MTBLS194: Matrix Effect on Chemical Isotope Labeling and Its Implication in Metabolomic Sample Preparation for Quantitative Metabolomics

Abstract

Matrix effect from various constituents in biological samples can reduce the accuracy of quantitative metabolomics. Differential chemical isotope labeling liquid chromatography mass spectrometry (CIL LC-MS) can overcome the matrix effect on MS detection based on measuring the intensity ratios of metabolite peak pairs detected in a mixture of a light-isotope labeled sample and a heavy-isotope labeled reference sample. However, the chemical labeling process itself may encounter matrix effect which can influence the overall quantitative results. In this work, we report the effects of salts and buffers commonly present in metabolomic samples on dansylation labeling. It is shown that high concentrations of NaCl and phosphate buffer (>50 mM) or PBS can reduce or enhance the labeling efficiencies of metabolites. By maintaining similar matrix contents in an individual sample vs. a reference sample, relative quantification of metabolites can be performed without compromising the metabolomic profiling results. For samples containing varying amounts of high salts such as urine, we demonstrate that the matrix effect can be largely overcome by diluting the original sample before dansylation labeling (e.g., 4-fold dilution for urine).

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 Authors: Wei Han, Liang Li

  Release date: 01-Jul-2015

 Status: Public

Organism(s)

Mus musculus

  Study Design

Matrix effect

CHMO:high-performance liquid chromatography-mass spectrometry

Chemical isotope Labeling

targeted metabolites

  Experimental Factors

Sample Matrix

Protocol Description
Sample collection Urine samples were collected from five age-matched healthy mice. Equal volumes of the five individual samples were mixed together to make a pooled sample. After sample collection, the urine samples were immediatelystored in -80 °C freezer for further use.
Extraction The frozen urine samples were thawed in an ice-bath and then centrifuged at 14000 rpm for 15 min. 12.5 µl supernatant was taken into an Eppendorf tube and totally dried using a Speed Vac. The sample was re-dissolved to 50 µL with water or a specific matrix solution. Then 25 µl of 250 mM sodium carbonate/sodium bicarbonate buffer and 25 µl of ACN were added into the sample. The solution was vortexed, spun down, and mixed with 50 µL of freshly prepared 12C-dansyl chloride solution (18 mg/ml) (for light labeling) or 13C-dansyl chloride solution (18 mg/ml) (for heavy labeling). After 45 min incubation at 40 °C, 10 µl of 250 mM NaOH was added to the reaction mixture to quench the excess dansyl chloride. The solution was then incubated at 40 °C for another 10 min. Finally, formic acid in 50/50 ACN/H2O was added to consume excess NaOH and to make the solution acidic. The 12C- or 13C-labeled sample was centrifuged at 14000 rpm for 10 min before injecting onto the ultrahigh performance liquid chromatography (UPLC) column for UV quantification (see below). For LC-MS analysis, the 12C- and 13C-labeled samples were mixed in equal amounts based on the quantification results.
Chromatography An Agilent 1100 series binary system (Agilent, Palo Alto, CA) and an Agilent reversed-phase Eclipse plus C18 column (2.1 mm x 100 mm, 1.8 µm particle size, 95 Å pore size) were used for LC-MS. LC solvent A was 0.1% (v/v) formic acid in 5% (v/v) ACN, and solvent B was 0.1% (v/v) formic acid in acetonitrile. The gradient elution profile was as follows: t = 0 min, 20% B; t = 3.5 min, 35% B; t = 18.0 min, 65% B; t = 24.0 min, 99% B; t = 32.0 min, 99% B. The flow rate was 180 µl/min.
Mass spectrometry The flow from HPLC was split 1:2 and a 60 µl/min flow was loaded to the electrospray ionization (ESI) source of a Bruker 9.4 Tesla Apex-Qe Fourier transform ion-cyclotron resonance (FTICR) mass spectrometer (Bruker, Billerica, MA, USA), while the rest of the flow was delivered to waste. All MS spectra were obtained in the positive ion mode. To monitor the instrumental performance, a quality control sample (i.e., a differentially labeled urine sample) was injected every 10–12 sample injections.
Data transformation The 12C/13C peak pairs were extracted by the IsoMS software reported [1]. IsoMS-Align was used to align the peak pair data from different samples by retention time and accurate mass [1]. The missing values were filled back by using the Zero-fill program [2]. Multivariate statistical analysis was carried out using SIMCA-P+ 12 (Umetrics AB, Umea, Sweden).

