SE134:/S1/M1

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Sample Set Information

ID SE134
Title Unbiased profiling of volatile organic compounds in the headspace of Allium plants using an in-tube extraction device.
Description Plants produce and emit important volatile organic compounds (VOCs), which have an essential role in biotic and abiotic stress responses and in plant–plant and plant–insect interactions. In order to study the bouquets from plants qualitatively and quantitatively, a comprehensive, analytical method yielding reproducible results is required.

We applied in-tube extraction (ITEX) and solid-phase microextraction (SPME) for studying the emissions of Allium plants. The collected HS samples were analyzed by gas chromatography–time-of-flight–mass spectrometry (GC-TOF–MS), and the results were subjected to multivariate analysis. In case of ITEX-method Allium cultivars released more than 300 VOCs, out of which we provisionally identified 50 volatiles. We also used the VOC profiles of Allium samples to discriminate among groups of A. fistulosum, A. chinense (rakkyo), and A. tuberosum (Oriental garlic). As we found 12 metabolite peaks including dipropyl disulphide with significant changes in A. chinense and A. tuberosum when compared to the control cultivar, these metabolite peaks can be used for chemotaxonomic classification of A. chinense, tuberosum, and A. fistulosum.

Authors Kusano M, Kobayashi M, Iizuka Y, Fukushima A, Saito K.
Reference BMC Res Notes. 2016 Feb 29;9:133. doi: 10.1186/s13104-016-1942-5.
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Sample Information

ID S1
Title Allium fistulosum species
Organism - Scientific Name Allium fistulosum L.
Organism - ID NCBI taxonomy:35875
Compound - ID
Compound - Source
Preparation Ten Allium (A.) fistulosum species, six spring onion cultivars, two scallions, and two Japanese-leek cultivars, rakkyo (A. chinense) and Oriental garlic (A. tuberosum), were purchased from a grocer in Kawasaki, Japan or harvested in a Japanese field (see Table 1 and Additional file 2). After removing the roots, a 10-cm length of the sheath and the basal plate of each plant sample were collected and chopped with stainless steel surgical blades (Feather, Tokyo, Japan). Out of the A. fistulosum cultivars, four were grown by applying a method (hilling) similar to that used for growing the leek A. ampeloprasum var. porrum to obtain longer white stems for consumption in Japan (Fig. 1f, g, h, l). Each sample was immediately frozen in liquid nitrogen and kept at −80 °C until use. As the group of samples of Mikata spring onion (class01) was gathered center of the PCA score scatter plot (Fig. 4), this cultivar was chosen as the control.
Sample Preparation Details ID
Comment


Table 1
Allium species used in this study
Class in
PCA
Binomial
name
Species
name
Bland name Harvested field
in Japan
08 Allium
chinense
Rakkyo Young rakkyo Namegata,Ibaraki
01 Allium
fistulosum
Spring onion Mikata spring onion Hamamatsu,
Shizuoka
02 Allium
fistulosum
Green spring onion
Aoi-chan green spring onion Akitakata,
Hiroshima
03 Allium
fistulosum
Scallion Hakata scallion Hakata, Fukuoka
04 Allium
fistulosum
Green spring
onion
Green spring onion from
Nagareyama chiba
Nagareyama, Chiba
05 Allium
fistulosum
White spring
onion
White spring onion from
Nagano
Nagano
06 Allium
fistulosum
Leek Shimonita leek Gunma
07 Allium
fistulosum
Leek Shirakami leek Noshiro, Akita
09 Allium
fistulosum
Scallion Kujo scallion Nagahama, Gifu
11 Allium
fistulosum
Spring onion Goudo spring onion Anpachi, Gifu
10 Allium
tuberosum
Oriental garlic Oriental garlic Nagahama, Shiga
12 Allium
fistulosum
Red spring
onion
Red spring onion Tsuruoka, Yamagata

