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39 results for “mass spectrometry imaging”
Supplementary data to accompany "Abundant metabolite-matrix adducts illuminate the dark metabolome of MALDI-mass-spectrometry imaging datasets"
<p>This dataset accompanies the publication "Abundant metabolite-matrix adducts illuminate the dark metabolome of MALDI-mass-spectrometry imaging datasets". The dataset includes all files, scripts and results that are included in the associated publication.</p> <p>Spatial metabolomics using mass spectrometry imaging (MSI) is a powerful tool to map hundreds or thousands of metabolites across biological systems. One major challenge is the complexity of the data, which includes signals from experimental artifacts. Formation of adducts (<em>e.g. </em>with Na+or K+) or abundant matrix-cluster, in the case of matrix-assisted laser desorption ionization (MALDI)-MSI, strongly increase peak counts. We developed <em>mass2adduct</em>, a universally applicable tool for adduct abundance estimations in high-mass-resolution spatial metabolomics datasets. Our study illustrates that MALDI-MSI data density is remarkably driven by adduct formation and revealed a major influence of so far unrecognized metabolite-matrix adducts on total peak counts. Current data analyses neglect those matrix adducts and therefore overestimate total metabolite numbers, thereby inflating the dark metabolome size.</p> <p>mass2adduct zenodo doi (10.5281/zenodo.1405088)</p> <p>mass2adduct gihub: https://github.com/kbseah/mass2adduct</p>
mzML mass spectrometry and imzML mass spectrometry imaging test data
<p>The repository contains three mzML and four imzML mass spectrometry datasets, </p><p>The mzML data are compiled in a <strong>single directory 'mzML' and zipped</strong>:</p><ul><li><strong>Col_1.mzML </strong>is a liquid chromatography (LC) ESI MS dataset from an Arabidopsis extraction published in: Sotelo-Silveira, M., Chauvin, A.-L., Marsch-Martínez, N., Winkler, R. & De Folter, S. Metabolic fingerprinting of Arabidopsis thaliana accessions. Frontiers in Plant Science 6, 1–13 (2015). <a href="https://doi.org/10.3389/fpls.2015.00365">https://doi.org/10.3389/fpls.2015.00365</a>.</li><li><strong>Cytochrome_C.mzML</strong> is an electrospray mass spectrometry (ESI MS) dataset of Cytochrome C. The data were discussed in: Winkler, R. ESIprot: a universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data. Rapid Communications in Mass Spectrometry 24, 285- 294 (2010). <a href="https://doi.org/10.1002/rcm.4384">https://doi.org/10.1002/rcm.4384</a>.</li><li><strong>T9_A1.mzML </strong>is a low-temperature plasma (LTP) MS dataset of the interaction between Arabidopsis and Trichoderma, published in 1. Torres-Ortega, R. et al. In Vivo Low-Temperature Plasma Ionization Mass Spectrometry (LTP-MS) Reveals Regulation of 6-Pentyl-2H-Pyran-2-One (6-PP) as a Physiological Variable during Plant-Fungal Interaction. Metabolites 12, 1231 (2022). <a href="https://doi.org/10.3390/metabo12121231">https://doi.org/10.3390/metabo12121231</a>.</li></ul><p>The imzML mass spectrometry imaging data are zipped individually:</p><ul><li><strong>imzML_AP_SMALDI.zip </strong>contains an AP-SMALDI mass spectrometry imaging data set of mouse urinary bladder slides, published by Römpp A, Guenther S, Schober Y, Schulz O, Takats Z, Kummer W, Spengler B., ProteomeXchange dataset PXD001283. 2014., and available from <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD001283">https://www.ebi.ac.uk/pride/archive/projects/PXD001283</a>; Publication: Römpp A, Guenther S, Schober Y, Schulz O, Takats Z, Kummer W, Spengler B; Histology by mass spectrometry: label-free tissue characterization obtained from high-accuracy bioanalytical imaging., Angew Chem Int Ed Engl, 49, 22, 3834-8 (2014). <a href="https://doi.org/10.1002/anie.200905559">https://doi.org/10.1002/anie.200905559</a>, PubMed: 20397170. </li><li><strong>imzML_DESI.zip </strong>is a DESI mass spectrometry imaging data set of human colorectal cancer tissue by Oetjen J, Veselkov K, Watrous J, McKenzie JS, Becker M, Hauberg-Lotte L, Kobarg JH, Strittmatter N, Mróz AK, Hoffmann F, Trede D, Palmer A, Schiffler S, Steinhorst K, Aichler M, Goldin R, Guntinas-Lichius O, von Eggeling F, Thiele H, Maedler K, Walch A, Maass P, Dorrestein PC, Takats Z, Alexandrov T. 2015. Benchmark datasets for 3D MALDI-and DESI-imaging mass spectrometry. GigaScience 4(1):2105 <a href="https://doi.org/10.1186/s13742-015-0059-4">https://doi.org/10.1186/s13742-015-0059-4</a>.