Ref:
[1] Zhou, R., Tseng, C. L., Huan, T., & Li, L. (2014). IsoMS: automated processing of LC-MS data generated by a chemical isotope labeling metabolomics platform. Analytical Chemistry, 86(10), 4675–4679. doi:10.1021/ac5009089. PMID:24766305
[2] Huan, T., & Li, L. (2015). Counting missing values in a metaboliteintensity data set for measuring the analytical performance of a metabolomics platform. Analytical Chemistry, 87(2), 1306–1313. doi:10.1021/ac5039994. PMID:25496403
Metabolite identification Metabolite identification was based on available standards.
Source Name Organism Organism part Protocol REF Sample Name Sample Matrix
Mouse Urine Mus musculus urine Sample collection PP1_1 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP1_2 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP1_3 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP2_1 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP2_2 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP2_3 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP3_1 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP3_2 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP3_3 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP4_1 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP4_2 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP4_3 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP5_1 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP5_2 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PP5_3 PBS C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection PW1_1 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW1_2 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW1_3 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW2_1 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW2_2 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW2_3 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW3_1 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW3_2 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW3_3 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW4_1 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW4_2 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW4_3 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW5_1 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW5_2 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection PW5_3 PBS C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WP1_1 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP1_2 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP1_3 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP2_1 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP2_2 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP2_3 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP3_1 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP3_2 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP3_3 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP4_1 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP4_2 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP4_3 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP5_1 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP5_2 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WP5_3 Water C12/ PBS C13
Mouse Urine Mus musculus urine Sample collection WW1_1 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW1_2 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW1_3 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW2_1 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW2_2 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW2_3 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW3_1 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW3_2 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW3_3 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW4_1 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW4_2 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW4_3 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW5_1 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW5_2 Water C12/ Water C13
Mouse Urine Mus musculus urine Sample collection WW5_3 Water C12/ Water C13

Assay 

Assay file name: a_cil_matrix_effect_metabolite_profiling_mass_spectrometry.txt
Measurement: metabolite profiling
Technology: mass spectrometry
Platform: apex-ultra hybrid Qq-FTMS (Bruker)

Instrumentation

Sample Name Protocol REF Post Extraction Derivatization Extract Name Protocol REF Chromatography Instrument 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
PP1_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP1_1.csv Data transformation Metabolite identification
PP1_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP1_2.csv Data transformation Metabolite identification
PP1_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP1_3.csv Data transformation Metabolite identification
PP2_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP2_1.csv Data transformation Metabolite identification
PP2_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP2_2.csv Data transformation Metabolite identification
PP2_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP2_3.csv Data transformation Metabolite identification
PP3_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP3_1.csv Data transformation Metabolite identification
PP3_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP3_2.csv Data transformation Metabolite identification
PP3_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP3_3.csv Data transformation Metabolite identification
PP4_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP4_1.csv Data transformation Metabolite identification
PP4_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP4_2.csv Data transformation Metabolite identification
PP4_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP4_3.csv Data transformation Metabolite identification
PP5_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP5_1.csv Data transformation Metabolite identification
PP5_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP5_2.csv Data transformation Metabolite identification
PP5_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PP5_3.csv Data transformation Metabolite identification
PW1_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW1_1.csv Data transformation Metabolite identification
PW1_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW1_2.csv Data transformation Metabolite identification
PW1_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW1_3.csv Data transformation Metabolite identification
PW2_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW2_1.csv Data transformation Metabolite identification
PW2_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW2_2.csv Data transformation Metabolite identification
PW2_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW2_3.csv Data transformation Metabolite identification
PW3_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW3_1.csv Data transformation Metabolite identification
PW3_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW3_2.csv Data transformation Metabolite identification
PW3_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW3_3.csv Data transformation Metabolite identification
PW4_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW4_1.csv Data transformation Metabolite identification
PW4_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW4_2.csv Data transformation Metabolite identification
PW4_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW4_3.csv Data transformation Metabolite identification
PW5_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW5_1.csv Data transformation Metabolite identification
PW5_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW5_2.csv Data transformation Metabolite identification
PW5_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS PW5_3.csv Data transformation Metabolite identification
WP1_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP1_1.csv Data transformation Metabolite identification
WP1_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP1_2.csv Data transformation Metabolite identification
WP1_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP1_3.csv Data transformation Metabolite identification
WP2_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP2_1.csv Data transformation Metabolite identification
WP2_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP2_2.csv Data transformation Metabolite identification
WP2_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP2_3.csv Data transformation Metabolite identification
WP3_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP3_1.csv Data transformation Metabolite identification
WP3_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP3_2.csv Data transformation Metabolite identification
WP3_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP3_3.csv Data transformation Metabolite identification
WP4_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP4_1.csv Data transformation Metabolite identification
WP4_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP4_2.csv Data transformation Metabolite identification
WP4_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP4_3.csv Data transformation Metabolite identification
WP5_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP5_1.csv Data transformation Metabolite identification
WP5_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP5_2.csv Data transformation Metabolite identification
WP5_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WP5_3.csv Data transformation Metabolite identification
WW1_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW1_1.csv Data transformation Metabolite identification
WW1_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW1_2.csv Data transformation Metabolite identification
WW1_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW1_3.csv Data transformation Metabolite identification
WW2_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW2_1.csv Data transformation Metabolite identification
WW2_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW2_2.csv Data transformation Metabolite identification
WW2_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW2_3.csv Data transformation Metabolite identification
WW3_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW3_1.csv Data transformation Metabolite identification
WW3_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW3_2.csv Data transformation Metabolite identification
WW3_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW3_3.csv Data transformation Metabolite identification
WW4_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW4_1.csv Data transformation Metabolite identification
WW4_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW4_2.csv Data transformation Metabolite identification
WW4_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW4_3.csv Data transformation Metabolite identification
WW5_1 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW5_1.csv Data transformation Metabolite identification
WW5_2 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW5_2.csv Data transformation Metabolite identification
WW5_3 Extraction Chemical Isotope Labeling other CIL Chromatography Agilent 1100 Series HPLC System ZORBAX Eclipse Plus C18 (1.8 µm, 2.1 mm x 100 mm; Agilent Technologies) reverse phase Mass spectrometry positive 200-1000 Bruker APEX-Qe 9.4T electrospray ionization CHMO:ion cyclotron resonance cell LC-MS WW5_3.csv Data transformation Metabolite identification
   Download study (FTP)  |     Download metadata    

