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Data files for:Critical assessment of the chemical space covered by LC-HRMS non-targeted analysis
<p>This upload contains the data for the review: "Critical assessment of the chemical space covered by LC-HRMS non-targeted analysis".</p> <p>All the files needed to run the code uploaded to GitHub (https://github.com/tobihul/CEC_review_code) can be found here.</p> <p>Included is: </p> <ul> <li>All 2657 structures found in the studied papers with their CID, InChIKey, and SMILES and whether they can be found in MassBank</li> <li>All the experimental parameters retrieved for each study in each category along with the general scope of each study</li> <li>The file with the CID, MW, XLogP3 and experimental parameters for each of the 61 papers</li> <li>The CSV file containing all classes of each of the compounds from the papers</li> <li>The CSV with all of the structures used to plot the chemical space of NORMAN SusDat (their CIDs)</li> </ul> <p> </p> <p> </p>
LC MS/MS spectra
<p>compilation of open source LC MS/MS databases necessary for MS2ID, an R annotation package </p>
Figure 12 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 12 – Pupa of Colotis euippe omphale. This pupa was reared from a larva collected on 19 December 2021 on Cadaba aphylla shrub C aphy 14, north of the Dedeben Research Centre, Tswalu Kalahari, South Africa. The CRG reference number for this pupa is RFT21H79. Photo: R.F. Terblanche.
Figure 14 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 14 – Cadaba aphylla (CAPPARACEAE), C aphy 14, photographed on 26 September 2022, north of the Dedeben Research Centre, Tswalu Kalahari, South Africa. When conditions are favourable, many shoots with small leaves can be produced by some individuals of the species, as depicted here. No flowers were present on this plant when the photograph was taken. Photo: R.F. Terblanche.
Figure 11 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 11 – Pupa of Colotis lais. This pupa was reared from a larva collected on 19 September 2022 on a Cadaba aphylla shrub C aphy 13, north of the Dedeben Research Centre, Tswalu Kalahari, South Africa. The CRG reference number for this pupa is RFT22H43. Photo: R.F. Terblanche.
Figure 10 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 10 – Final instar larva of Colotis euippe omphale collected on 3 January 2022 on Cadaba aphylla shrub C aphy 11, near the Dedeben Research Centre in Tswalu Kalahari, South Africa. The CRG reference number for this larva is RFT22H2. Photo: R.F. Terblanche.
Figure 9 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 9 – Final instar larva of Colotis lais. The larva was collected on 19 December 2021 on Cadaba aphylla shrub C aphy 13, north of the Dedeben Research Centre, Tswalu Kalahari, South Africa. The larva had been successfully reared on new shoots (young stems with small leaves) of Cadaba aphylla. The CRG reference number for this larva is RFT21H78. Photo: R.F. Terblanche.
Figure 15 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 15 – Cadaba aphylla (CAPPARACEAE) photographed on 21 January 2019 at Tswalu Kalahari, South Africa. A commonly used English name for Cadaba aphylla is "leafless wormbush," because leaves are often not present or obscured by many leafless stems. Photo: R.F. Terblanche.
Figure 7 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 7 – Depiction of GPS-marked Cadaba aphylla host plants (white markers) selected for ecological monitoring, north and north-west of the Dedeben Research Centre at Tswalu Kalahari.
Figure 5 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 5 – Colotis euippe omphale male puddling (imbibing water and nutrients from wet soil) at a damp area near the Dedeben Research Centre, Tswalu Kalahari, South Africa, 22 December 2021. Photo: R.F. Terblanche.
Figure 3 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 3 – Colotis lais female resting on bare ground with open wings in typical fashion, north-west of the Dedeben Research Centre, Tswalu Kalahari, South Africa, 22 December 2021. Photo: R.F. Terblanche.
Figure 4 – Freshly emerged Colotis euippe omphale reared from a in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 4 – Freshly emerged Colotis euippe omphale reared from a larva collected on 19 December 2021 on a Cadaba aphylla shrub, north of the Dedeben Research Centre, Tswalu Kalahari, South Africa. The CRG reference number for this rearing is RFT21H79. Photo: R.F. Terblanche.
Figure 2 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 2 – Colotis lais male, puddling (imbibing water and nutrients from wet soil) at a damp area near the Dedeben Research Centre, Tswalu Kalahari, South Africa, 24 December 2021. Photo: R.F. Terblanche.
Figure 1 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 1 – Freshly emerged adult male of Colotis lais reared from a larva collected on 19 December 2021 on a Cadaba aphylla shrub, north of the Dedeben Research Centre, Tswalu Kalahari, South Africa. The CRG reference number for this rearing is RFT21H78. Photo: R.F. Terblanche.
