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MB Sample ID: SA249108
| Local Sample ID: | FB06135262 |
| Subject ID: | SU002586 |
| Subject Type: | Plant |
| Subject Species: | Malus domestica/Musa acuminata/Solanum lycopersicum/Lactuca sativa/Fragaria x ananassa/Daucus carota/Prunus persica/Allium cepa/Spinacia oleracea/Capsicum annuum/Zea mays/Allium sativum/Ocimum basilicum/Solanum tuberosum/Glycine max/Phaseolus vulgaris/Olea europaea/Cicer arietinum/Beta vulgaris/Pyrus communis |
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Subject:
| Subject ID: | SU002586 |
| Subject Type: | Plant |
| Subject Species: | Malus domestica/Musa acuminata/Solanum lycopersicum/Lactuca sativa/Fragaria x ananassa/Daucus carota/Prunus persica/Allium cepa/Spinacia oleracea/Capsicum annuum/Zea mays/Allium sativum/Ocimum basilicum/Solanum tuberosum/Glycine max/Phaseolus vulgaris/Olea europaea/Cicer arietinum/Beta vulgaris/Pyrus communis |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| FB06135262 | SA249108 | FL031472 | Onion | Species |
| FB06135262 | SA249108 | FL031472 | Yellow | Variety |
Collection:
| Collection ID: | CO002579 |
| Collection Summary: | Metabolomics experiments were performed on 20 food items collected from two local grocery stores (Whole Foods Market and Stop & Shop) depending on availability, freshness, and level of processing. Six food items of each food: apple, banana, basil, black bean, carrot, chickpeas, corn, garlic, lettuce, olives, onion, peach, pear, pepper, potato, spinach, soybean, strawberry, sugarbeet, and tomato, were bought for analysis. |
| Sample Type: | Plant |
Treatment:
| Treatment ID: | TR002598 |
| Treatment Summary: | Since we bought the plant-based food items from local grocery stores, the only treatment prior to metabolomics analysis would be those performed by the distribution pipeline to get the items to the grocery stores. We did not perform any treatments of our own prior to metabolomics analysis. |
Sample Preparation:
| Sampleprep ID: | SP002592 |
| Sampleprep Summary: | After purchase the items are directly taken into a humidity-controlled room and exposure to light was minimized. The foods are prepared following how they are commonly eaten; for example, apples cores are removed, and bananas are peeled. Food items are rinsed with water if the consumed part is exposed; for example, apples are washed while bananas are not. The edible parts are sliced and chopped into small 1 cm^3 pieces with a knife on a glass cutting board. This process is repeated for all six items. About 120 g of each item are frozen at -80C for 16 hrs and after transferred into a freeze dryer (Catalog No. 10-269-56B from LabConco/Fisher) and a dark room for 24 hrs. Afterwards the pieces are put into a coffee grinder (Kitchen Aid, 170W, Model No. BCG111OBO) and pulverized to yield a fine powder. The powder is stored at -80C and 200 mg is shipped in argon filled vials under dry ice to the metabolomics center for analysis. Three vials, technical replicates, for each food item were sent. |
Combined analysis:
| Analysis ID | AN004081 | AN004082 | AN004083 | AN004084 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | HILIC |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Focus | Thermo Q Exactive Focus | Thermo Q Exactive Focus | Thermo Q Exactive Focus |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | Peak area | Peak area | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH003023 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 65C |
| Flow Gradient: | 0-1 min 99% (A), 1-13min 99%-65% (A), 13-14.5min 65%-30% (A), 14.5-15.5min 30%-1% (A), 15.5-17min 1% (A), 17-17.5min 1%-99% (A) |
| Flow Rate: | 0.6 mL/min |
| Solvent A: | 100% water; 0.05% perfluoropentanoic acid; 0.1% formic acid |
| Solvent B: | 95% methanol/5% water; 0.05% perfluoropentanoic acid; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003024 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 65C |
| Flow Gradient: | 0-1min 45% (A), 1-4min 45%-35% (A), 4-12min 25%-11% (A), 12-15min 11%-1% (A) |
| Flow Rate: | 0.6 mL/min |
| Solvent A: | 95% methanol/5% water; 6.5mM Ammonium Bicarbonate at pH 8 |
| Solvent B: | 70% acetonitrile/30% water; 6.5mM Ammonium Bicarbonate at pH 8 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003025 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| Column Temperature: | 40C |
| Flow Gradient: | 0-4min 100% (A), 4-6min 100%-50% (A), 6-11min 50%-20% (A), 11-12min 20%-0% (A), 12-14min 0% (A) |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% water; 10mM Ammonium Formate, pH 10.8 |
| Solvent B: | 100% acetonitrile; 10mM Ammonium Formate, pH 10.8 |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003828 |
| Analysis ID: | AN004081 |
| Instrument Name: | Thermo Q Exactive Focus |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | This is for RP in positive ion mode optimized for hydrophilic compounds. Different from (2) because it uses different mobile phases. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003829 |
| Analysis ID: | AN004082 |
| Instrument Name: | Thermo Q Exactive Focus |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | This is for RP in positive ion mode optimized for hydrophobic compounds by changing the mobile phases from (1). |
| Ion Mode: | POSITIVE |
| MS ID: | MS003830 |
| Analysis ID: | AN004083 |
| Instrument Name: | Thermo Q Exactive Focus |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | This is for RP in Negative ion mode optimized for hydrophilic compounds. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS003831 |
| Analysis ID: | AN004084 |
| Instrument Name: | Thermo Q Exactive Focus |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | This is for HILIC in Negative ion mode optimized for hydrophilic compounds. |
| Ion Mode: | NEGATIVE |
