MTBLS893: Metabolic alterations in pea leaves during arbuscular mycorrhiza development.

Abstract

Arbuscular mycorrhiza (AM) is known to be a mutually beneficial plant-fungal symbiosis; however, the effect of mycorrhization is heavily dependent on multiple biotic and abiotic factors. Therefore, for the proper employment of such plant-fungal symbiotic systems in agriculture, a detailed understanding of the molecular basis of the plant developmental response to mycorrhization is needed. The aim of this work was to uncover the physiological and metabolic alterations in pea (Pisum sativum L.) leaves associated with mycorrhization at key plant developmental stages. Plants of pea cv. Finale were grown in constant environmental conditions under phosphate deficiency. The plants were analyzed at six distinct time points, which corresponded to certain developmental stages of the pea: I: 7 days post inoculation (DPI) when the second leaf is fully unfolded with one pair of leaflets and a simple tendril; II: 21 DPI at first leaf with two pairs of leaflets and a complex tendril; III: 32 DPI when the floral bud is enclosed; IV: 42 DPI at the first open flower; V: 56 DPI when the pod is filled with green seeds; and VI: 90-110 DPI at the dry harvest stage. Inoculation with Rhizophagus irregularis had no effect on the fresh or dry shoot weight, the leaf photochemical activity, accumulation of chlorophyll a, b or carotenoids. However, at stage III (corresponding to the most active phase of mycorrhiza development), the number of internodes between cotyledons and the youngest completely developed leaf was lower in the inoculated plants than in those without inoculation. Moreover, inoculation extended the vegetation period of the host plants, and resulted in increase of the average dry weight per seed at stage VI. The leaf metabolome, as analyzed with GC-MS, included about three hundred distinct metabolites and showed a strong correlation with plant age, and, to a lesser extent, was influenced by mycorrhization. Metabolic shifts influenced the levels of sugars, amino acids and other intermediates of nitrogen and phosphorus metabolism. The use of unsupervised dimension reduction methods showed that (i) at stage II, the metabolite spectra of inoculated plants were similar to those of the control, and (ii) at stages IV and V, the leaf metabolic profiles of inoculated plants shifted towards the profiles of the control plants at earlier developmental stages. At stage IV the inoculated plants exhibited a higher level of metabolism of nitrogen, organic acids, and lipophilic compounds in comparison to control plants. Thus, mycorrhization led to the retardation of plant development, which was also associated with higher seed biomass accumulation in plants with an extended vegetation period. The symbiotic crosstalk between host plant and AM fungi leads to alterations in several biochemical pathways the details of which need to be elucidated in further studies.

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 Authors: Roman K Puzanskiy

  Release date: 09-Feb-2020

 Status: Public

Organism(s)

Pisum sativum

  Study Design

MTBLS:untargeted metabolites

CHMO:gas chromatography-mass spectrometry

IOBC:Arbuscular mycorrhiza

IOBC:plant growth

PATO:physiological state

  Experimental Factors

Days post inoculation

Mycorrhization

Plant growth stage

Protocol Description
Sample collection

The low, determinate pea (Pisum sativum L.) cv. Finale (Cebeco, Rotterdam, The Netherlands) with dark green leaves, white flowers and round green seeds[1] was used to study Arbuscular mycorrhiza (AM) mediated metabolic alterations in leaves. This cultivar was used because of its stable yields and wide adaptation[1].


The fungal isolate Rhizophagus irregularis BEG144 used in the study was previously characterized as forming highly effective AM symbioses with many agricultural crops.


Pea seeds were surface-disinfected as follows: 1 min in 96% ethanol, a rinse with sterile water, 8 min in a 5% NaClO aqueous solution, and a thorough rinse with sterile water. Disinfected pea seeds were germinated on sterile humid vermiculite in Petri dishes for 3 days at 27 °C in the dark. 2 pea seedlings of equal size were planted into a 300-ml ceramic flower pot with the growth substrate consisting of sterile soil and quartz sand mixture (1:2 v/v), supplemented with 1 g/l Ca3PO4 as a source of phosphate. Half of the pots were supplemented with 15 g/l R. irregularis inoculum before planting; the other half was left as control.


The plants were analyzed at 6 points in time, which corresponded to specific developmental stages for the growth of this species. I (7 days post inoculation, DPI); II (21 DPI); III (32 DPI); IV (42 DPI); V (56 DPI); and VI (90–110 DPI).


At stages II, IV and V, 10 or more plants per treatment were taken at random at each stage. The plants were removed from the soil and their root systems thoroughly washed. The total fresh weight, the fresh weight of the aerial part of the plants and the number of internodes were determined. After measuring the growth parameters, the youngest fully-developed leaf from each analyzed plant was cut off. Leaves from 3 to 5 plants were allocated to a single biological replicate, weighed and snap-frozen in liquid nitrogen in 2 ml Eppendorf Safe-Lock tube, and then stored at −80 °C. At least 3 biological replicates for each time point were collected. At stage VI, the aerial parts of all remaining plants were collected and their dry weight was measured after drying at room temperature for 3 months.


