding scale and nature of rice fraud in the global food system has caused major economic and human health concerns. Herein, an untargeted metabolomics approach based on the UHPLC-Q-Orbitrap-HRMS system was utilized for the discrimination between authentic and commercial Sengcu rice, a local specialty cultivated by terraced farming in northern Vietnam. A total of 8398 positive and 5250 negative mode compounds were introduced to multivariate statistical analyses for the construction of classification models. The first two principal components explaining 52% of the total variance in both datasets exhibited distinguished clusters of authentic against commercial Sengcu rice. Partial least squares-discriminant analysis models were optimized to obtain the optimal number of retained components, the optimal number of variables retained in each component and the best prediction distance type for model evaluation. One component containing five positive (DMG, RSA, RCA, PAL and BOSe) and six negative mode variables (PXP, RXP, TDHP, ISS, MXP and RGB) was sufficient to discriminate between authentic and commercial Sengcu rice. The classification error rate was less than 1.1310-4, as determined from repeated k-fold cross validation. These putative signature metabolites clearly separated authentic and commercial Sengcu rice in the hierarchical clustering models. In addition, the isolated metabolites also reflected the cultivation practices of terraced farming of authentic Sengcu rice. Overall, we have proposed an effective method for the identification of key metabolites from fingerprinting metabolomics, and it could serve as a fundamental approach for other in-depth food authentication studies.
Institute
Institute of Chemistry, Vietnam Academy of Science and Technology
LaboratoryLaboratory of Environmental and Bioorganic Chemistry
Last NameDao
First NameYen Hai
Address18 Hoang Quoc Viet Street, Hanoi, 100000, Vietnam
Emailhoasinhmoitruong.vast@gmail.com
Phone+84 985859795
Submit Date2022-05-08
Num Groups2
Total Subjects71
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-06-08
Release Version1
Yen Hai Dao Yen Hai Dao
https://dx.doi.org/10.21228/M8BH86
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001380
Project DOI:doi: 10.21228/M8BH86
Project Title:Metabolomics for the authentication of Sengcu rice
Project Type:MS Untargeted analysis
Project Summary:Identifying putative key metabolites from fingerprinting metabolomics for the authentication of rice origin: A case study of Sengcu rice
Institute:Institute of Chemistry, Vietnam Academy of Science and Technology
Laboratory:Laboratory of Environmental and Bioorganic Chemistry
Last Name:Dao
First Name:Yen Hai
Address:18 Hoang Quoc Viet Street, Hanoi, 100000, Vietnam
Email:hoasinhmoitruong.vast@gmail.com
Phone:+84 985859795
Funding Source:Vietnam Academy of Science and Technology
Project Comments:Grant number TĐNDTP.03/19-21

Subject:

Subject ID:SU002255
Subject Type:Plant
Subject Species:Oryza sativa

Factors:

Subject type: Plant; Subject species: Oryza sativa (Factor headings shown in green)