LC-MS/MS, PSM and BLG properties data from "Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins"
<p>This dataset contains the data analyzed in:</p> <p>Rodriguez Palomo I, Nair B, Chang Y, Dartigues B, Dekker K, Mackie M, Evans M, Macleod R, Olsen JV, Collins MJ. (2023) "<em>Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins"</em></p> <p>It contains the following data:</p> <ul> <li>raw_files.zip Thermo RAW files for the 0, 4 and 128 days samples</li> <li>benchmark_results.zip PSMs data from the analysis of the RAW files <ul> <li>Data from runs in Mascot, Fragpipe, pFind, Metamorpheus, MaxQuant and DeNovoGUI</li> <li>Parameters and workflow files for MaxQuant and Fragpipe</li> </ul> </li> <li>bovin_blg_prop.zip BLG properties files: amyloid formation, 3D structure and solvent accessibility</li> <li>benchmark_table.csv Table with runs settings for benchmarking</li> <li>parameters_table.xlsx Spreadsheet with software parameters, derived from files used to run each software</li> </ul> <p> </p>
Data for: Mapping the Limits of Passive Samplers in Water: Chemical Space Coverage Using Nontargeted LC-HRMS Analysis
<p>This dataset provides files for passive samplers nad blanks analyzed by LC-HRMS fullscan DIA MS2.</p> <p>Excel file provides information about passive samplers, sampling site and sample files.</p>
Portimine A toxin causes skin pathology through ZAKα-dependent NLRP1 inflammasome activation: LC-MS/MS raw data for Figure 1. C
<p>This dataset pertains to the LC-MS/MS analyses conducted as part of a study on microalgal toxins present in samples from Senegal, published in the paper entitled <em>"Portimine A toxin causes skin pathology through ZAK</em><em>α</em><em>-dependent NLRP1 inflammasome activation."</em> The data correspond to the quantification results of environmental samples presented in Figure 1C.</p> <p>The raw data were acquired using Analyst software (Applied Biosystems proprietary software). The materials and methods used to generate these data are detailed in the associated publication in <em>EMBO Molecular Medicine</em> (ISSN: 1757-4676, 2024).</p>
LC-MS raw data_Lysophosphatidic Acid Shifts Metabolic and Transcriptional Landscapes to Induce a Distinct Cellular State in Human Pluripotent Stem Cells
<p><strong>LC-MS/MS analysis</strong></p> <p><strong>Metabolite extraction</strong></p> <p>For LC-MS/MS quantification, cell sample preparation was conducted as described in the previous literatures (Ying, Kimmelman et al. 2012, Zhang, Badur et al. 2016). Briefly, the spent medium was removed, and cells were rinsed with 1 mL/well 0.9% (w/v) saline twice. Then 0.5 mL/well -80°C 0.2 μg/mL norvaline containing 80% methanol was added to quench the metabolism. Cells were scraped off into 1.5-mL eppendorf tube and stored in -80℃ overnight. The mixtures were vortexed and then centrifuged 12500 × <em>g </em>for 15 min at 4℃. The supernatant was used for LC-MS analysis.</p> <p><strong>LC-MS/MS method</strong></p> <p>Waters Xevo TQD coupled with Waters Acquity UPLC system was used for quantification. Acquity UPLC BEH HILIC column (2.1 × 100 mm, 1.7 μm), Acquity UPLC BEH C18 column (2.1 × 100 mm, 1.7 μm), and Acquity UPLC BEH amide column (2.1 × 100 mm, 1.7 μm) were used for the separation of metabolites. Column temperature was set at 40 °C.</p> <p>For the quantification of norvaline, amino acids, GSH, GSSG, SAH, SAM, ascorbic acid and myo-inositol, amide column was used for the separation. Acetonitrile with 0.1% formic acid (A) and water with 0.1% formic acid (B) were used as mobile phases. The gradient setting is: 0-4 min, 99% A to 90% A; 4-10 min, 90% A to 67% A; 10-13 min, 67% A to 1% A; 13-15 min, 1% A; 15-16.5 min, 1% A to 99% A; 16.5-20 min, 99% A. Flowrate was set as 0.4 mL/min.</p> <p>For the quantification of metabolites involved in TCA cycle, energy related and ribonucleotides, an amide column was used for the separation. Acetonitrile with 0.1% formic acid (A) and water with 0.1% formic acid (B) were used as mobile phases. The gradient setting is: 0-2 min, 80% A; 2-3 min, 80% A to 20% A; 3-5 min, 20% A; 5-6 min, 20% A to 80% A; 6-10 min, 80% A. Flowrate was set as 0.4 mL/min.