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MB Sample ID: SA174211
| Local Sample ID: | Sample_16A_Jeanmaire_LIU_GA7_01_2912 |
| Subject ID: | SU001931 |
| Subject Type: | Plant |
| Subject Species: | Tetrastigma loheri |
| Taxonomy ID: | 1006131 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001931 |
| Subject Type: | Plant |
| Subject Species: | Tetrastigma loheri |
| Taxonomy ID: | 1006131 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Sample_16A_Jeanmaire_LIU_GA7_01_2912 | SA174211 | FL021368 | Infected | factor |
Collection:
| Collection ID: | CO001924 |
| Collection Summary: | Cuttings of Rafflesia lagascae-infected Tetrastigma loheri Gagnep. and non-infected shoots were collected from San Lorenzo Ruiz Municipality, Mt. Guinatungan, Camarines Norte, Philippines. The non-infected cuttings were taken from sufficiently mature woody host vines that did not have any visible sign of Rafflesia infection (i.e. Rafflesia floral buds/scars absent), but mature enough that they could presumably support an infection since Rafflesia has never been observed to infect juvenile vines. Sections within ca. 5 cm of a Rafflesia bud, as well as comparable sections from non-infected cuttings, were subjected to LC-MS experiments. |
| Sample Type: | Plant |
Treatment:
| Treatment ID: | TR001943 |
| Treatment Summary: | Sections within ca. 5 cm of a Rafflesia bud (i.e. infected), as well as comparable sections from non-infected cuttings, were subjected to LC-MS experiments. |
Sample Preparation:
| Sampleprep ID: | SP001937 |
| Sampleprep Summary: | Samples were first extracted in methanol (25 mg ground in 700 µL methanol). The extracts were evaporated to dryness under a gentle stream of nitrogen. Samples were prepared for injection by reconstituting in 0.3 mL of 1:1 MeOH/water. |
Combined analysis:
| Analysis ID | AN003005 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Scientific Ultimate-3000 UHPLC system |
| Column | Agilent Acclaim 120 C18-column (2.1 mm x 100 mm, 5 µm) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Bruker Daltonics maXis-II UHR-ESI-QqTOF |
| Ion Mode | POSITIVE |
| Units | ion intensity |
Chromatography:
| Chromatography ID: | CH002228 |
| Instrument Name: | Thermo Scientific Ultimate-3000 UHPLC system |
| Column Name: | Agilent Acclaim 120 C18-column (2.1 mm x 100 mm, 5 µm) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002794 |
| Analysis ID: | AN003005 |
| Instrument Name: | Bruker Daltonics maXis-II UHR-ESI-QqTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Raw data were analyzed by using the online version of XCMS metabolomics software (version 1.10.9; Tautenhahn et al. 2012). To analyze the data in XCMS, we applied a pairwise comparison between infected and non-infected samples with default parameters for Bruker Q-TOF. After XCMS analysis, the difference reports were filtered. The features from XCMS with p-value < 0.05, intensities above 50000, and fold difference of at least 5, were analyzed further in Bruker Compass Data Analysis v4.3 and Metfrag Web (Ruttkies et al. 2016; https://msbi.ipb-halle.de/MetFragBeta/) to identify metabolites of interest. The neutral molecular formula of the precursor ions (desired features) and their MS/MS fragmentation spectra were then obtained in Bruker Compass Data Analysis and given as input in the MS/MS peak list in Metfrag. All other settings were kept at default values. Candidate metabolites were then retrieved with the highest scoring candidates subjected to additional analysis in CFM-ID (Allen et al. 2014; http://cfmid.wishartlab.com/) to confirm Metfrag candidates. Metfrag and CFM-ID are silico fragmentation tools that utilize known compounds from structure databases to calculate fragments that are matched to experimentally obtained spectra (Blaženović et al. 2018). In addition to these automated approaches, we have also performed a manual dereplication approach to verify the metabolites of interest, as described in previous publications (Gödecke et al. 2009; Nikolić et al. 2012; Nikolić et al. 2015; Nikolic et al. 2017). |
| Ion Mode: | POSITIVE |