Ref:

[1] Engvild KC. Nodulation and nitrogen fixation mutants of pea, Pisum sativum. Theor Appl Genet. 1987 Oct;74(6):711-3. doi:10.1007/BF00247546. PMID:24240329

Extraction

The samples (0.1–0.2 g) were ground as previously described[1] and subjected to a single-stage extraction with 2 ml methanol:chloroform:water (5:2:1) mixture. Tissue debris was removed by centrifugation at 12,000 x g for 10 min at −5 °C. The supernatant was collected and evaporated in a vacuum evaporator (Eppendorf, Germany). The dried material was dissolved in pyridine with the internal tricosane standard (nC23). The samples were then supplied with the silylating agent BSTFA:TMCS 99:1 (Sigma-Aldrich) and derivatizated at 90 °C for 20 min[1][2].


Leaf metabolome analysis was performed on 3 biological and 2 technical replicates.


Ref:

[1] Puzanskiy RK, Yemelyanov VV, Kliukova MS, Shavarda AL, Shtark OY, Yurkov AP, Shishova MF. Optimization of metabolite profiling for black medick (Medicago lupulina) and peas (Pisum sativum). Applied Biochemistry and Microbiology. 2018;54:442–448. doi:10.1134/S0003683818040129

[2] Puzanskiĭ RK, Shavarda AL, Tarakhovskaia ER, Shishova MF. Analysis of metabolic profile of Chlamydomonas reinhardtii cultivated under autotrophic conditions. Prikl Biokhim Mikrobiol. 2015 Jan-Feb;51(1):73-85. doi:10.7868/s0555109915010134. PMID:25842907

Chromatography

GC-MS analysis was performed on an Agilent 5860 gas chromatograph using Agilent ChemStation E.02.02.1431 software (Agilent Technologies, Santa Clara, CA, USA). Separation was performed on a J&W HP-5ms capillary column, 30 m long, 0.25 mm in diameter, stationary phase film (95% dimethylpolyoxane, 5% diphenyl), and thickness 0.1 µm. The helium gas flow rate was 1 ml/min. Inlet temperature was 250 °C at splitless mode. The temperature conditions of the column thermostat were: an initial temperature of 70 °C, increased by 5 °C/min up to 320 °C.

Mass spectrometry

The mass spectrometry peaks were recorded by an Agilent 5975S mass selective detector (Agilent Technologies, Santa Clara, CA, USA). Electron impact ionization was performed at 70 V and an ion source temperature of 230 °C.

Data transformation

The analysis of the GC-MS data was processed using the PARADISe program (Department of Food Science Faculty of Science, University of Copenhagen, Denmark, http://www.models.life.ku.dk/paradise).

Metabolite identification

Metabolites were identified using the PARADISe program (Department of Food Science Faculty of Science, University of Copenhagen, Denmark, http://www.models.life.ku.dk/paradise) coupled with NIST MS Search (National Institute of Standards and Technology (NIST), USA). In addition, the AMDIS (Automated Mass Spectral Deconvolution and Identification System, NIST, USA) were used. The following mass-spectrometer libraries were applied: NIST2010, the library of the Resource Center of the Science Park 'Center for Molecular and Cell Technologies' (St. Petersburg University), the Golm Metabolome Database (GMD) and MoNA (Massbank of North America). Retention index (RI) was determined by calibration with standard alkanes.