mb_sample_id local_sample_id Group Treatment
SA208726M7_NegativeAuthentic Sengcu rice Negative
SA208727M4_NegativeAuthentic Sengcu rice Negative
SA208728M34_LAN_NegativeAuthentic Sengcu rice Negative
SA208729M10_NegativeAuthentic Sengcu rice Negative
SA208730M15_NegativeAuthentic Sengcu rice Negative
SA208731M23_VINH_NegativeAuthentic Sengcu rice Negative
SA208732M16_NegativeAuthentic Sengcu rice Negative
SA208733M33_MINH_NegativeAuthentic Sengcu rice Negative
SA208734M12_NegativeAuthentic Sengcu rice Negative
SA208735M25_BICH_NegativeAuthentic Sengcu rice Negative
SA208736M35_HUYEN_NegativeAuthentic Sengcu rice Negative
SA208737M29_QUANG_NegativeAuthentic Sengcu rice Negative
SA208738M22_HOA_NegativeAuthentic Sengcu rice Negative
SA208739M38_UT_NegativeAuthentic Sengcu rice Negative
SA208740M39_THO_NegativeAuthentic Sengcu rice Negative
SA208741M24_TRUYEN_NegativeAuthentic Sengcu rice Negative
SA208742MV28_SANG_NegativeAuthentic Sengcu rice Negative
SA208743M26_NegativeAuthentic Sengcu rice Negative
SA208744M30_PHONG_NegativeAuthentic Sengcu rice Negative
SA208745M14_NegativeAuthentic Sengcu rice Negative
SA208746M13_NegativeAuthentic Sengcu rice Negative
SA208747M11_NegativeAuthentic Sengcu rice Negative
SA208748M17_NegativeAuthentic Sengcu rice Negative
SA208749M27_CAU_NegativeAuthentic Sengcu rice Negative
SA208750M18_NegativeAuthentic Sengcu rice Negative
SA208751M36_THOM_NegativeAuthentic Sengcu rice Negative
SA208752M9_NegativeAuthentic Sengcu rice Negative
SA208753M6_NegativeAuthentic Sengcu rice Negative
SA208754M37_HANG_NegativeAuthentic Sengcu rice Negative
SA208755M32_KIEN_NegativeAuthentic Sengcu rice Negative
SA208756M31_BINH_NegativeAuthentic Sengcu rice Negative
SA208757M1_NegativeAuthentic Sengcu rice Negative
SA208758M2_NegativeAuthentic Sengcu rice Negative
SA208759M5_NegativeAuthentic Sengcu rice Negative
SA208760M3_NegativeAuthentic Sengcu rice Negative
SA208761M20_SUNG_NegativeAuthentic Sengcu rice Negative
SA208762M19_NegativeAuthentic Sengcu rice Negative
SA208763M1_PositiveAuthentic Sengcu rice Positive
SA208764M2_PositiveAuthentic Sengcu rice Positive
SA208765M3_PositiveAuthentic Sengcu rice Positive
SA208766M37_HANG_PositiveAuthentic Sengcu rice Positive
SA208767M32_KIEN_PositiveAuthentic Sengcu rice Positive
SA208768M30_PHONG_PositiveAuthentic Sengcu rice Positive
SA208769M31_BINH_PositiveAuthentic Sengcu rice Positive
SA208770M5_PositiveAuthentic Sengcu rice Positive
SA208771M6_PositiveAuthentic Sengcu rice Positive
SA208772M17_PositiveAuthentic Sengcu rice Positive
SA208773M27_CAU_PositiveAuthentic Sengcu rice Positive
SA208774M36_THOM_PositiveAuthentic Sengcu rice Positive
SA208775M14_PositiveAuthentic Sengcu rice Positive
SA208776M13_PositiveAuthentic Sengcu rice Positive
SA208777M9_PositiveAuthentic Sengcu rice Positive
SA208778M11_PositiveAuthentic Sengcu rice Positive
SA208779M23_VINH_PositiveAuthentic Sengcu rice Positive
SA208780M16_PositiveAuthentic Sengcu rice Positive
SA208781M38_UT_PositiveAuthentic Sengcu rice Positive
SA208782M39_THO_PositiveAuthentic Sengcu rice Positive
SA208783MV28_SANG_PositiveAuthentic Sengcu rice Positive
SA208784M35_HUYEN_PositiveAuthentic Sengcu rice Positive
SA208785M29_QUANG_PositiveAuthentic Sengcu rice Positive
SA208786M20_SUNG_PositiveAuthentic Sengcu rice Positive
SA208787M22_HOA_PositiveAuthentic Sengcu rice Positive
SA208788M24_TRUYEN_PositiveAuthentic Sengcu rice Positive
SA208789M25_BICH_PositiveAuthentic Sengcu rice Positive
SA208790M10_PositiveAuthentic Sengcu rice Positive
SA208791M12_PositiveAuthentic Sengcu rice Positive
SA208792M15_PositiveAuthentic Sengcu rice Positive
SA208793M7_PositiveAuthentic Sengcu rice Positive
SA208794M4_PositiveAuthentic Sengcu rice Positive
SA208795M33_MINH_PositiveAuthentic Sengcu rice Positive
SA208796M34_LAN_PositiveAuthentic Sengcu rice Positive
SA208797M18_PositiveAuthentic Sengcu rice Positive
SA208798M26_PositiveAuthentic Sengcu rice Positive
SA208799M19_PositiveAuthentic Sengcu rice Positive
SA208800LC3_NegativeCommercial Sengcu rice Negative
SA208801LC2_NegativeCommercial Sengcu rice Negative
SA208802LC1_NegativeCommercial Sengcu rice Negative
SA208803LC4_NegativeCommercial Sengcu rice Negative
SA208804LC5_NegativeCommercial Sengcu rice Negative
SA208805LC7_NegativeCommercial Sengcu rice Negative
SA208806LC6_NegativeCommercial Sengcu rice Negative
SA208807DB10_NegativeCommercial Sengcu rice Negative
SA208808DB9_NegativeCommercial Sengcu rice Negative
SA208809DB4_NegativeCommercial Sengcu rice Negative
SA208810DB3_NegativeCommercial Sengcu rice Negative
SA208811DB5_NegativeCommercial Sengcu rice Negative
SA208812DB6_NegativeCommercial Sengcu rice Negative
SA208813DB8_NegativeCommercial Sengcu rice Negative
SA208814DB7_NegativeCommercial Sengcu rice Negative
SA208815LC8_NegativeCommercial Sengcu rice Negative
SA208816LC10_NegativeCommercial Sengcu rice Negative
SA208817LC20_NegativeCommercial Sengcu rice Negative
SA208818LC19_NegativeCommercial Sengcu rice Negative
SA208819LC18_NegativeCommercial Sengcu rice Negative
SA208820LC21_NegativeCommercial Sengcu rice Negative
SA208821LC22_NegativeCommercial Sengcu rice Negative
SA208822LC24_NegativeCommercial Sengcu rice Negative
SA208823LC23_NegativeCommercial Sengcu rice Negative
SA208824LC17_NegativeCommercial Sengcu rice Negative
SA208825LC16_NegativeCommercial Sengcu rice Negative
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 142