Aspera Download Details:

List of study files   Subset

File
PP1_2.csv
PP3_2.csv
PP1_1.csv
PP2_1.csv
PP1_3.csv
PP3_1.csv
PP2_2.csv
PP2_3.csv
validation_report.json
PP3_3.csv
PP4_3.csv
PW3_2.csv
WP3_3.csv
WP3_1.csv
WP4_2.csv
PP5_2.csv
PW1_3.csv
PW3_1.csv
PW5_3.csv
WP2_1.csv
WP4_3.csv
PP4_2.csv
PP5_1.csv
PW3_3.csv
WP2_2.csv
PW5_2.csv
PW1_2.csv
WP1_2.csv
WP1_3.csv
PP5_3.csv
WP1_1.csv
PW5_1.csv
WP4_1.csv
WP3_2.csv
PW2_2.csv
PW2_1.csv
WP2_3.csv
PW4_1.csv
PW4_3.csv
PW1_1.csv
PP4_1.csv
PW4_2.csv
PW2_3.csv
WW1_3.csv
WW2_3.csv
WW2_1.csv
WP5_3.csv
WW3_1.csv
WW4_2.csv
WW3_2.csv
WW5_2.csv
a_cil_matrix_effect_metabolite_profiling_mass_spectrometry.txt
WW1_1.csv
WP5_2.csv
WW5_1.csv
WW3_3.csv
i_Investigation.txt
WW4_1.csv
WW4_3.csv
WW1_2.csv
s_CIL Matrix Effect.txt
WW5_3.csv
WP5_1.csv
WW2_2.csv
audit

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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
PASSES Study Contact(s) have listed email MANDATORY CONTACT OK
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 Raw files reported in the Assay(s), are not of valid format or the raw file folders are empty: WP5_3.csv, PW4_1.csv, WW5_2.csv, PP4_3.csv, PP4_2.csv, WW1_3.csv, WW5_1.csv, PW1_1.csv, PP1_1.csv, WP2_2.csv, PW3_3.csv, WW1_2.csv, WW5_3.csv, PP4_1.csv, WP2_3.csv, PP5_2.csv, PP3_3.csv, PW5_1.csv, WP3_1.csv, PP5_3.csv, PW1_3.csv, WW4_3.csv, PP3_2.csv, WW2_2.csv, WP3_2.csv, PW4_3.csv, PW1_2.csv, PW4_2.csv, WW2_1.csv, WP3_3.csv, PP3_1.csv, PW2_2.csv, PP2_3.csv, WW3_2.csv, WP4_1.csv, PW5_3.csv, PW2_1.csv, WP4_2.csv, WP1_1.csv, PP2_2.csv, WW3_1.csv, PW5_2.csv, WW2_3.csv, WW4_2.csv, PP2_1.csv, WP4_3.csv, WW1_1.csv, WP1_2.csv, WP5_1.csv, PW3_2.csv, PP1_3.csv, PP5_1.csv, WW4_1.csv, PW2_3.csv, WP1_3.csv, WW3_3.csv, PP1_2.csv, PW3_1.csv, WP5_2.csv, WP2_1.csv
PASSES Assay(s) MANDATORY ASSAYS OK
* PASSES At least one assay has Metabolite Assignment Files (MAFs) referenced MANDATORY FILES Metabolite identification protocol is described but no Metabolite Assignment File (MAF) is referenced in the Assay table
PASSES ISA-Tab investigation file check MANDATORY ISATAB OK

Pathways - Assay 



MetExplore Pathways Mapping

Name DB Identifier Mapped Metabolite(s)