Source Name Organism Variant Organism part Protocol REF Sample Name Mycorrhization Days post inoculation Unit Plant growth stage
21d-AM-1 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 21d-AM-1 Arbuscular Mycorrhiza 21.0 day II
21d-AM-2 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 21d-AM-2 Arbuscular Mycorrhiza 21.0 day II
21d-AM-3 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 21d-AM-3 Arbuscular Mycorrhiza 21.0 day II
21d-AM-4 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 21d-AM-4 Arbuscular Mycorrhiza 21.0 day II
21d-AM-5 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 21d-AM-5 Arbuscular Mycorrhiza 21.0 day II
21d-AM-6 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 21d-AM-6 Arbuscular Mycorrhiza 21.0 day II
21d-contr-1 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 21d-contr-1 control 21.0 day II
21d-contr-2 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 21d-contr-2 control 21.0 day II
21d-contr-3 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 21d-contr-3 control 21.0 day II
21d-contr-4 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 21d-contr-4 control 21.0 day II
21d-contr-5 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 21d-contr-5 control 21.0 day II
21d-contr-6 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 21d-contr-6 control 21.0 day II
42d-AM-1 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 42d-AM-1 Arbuscular Mycorrhiza 42.0 day IV
42d-AM-2 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 42d-AM-2 Arbuscular Mycorrhiza 42.0 day IV
42d-AM-3 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 42d-AM-3 Arbuscular Mycorrhiza 42.0 day IV
42d-AM-4 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 42d-AM-4 Arbuscular Mycorrhiza 42.0 day IV
42d-AM-5 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 42d-AM-5 Arbuscular Mycorrhiza 42.0 day IV
42d-AM-6 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 42d-AM-6 Arbuscular Mycorrhiza 42.0 day IV
42d-contr-1 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 42d-contr-1 control 42.0 day IV
42d-contr-2 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 42d-contr-2 control 42.0 day IV
42d-contr-3 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 42d-contr-3 control 42.0 day IV
42d-contr-4 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 42d-contr-4 control 42.0 day IV
42d-contr-5 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 42d-contr-5 control 42.0 day IV
42d-contr-6 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 42d-contr-6 control 42.0 day IV
56d-AM-1 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 56d-AM-1 Arbuscular Mycorrhiza 56.0 day V
56d-AM-2 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 56d-AM-2 Arbuscular Mycorrhiza 56.0 day V
56d-AM-3 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 56d-AM-3 Arbuscular Mycorrhiza 56.0 day V
56d-AM-4 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 56d-AM-4 Arbuscular Mycorrhiza 56.0 day V
56d-AM-5 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 56d-AM-5 Arbuscular Mycorrhiza 56.0 day V
56d-AM-6 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 56d-AM-6 Arbuscular Mycorrhiza 56.0 day V
56d-contr-1 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 56d-contr-1 control 56.0 day V
56d-contr-2 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 56d-contr-2 control 56.0 day V
56d-contr-3 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 56d-contr-3 control 56.0 day V
56d-contr-4 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 56d-contr-4 control 56.0 day V
56d-contr-5 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 56d-contr-5 control 56.0 day V
56d-contr-6 Pisum sativum Pisum sativum L. cv. Finale leaf Sample collection 56d-contr-6 control 56.0 day V

Assay 

Assay file name: a_MTBLS893_GC-MS___metabolite_profiling.txt
Measurement: metabolite profiling
Technology: mass spectrometry
Platform: Gas Chromatography MS -

Instrumentation

Sample Name Protocol REF Post Extraction Derivatization Extract Name Protocol REF Chromatography Instrument Autosampler model Column model Column type Labeled Extract Name Label Protocol REF Scan polarity Scan m/z range Instrument Ion source Mass analyzer MS Assay Name Raw Spectral Data File Protocol REF Normalization Name Derived Spectral Data File Protocol REF Data Transformation Name Metabolite Assignment File
21d-AM-1 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 21d-AM-1 21d-AM-1.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
21d-AM-2 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 21d-AM-2 21d-AM-2.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
21d-AM-3 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 21d-AM-3 21d-AM-3.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
21d-AM-4 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 21d-AM-4 21d-AM-4.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
21d-AM-5 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 21d-AM-5 21d-AM-5.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
21d-AM-6 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 21d-AM-6 21d-AM-6.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
21d-contr-1 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 21d-contr-1 21d-contr-1.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
21d-contr-2 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 21d-contr-2 21d-contr-2.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
21d-contr-3 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 21d-contr-3 21d-contr-3.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
21d-contr-4 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 21d-contr-4 21d-contr-4.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
21d-contr-5 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 21d-contr-5 21d-contr-5.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
21d-contr-6 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 21d-contr-6 21d-contr-6.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
42d-AM-1 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 42d-AM-1 42d-AM-1.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
42d-AM-2 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 42d-AM-2 42d-AM-2.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
42d-AM-3 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 42d-AM-3 42d-AM-3.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
42d-AM-4 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 42d-AM-4 42d-AM-4.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
42d-AM-5 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 42d-AM-5 42d-AM-5.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
42d-AM-6 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 42d-AM-6 42d-AM-6.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
42d-contr-1 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 42d-contr-1 42d-contr-1.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
42d-contr-2 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 42d-contr-2 42d-contr-2.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
42d-contr-3 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 42d-contr-3 42d-contr-3.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
42d-contr-4 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 42d-contr-4 42d-contr-4.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
42d-contr-5 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 42d-contr-5 42d-contr-5.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
42d-contr-6 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 42d-contr-6 42d-contr-6.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
56d-AM-1 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 56d-AM-1 56d-AM-1.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
56d-AM-2 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 56d-AM-2 56d-AM-2.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
56d-AM-3 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 56d-AM-3 56d-AM-3.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
56d-AM-4 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 56d-AM-4 56d-AM-4.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
56d-AM-5 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 56d-AM-5 56d-AM-5.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
56d-AM-6 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 56d-AM-6 56d-AM-6.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
56d-contr-1 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 56d-contr-1 56d-contr-1.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
56d-contr-2 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 56d-contr-2 56d-contr-2.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
56d-contr-3 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 56d-contr-3 56d-contr-3.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
56d-contr-4 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 56d-contr-4 56d-contr-4.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
56d-contr-5 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 56d-contr-5 56d-contr-5.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
56d-contr-6 Extraction methanol/chloroform/water (5/2/1) sylilation Chromatography Agilent 8860 GC Agilent 7693 Automatic Liquid Sampler HP-5ms GC (0.1 µm, 0.25 mm x 30 m; J&W Scientific) low polarity Mass spectrometry positive 40-600 Agilent 5975C MSD electron ionization quadrupole 56d-contr-6 56d-contr-6.CDF Data transformation Metabolite identification m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
   Download study (FTP)  |     Download metadata    