Collection:

Collection ID:CO002248
Collection Summary:A total of 71 Sengcu rice samples (hereafter referred to as ‘Sengcu samples’) of the 2020 spring crop were employed for the assessment of metabolic variation between authentic (n = 37) and commercial groups (n = 34). The authentic group comprised 37 samples, each of which was originally cultivated from a separate rice paddy in Muong Vi village, Bat Xat district, Lao Cai province (22.607916 N, 103.704403 E, approximately 2314 m above sea level). Meanwhile, the commercial Sengcu samples were collectively obtained from different local market vendors in Lao Cai and Dien Bien provinces, with 24 and 10 samples per region, respectively. Since the cultivation locations of those commercial samples were not available, each commercial sample was collected from a local market, and the distance between every two markets ranged from 10 to 15 km to minimize pseudoreplication. These commercial samples were intentionally gathered immediately after the spring harvesting season of 2020 to ensure compatibility with authentic samples.
Sample Type:Rice grain

Treatment:

Treatment ID:TR002267
Treatment Summary:A total of 71 Sengcu rice samples of the 2020 spring crop were employed for the assessment of metabolic variation between authentic (n = 37) and commercial groups (n = 34). Two analysis polarity modes, positive and negative ionization, were implemented on the samples. The capillary voltage was 3.0 kV in positive mode and -2.5 kV in negative mode.