</li><li><strong>imzML_LA-ESI.zip</strong> is an LA-ESI mass spectrometry imaging data set of an <i>Arabidopsis thaliana</i> leaf by Zheng, Z., Bartels, B., & Svatoš, A. (2020). Laser Ablation Electrospray Ionization Mass Spectrometry Imaging (LAESI MSI) of Arabidopsis thaliana leaf [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.3678473">https://doi.org/10.5281/zenodo.3678473</a>. </li><li>imzML_LTP.zip was generated by low-temperature plasma ionization ambient mass spectrometry imaging of a chili fruit, published by Maldonado-Torres M, López-Hernández Jé F, Jiménez-Sandoval P, Winkler R. 2014. Plug and play' assembly of a low-temperature plasma ionization mass spectrometry imaging (LTP-MSI) system. Journal of Proteomics 102C:60–65 <a href="https://doi.org/10.1016/j.jprot.2014.03.003">https://doi.org/10.1016/j.jprot.2014.03.003</a>; Mauricio Maldonado-Torres, José Fabricio López-Hernández, Pedro Jiménez-Sandoval, & Robert Winkler. (2017). Low-temperature plasma mass spectrometry imaging (LTP-MSI) of Chili pepper [Data set]. In Journal of proteomics (Vol. 102, pp. 60–65). Zenodo. <a href="https://doi.org/10.5281/zenodo.484496">https://doi.org/10.5281/zenodo.484496</a>.</li></ul><p>All these datasets are publicly available from different repositories; however, If you reuse them, <strong>please attribute the original authors!</strong></p>
Fig. 5 in Unique localization of jasmonic acid-related compounds in developing Phaseolus vulgaris L. (common bean) seeds revealed through desorption electrospray ionization-mass spectrometry imaging
Fig. 5. DESI-MS/MSI of OPDA and OPC-8 in the developing Phaseolus vulgaris seeds. (a) Optical image of the seed section for OPDA analysis. (b) MS/MS spectrum of precursor ion at m/z 291.1966 ± 1 Da obtained at the target enhanced mode for m/z 165.1. (c) Ion image at m/z 165.1300. (d) Optical image of the seed section for OPC-8:0 analysis. (e) MS/MS spectrum of precursor ion at m/z 293.2122 ± 1 Da obtained at the target enhanced mode for m/z 225.1. Ion images at m/z (f) 223.1400 and (g) 231.2142. Scale bar = 2 mm. Compound names are defined in Table 1.
Fig. 4 in Unique localization of jasmonic acid-related compounds in developing Phaseolus vulgaris L. (common bean) seeds revealed through desorption electrospray ionization-mass spectrometry imaging
Fig. 4. LC-ESI-MS/MS analysis of JA-related compounds in the extracts from the radicle and seed coat of developing Phaseolus vulgaris seeds. MS/MS spectra of peaks at (a) 5.3 min in Fig. 3c, (b) 5.3 min in Fig. 3d, (c) 6.5 min in Fig. 3c and (d) 6.5 min in Fig. 3d and (e) 6.3 min in Fig. 3e and (f) 6.3 min in Fig. 3f and (g) 6.4 min in Fig. 3e, (h) 6.4 min in Fig. 3f, (i) 6.7 min in Fig. 3e, and (j) 6.7 min in Fig. 3f. Compound names are defined in Table 1.
Fig. 2 in Unique localization of jasmonic acid-related compounds in developing Phaseolus vulgaris L. (common bean) seeds revealed through desorption electrospray ionization-mass spectrometry imaging
Fig. 2. LC-ESI-MS/MS analysis of JA-related compound standards. Spectra of (a) OPDA, (b) OPC-8:0, and (c) JA standards. Compound names are defined in Table 1.
Fig. 1 in Unique localization of jasmonic acid-related compounds in developing Phaseolus vulgaris L. (common bean) seeds revealed through desorption electrospray ionization-mass spectrometry imaging
Fig. 1. DESI-MSI analysis of JA-related compounds in the developing Phaseolus vulgaris seeds. (a) Optical image of the section. (b) Mass spectrum obtained from the section. Ion images of m/z (c) 277.2172, (d) 291.1953, and (e) 293.2117. Three different developing seeds were analyzed, and the results from one are shown as representative data. Scale bar = 2 mm. Compound names are defined in Table 1.