Aspera Download Details:

List of study files   Subset

File
i_Investigation.txt
56d-AM-3.CDF
audit
s_MTBLS893.txt
56d-AM-2.CDF
42d-contr-5.CDF
56d-AM-5.CDF
42d-AM-6.CDF
21d-contr-6.CDF
21d-contr-3.CDF
42d-contr-2.CDF
21d-contr-5.CDF
56d-contr-1.CDF
42d-AM-4.CDF
21d-AM-3.CDF
42d-contr-6.CDF
42d-AM-1.CDF
56d-contr-6.CDF
56d-contr-4.CDF
21d-contr-1.CDF
42d-AM-3.CDF
21d-AM-5.CDF
42d-contr-3.CDF
42d-AM-2.CDF
56d-contr-2.CDF
56d-AM-4.CDF
21d-AM-6.CDF
56d-contr-3.CDF
42d-AM-5.CDF
21d-AM-4.CDF
42d-contr-4.CDF
21d-AM-1.CDF
21d-contr-2.CDF
56d-contr-5.CDF
56d-AM-1.CDF
21d-AM-2.CDF
a_MTBLS893_GC-MS___metabolite_profiling.txt
m_MTBLS893_GC-MS___metabolite_profiling_v2_maf.tsv
metexplore_mapping.json
21d-contr-4.CDF
42d-contr-1.CDF
56d-AM-6.CDF

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Validations marked with (*) have been allowed by the MetaboLights Curators.
Click here for the detailed description of Validations.
Condition Status Description Requirement Group Message
PASSES Study Title MANDATORY STUDY OK
PASSES Study Description MANDATORY STUDY OK
PASSES Study text successfully parsed OPTIONAL STUDY OK
FAILS Study Contact(s) have listed email MANDATORY CONTACT Not all Study Contacts have their emails listed
PASSES Sample(s) MANDATORY SAMPLES OK
PASSES Sample Name consistency check MANDATORY ASSAYS OK
PASSES Publication(s) associated with this Study MANDATORY PUBLICATION OK
PASSES Minimal Experimental protocol MANDATORY PROTOCOLS OK
PASSES Comprehensive Experimental protocol OPTIONAL PROTOCOLS OK
PASSES Extraction protocol description MANDATORY PROTOCOLS OK
PASSES Data transformation protocol description MANDATORY PROTOCOLS OK
PASSES Metabolite Identification protocol description MANDATORY PROTOCOLS OK
PASSES Mass spectrometry protocol description MANDATORY PROTOCOLS OK
PASSES Chromatography protocol description MANDATORY PROTOCOLS OK
PASSES Sample Collection protocol description MANDATORY PROTOCOLS OK
PASSES Protocols text successfully parsed OPTIONAL PROTOCOLS OK
PASSES Organism name MANDATORY ORGANISM OK
PASSES Organism part MANDATORY ORGANISM OK
PASSES Study Factors MANDATORY FACTORS OK
PASSES Assay platform information OPTIONAL ASSAYS OK
PASSES Assay has raw files referenced MANDATORY FILES OK
PASSES Assay referenced raw files detection in filesystem MANDATORY FILES OK
PASSES Raw files in the Assay(s) have the correct format MANDATORY FILES OK
PASSES Assay(s) MANDATORY ASSAYS OK
PASSES All Assays have Metabolite Assignment File (MAF) referenced OPTIONAL FILES OK
PASSES Metabolite Assignment File (MAF) is present in Study folder MANDATORY FILES OK
PASSES Metabolite Assignment File (MAF) has correct format MANDATORY FILES OK
PASSES Metabolite Identification File (MAF) content MANDATORY FILES OK
PASSES ISA-Tab investigation file check MANDATORY ISATAB OK

Pathways - Assay 



MetExplore Pathways Mapping

Name DB Identifier Mapped Metabolite(s)