</p> <p>For the quantification of acetate, acetyl-CoA and metabolites involved in glycolysis and pentose phosphate pathway, HILIC column was used for the separation. Acetonitrile (A) and 10 mM ammonium bicarbonate were used as mobile phases. The gradient setting is: 0-2 min, 10% A; 2-5 min, 10% A to 5% A; 5-6 min, 5% A to 10% A; 6-10 min, 10% A. Flowrate was set as 0.2 mL/min.</p> <p>For the quantification of LPA, LPC and PC, HILIC column was used for the separation. Acetonitrile (A) and 10 mM ammonium bicarbonate aqueous solution (B) were used as mobile phases. The gradient setting is: 0-2 min, 95% A; 2-4 min, 95% A to 10% A; 4-7 min, 10% A; 7-9 min, 10% A to 95% A; 9-15 min, 95% A. Flowrate was set as 0.2 mL/min.</p> <p>For the quantification of CDL lipids, C18 column was used for the separation. 98% Acetonitrile aqueous solution (A) and 10 mM ammonium acetate 90% acetonitrile aqueous solution (B) were used as mobile phases. The gradient setting is: 0-5 min, 0.1% A; 5-6 min, 0.1% A to 99.9% A; 6-11 min, 99.9% A; 11-12 min, 99.9% A to 0.1% A; 12-15 min, 0.1% A. Flowrate was set as 0.4 mL/min.</p> <p>Argon was used as source gas, capillary voltage was 3500 V, and desolvation temperature was 500 °C. Multiple reaction monitoring (MRM) was conducted, and the ion transitions are listed in the supplemental Table S2. Selected ion recording (SIR) was conducted for the detection of CDL-related lipids, and the setting is listed in the supplemental Table S3.</p> <p>Standard solutions of TCA metabolites (100 μg/mL) and intermediates of glycolysis and pentose phosphate pathway (10 μg/mL) were prepared to confirm the retention time. Peak intensity of product ion was used for the quantification. Data analysis was performed by TargetLynx software (Waters) with statistical analysis in Graphpad Prism (version 8.4.0) and R.</p>
LC-MS² meta data for each MassBank (MB) subset
<p>The CSV-file (tab used as separator) provides the Liquid-chromatography (LC) and Tandem-mass spectrometry (MS²) configurations for each MassBank (MB) subset used in the publication: "Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data" by Bach et al. (2022).</p>
Рис. 1. Номенклатура и условные обоЗначениЯ морфоструктур Замочной плоЩадки личиночных венерид (A, B; по Rees, 1950, с иЗменениЯми), ювенильных Turtonia minuta (С) и вЗрослых венерид Tapetinae (D): a, a0 – передний Зуб правой створки (RV); b, b0 – Задний Зуб RV; c, c0 – передний Зуб левой створки (LV); d, d0 – Задний Зуб LV; lc – лигаментнаЯ Ямка центрального расположениЯ; lp – лигаментнаЯ Ямка Заднего расположениЯ; L1 – передне-вентральный латеральный Зуб RV; L2 – передний латеральный Зуб LV; L3 – передне-дорсальный латеральный Зуб RV; n – нимфа вторичного лигамента;:a – Ямка Зуба переднего Зуба RV;:c – Ямка переднего Зуба LV; 1 – вентральный кардинальный Зуб RV; 2a – переднЯЯ часть кардинального Зуба 2 LV; 2b – ЗаднЯЯ часть кардинального Зуба 2 LV; 3а – переднЯЯ часть кардинального Зуба 3 RV; 3b – ЗаднЯЯ часть кардинального Зуба 3 RV; 4 – Задний кардинальный Зуб LV;:4 – Ямка Заднего кардинального Зуба LV. in Larval, juvenile and adult Turtonia minuta (Bivalvia: Turtoniidae) and comparative shell morphology of the veneroid and venerid taxa from Peter the Great Bay, Sea of Japan
Рис. 1. Номенклатура и условные обоЗначениЯ морфоструктур Замочной плоЩадки личиночных венерид (A, B; по Rees, 1950, с иЗменениЯми), ювенильных Turtonia minuta (С) и вЗрослых венерид Tapetinae (D): a, a0 – передний Зуб правой створки (RV); b, b0 – Задний Зуб RV; c, c0 – передний Зуб левой створки (LV); d, d0 – Задний Зуб LV; lc – лигаментнаЯ Ямка центрального расположениЯ; lp – лигаментнаЯ Ямка Заднего расположениЯ; L1 – передне-вентральный латеральный Зуб RV; L2 – передний латеральный Зуб LV; L3 – передне-дорсальный латеральный Зуб RV; n – нимфа вторичного лигамента;:a – Ямка Зуба переднего Зуба RV;:c – Ямка переднего Зуба LV; 1 – вентральный кардинальный Зуб RV; 2a – переднЯЯ часть кардинального Зуба 2 LV; 2b – ЗаднЯЯ часть кардинального Зуба 2 LV; 3а – переднЯЯ часть кардинального Зуба 3 RV; 3b – ЗаднЯЯ часть кардинального Зуба 3 RV; 4 – Задний кардинальный Зуб LV;:4 – Ямка Заднего кардинального Зуба LV.
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International Brain Laboratory public data
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OpenNeuro
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