Sample Preparation:

Sampleprep ID:SP002261
Sampleprep Summary:Extraction of rice samples followed the ultrasonically assisted extraction (UAE) procedure with slight adjustments (Xiao et al., 2018). An A&D HR-120 research-grade analytical balance (A&D, Tokyo, Japan), a Universal 320 centrifuge (Hettich, Georgia, USA) and an Elmasonic 80H ultrasonic bath (Elma Schmidbauer, Singen, Germany) were used for sample extraction. First, each sample was sieved through a 100-m sieve, and then 500  0.1 mg of each homogenized sample was inserted into a 15-mL falcon tube. Afterward, 5 mL of solvent containing ultra-pure water and methanol (1/1, v/v) was added to the tube, and the sample was sonicated for 30 min at 40C and then centrifuged at 6080 x g. The supernatant was filtered through a 0.22-m nylon filter. Consequently, 1 mL of filtered solution was transferred into a dark vial and analyzed by UHPLC-Q-Orbitrap-HRMS as described previously. Procedure blanks consisting of water and methanol (1/1, v/v) were injected after each analyzed sample for background interference removal. Two standard calibrated solutions, Pierce LTQ Velos ESI Positive Ion and Pierce LTQ Velos ESI Negative Ion, were used at the beginning, at the end of each run and after each batch of fifteen analyzed samples.

Combined analysis:

Analysis ID AN003553 AN003554
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Thermo Hypersil GOLD aQ C18 Polar Endcapped column (150 x 2.1 mm i.d. x 3 um) Thermo Hypersil GOLD aQ C18 Polar Endcapped column (150 x 2.1 mm i.d. x 3 um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Focus Thermo Q Exactive Focus
Ion Mode POSITIVE NEGATIVE
Units m/z values m/z values

Chromatography:

Chromatography ID:CH002625
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Thermo Hypersil GOLD aQ C18 Polar Endcapped column (150 x 2.1 mm i.d. x 3 um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003310
Analysis ID:AN003553
Instrument Name:Thermo Q Exactive Focus
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Signal detection was carried out in both positive and negative modes in the combination of “Full-scan” (FullMS) and “All-Ion Fragmentation” (AIF) experiments. Regarding FullMS, the inspected mass ranged from 100 to 1600 Da under a resolution of 70 000 FWHM with m/z = 200. The automatic gain control (AGC) target was 106, the maximum injection time (IT) was 50 ms in both modes, and the radio frequency (RF) lens was 50 Hz. Throughout the FullMS experiment, the higher-energy collisional dissociation collision cell was switched off. In terms of AIF, the precursor fragmentation in positive and negative polarities was between 80 and 1000 Da mass range under a resolution of 35 000 FWHM with m/z = 200 and a normalized collision energy of 35%. An isolation window of 2 m/z was used with an AGC target of 105, an IT of 50 ms in both modes and an RF lens of 50 Hz. The UHPLC-Q-Orbitrap-HRMS system was operated using XcaliburTM 4.1 software (Thermo Fisher Scientific, Massachusetts, USA).
Ion Mode:POSITIVE
  
MS ID:MS003311
Analysis ID:AN003554
Instrument Name:Thermo Q Exactive Focus
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Signal detection was carried out in both positive and negative modes in the combination of “Full-scan” (FullMS) and “All-Ion Fragmentation” (AIF) experiments. Regarding FullMS, the inspected mass ranged from 100 to 1600 Da under a resolution of 70 000 FWHM with m/z = 200. The automatic gain control (AGC) target was 106, the maximum injection time (IT) was 50 ms in both modes, and the radio frequency (RF) lens was 50 Hz. Throughout the FullMS experiment, the higher-energy collisional dissociation collision cell was switched off. In terms of AIF, the precursor fragmentation in positive and negative polarities was between 80 and 1000 Da mass range under a resolution of 35 000 FWHM with m/z = 200 and a normalized collision energy of 35%. An isolation window of 2 m/z was used with an AGC target of 105, an IT of 50 ms in both modes and an RF lens of 50 Hz. The UHPLC-Q-Orbitrap-HRMS system was operated using XcaliburTM 4.1 software (Thermo Fisher Scientific, Massachusetts, USA).
Ion Mode:NEGATIVE
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