Fig. 3 in Unique localization of jasmonic acid-related compounds in developing Phaseolus vulgaris L. (common bean) seeds revealed through desorption electrospray ionization-mass spectrometry imaging
Fig. 3. LC-ESI-MS analysis of JA-related compounds in the extracts from the radicle and seed coat of developing Phaseolus vulgaris seeds. Base peak chromatogram of m/z 277.2173 ±10 ppm for (a) radicle and (b) seed coat, m/z 291.1966 ± 10 ppm for (c) radicle and (d) seed coat, and m/z 293.2122 ± 10 ppm for (e) radicle and seed coat, respectively. Peaks with arrow indicates JA-related compounds: (a) and (b) αLA, (c) and (d) OPDA, and (e) and (f) OPC-8:0. Compound names are defined in Table 1.
Fig. 2 in Visualizing the spatial distribution of metabolites in Clausena lansium (Lour.) skeels using matrix-assisted laser desorption/ionization mass spectrometry imaging
Fig. 2. Comparison of sample pretreatment methods for MALDI-MSI analysis. (A) Intensities of ion peaks corresponding to organic acids, sugars, and alkaloids in the three different sections using airbrush, iMLayer or combined methods for matrix application. Data represent the mean ± SE of intensities of ions at m/z 230.9, 381.0, 264.1 and 367.1 (n = 3), respectively. Photographs of DHB matrix material prepared by different methods: (B) Spray by airbrush, (C) Sublimation by iMLayer, (D) Spray after sublimation. Films and crystals observation were recorded under the light microscope (× 40).
Fig. 5 in Visualizing the spatial distribution of metabolites in Clausena lansium (Lour.) skeels using matrix-assisted laser desorption/ionization mass spectrometry imaging
Fig. 5. Distribution of the main coumarins in diverse tissue parts in the plant of C. lansium. All the MSI were acquired in positive ion mode. The number of pixels in x and y axis was 243 × 248 for the fruit, and 100 × 70 for the stem and 65 × 37 for the leaf parts. The distributions are displayed as heat maps, with the color code between black (low) and red (high). Images were exported from the Shimadzu Imaging software. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4 in Visualizing the spatial distribution of metabolites in Clausena lansium (Lour.) skeels using matrix-assisted laser desorption/ionization mass spectrometry imaging
Fig. 4. Distribution of the main alkaloids in diverse tissue parts in the plant of C. lansium. All the MSI were acquired in positive ion mode. The number of pixels in x and y axis was 243 × 248 for the fruit, and 100 × 70 for the stem and 65 × 37 for the leaf parts. The distributions are displayed as heat maps, with the color code between black (low) and red (high). Images were exported from the Shimadzu Imaging software. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Visualizing the spatial distribution of metabolites in Clausena lansium (Lour.) skeels using matrix-assisted laser desorption/ionization mass spectrometry imaging
Fig. 1. Optical images of different tissue sections of Clausena lansium (Lour.) Skeels plants. (A) Fruit cross section, (B) Part of stem cross section, (C) Leaf cross section (magnification at 40x).
Application of matrix-assisted laser desorption/ionization mass spectrometry imaging in combination with LC–MS in pharmacokinetic study of metformin
<p>Application of matrix-assisted laser desorption/ionization mass spectrometry imaging in combination with LC-MS in a pharmacokinetic study of metformin</p> <p><a href="https://doi.org/10.4155/bio-2017-0190">https://doi.org/10.4155/bio-2017-0190</a></p> <p>MALDI MSI datasets</p>
Fig. 3 in Visualizing the spatial distribution of metabolites in Clausena lansium (Lour.) skeels using matrix-assisted laser desorption/ionization mass spectrometry imaging
Fig. 3. MALDI-MS spectrum of C. lansium fruit extract in positive ion mode.
Nucleolin-aptamer therapy in retinoblastoma: molecular changes and mass spectrometry–based imaging
GEO Series GSE89818. Homo sapiens. 4 samples. Type: Non-coding RNA profiling by array.
Skin Tumor Biomarkers by Mass Spectrometry Imaging
ClinicalTrials.gov study NCT06227416. IPD Sharing: NO. Countries: 1. Publications: 0.
Evaluating Mass Spectrometry And Intraoperative MRI In The Advanced Multimodality Image Guided Operating Suite (Amigo) In Breast-Conserving Therapy
ClinicalTrials.gov study NCT02335671. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Cell-intrinsic metabolic phenotypes identified in glioblastoma patients using mass spectrometry imaging of 13C-labeled glucose metabolism
GEO Series GSE288836. Homo sapiens. 35 samples. Type: Expression profiling by high throughput sequencing.
Matrix Selection for the Visualization of Small Molecules and Lipids in Brain Tumors Using Untargeted MALDI-TOF Mass Spectrometry Imaging
GEO Series GSE279139. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Mass spectrometry imaging and single-cell transcriptome reveal metabolic profiles of the postauricular glands of the Bufo gargarizans, and hypothesize Bufotoxin biosynthesis pathways
GEO Series GSE261560. Bufo gargarizans. 1 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.