Analytical Method Information

ID M1
Title GC-TOF MS
Method Details ID MS1
Sample Amount 500 μl
Comment


Analytical Method Details Information

ID MS1
Title GC-TOF MS
Instrument Pegasus III TOF mass spectrometer (LECO)
Instrument Type
Ionization EI
Ion Mode Positive
Description Sample preparation procedure

The samples were crushed into powder (2 min at 4 °C) in a Mixer Mill MM 311 instrument featuring a grinding jar with a stainless steel screw cap (Restech, Tokyo, Japan) and the frozen powder from each sample (flesh weight, 1 g) was weighed in a 20-ml HS vial (Supelco, MO, USA). For VOC profiling of Allium plants we used a modified method of Tikunov et al. and Kusano et al. Briefly, the 20-ml HS-GC vial (Supelco) containing the frozen powder was closed with a magnetic screw cap (AMR, Tokyo, Japan) for ITEX- and SPME-analysis. Then, 1 ml of 100 mM 2,2′,2′’,2′’’-(ethane-1,2-diyldinitrilo) tetraacetic acid (EDTA)- NaOH water solution (pH 7.5) was added to each vial; the water derived from an Allium sample was considered to be equal to 1 ml. After vortexing, 10 μl of solution containing n-decane (d 22 , 99 %; 50 μM), n-pentadecane (d 32 , 98 %; 50 μM), n-eicosane (d 42 , 98 %; 50 μM) for definition of RI and EPA524.2 fortification solution (20 μg/ml of fluorobenzene, 4-bromofluorobenzene, and 1,2-dichlorobenzene-d4) as ISs was mixed in methanol, then solution was added to each vial as IS. Solid CaCl2 was added to obtain a final concentration of 5 M and the samples were stored overnight at 22 °C.


HS collection using the SPME fiber

The SPME device for a CTC CombiPAL auto-sampler (CTC Analytics, Zwingen, Switzerland) was purchased from AMR (Tokyo, Japan). We used an SPME fiber comprised of a 65-μm-thick layer of polydimethylsiloxane (PDMS)/divinylbenzene (DVB)-fused silica (FS) fiber/stainless-steel (SS) tube. Before analysis, the fiber was conditioned at 250 °C for 30 s in the injection port of an Agilent 6890 N gas chromatograph (Agilent Technologies, Wilmington, USA) equipped with a 30 m × 0.25 mm inner diameter fused-silica capillary column with a chemically bound 0.25-μl film Rtx-5 Sil MS stationary phase (RESTEK, Bellefonte, USA). Collection of volatiles was carried out by inserting the SPME-fiber to the vial and by trapping the VOCs for 20 min at 80 °C under continuous agitation. After HS collection it was placed in the injection port of the gas chromatograph that was coupled to a Pegasus III TOF mass spectrometer (LECO, St. Joseph, USA). The thermodesorption of VOCs occurred for 15 s at 250 °C.


HS collection using the ITEX device

We used a CTC CombiPAL auto-sampler (PAL COMBI-xt) featuring the ITEX device PAL ITEX-2 option (CTC Analytics). The ITEX procedure was controlled with a PAL Cycle Composer (CTC analytics). We conducted preliminary experiments to choose an appropriate sorbent material from the four materials, Tenax TA, Tenax GR (TGR), Carbosieve SIII (CSIII) and mixed TGR and CSIII (TGR/CSIII), that are commercially available (data not shown). Then, we chose that the sorbent material for the ITEX-2 portion was TGR (80/100 mesh)/CSIII (60/80 mesh). The parameters for HS collection were as described in the Additional file 2. After HS collection, 500 μl of the HS sample were injected into the injection port of the gas chromatograph coupled to the mass spectrometer used for HS collection by ITEX.


GC-TOF–MS analysis

GC-TOF–MS conditions were as described in the Additional file 2. Data acquisition was on a Pegasus III TOF mass spectrometer (LECO); the acquisition rate was 30 spectra/s in the mass range of a mass-to-charge ratio of m/z = 30–550. Five ISs were used for data normalization.

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