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Lipid Landscape of the Human Retina and Supporting Tissues Revealed by High Resolution Imaging Mass Spectrometry
[article]
2020
bioRxiv
pre-print
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Data were acquired with 500 shots per pixel and a mass range of m/z 154-2000 using the 1M data size resulting in a 0.5592 second transient, mass resolution was ~60,000 at m/z 699.499. ...
Rod photoreceptors are slender (2-3 µm) and can be very long (100 µm). They are the dominant photoreceptor in human retina (20:1 rod:cone ratio), being absent only in the cone-only foveal center. ...
doi:10.1101/2020.04.08.029538
fatcat:kmcao3cjvrebxioskmdvx2y42i
Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry
2022
Frontiers in Physiology
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Technologies are characterized based on their spatial resolution from the level of anatomical structure (>500 µm), Functional Tissue Unit (FTU, ∼50-500 µm), cellular (∼10-50 µm), and subcellular (<10 µm ...
., 1997; Norris and Caprioli, 2013; Spraggins et al., 2019; Martín-Saiz et al., 2021) . ...
doi:10.3389/fphys.2022.837773
pmid:35222094
pmcid:PMC8874197
fatcat:jsymkizlyrfthehkawipmwb53i
MALDI Imaging of Lipid Biochemistry in Tissues by Mass Spectrometry
2011
Chemical Reviews
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Jeff Spraggins received his B.A. in Chemistry from the College of Wooster and his Ph.D. in
Analytical Chemistry from the University of Delaware (2009) where he studied gas phase
fragmentation mechanisms ...
[M+H] + , [M+Na] + , [M +K] + , or [M−H] − . ...
doi:10.1021/cr200280p
pmid:21942646
pmcid:PMC3199966
fatcat:texdypelhfgalnihgvatitbjqa
Optimized Workflow for High Spatial Resolution MALDI Imaging Mass Spectrometry of Fresh-Frozen Bone
[article]
2021
bioRxiv
pre-print
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High spatial resolution (10 μm) MALDI IMS was leveraged to characterize lipid distributions in fresh-frozen bone, and complementary microscopy modalities aided tissue and cell assignments. ...
m/z 760.59), [SM(34:1) + H] + (m/z 703.57), and [SM(42:2) + H] + (m/z 813.68; Figure ...
2 footprint and 8 µm 2 footprint for 20 µm and 10 µm spatial resolution imaging, respectively. ...
doi:10.1101/2021.10.01.462831
fatcat:bi7nwt7lobbphptirm4amzo2qm
Highly Multiplexed Immunofluorescence of the Human Kidney using Co-Detection by Indexing (CODEX)
[article]
2020
bioRxiv
pre-print
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M.; Kliegel, J. A.; Shuch, B. M.; Montgomery, R. R.; Moeckel, G. W.; Cantley, L. G. JCI Insight 2019, 4, e129477. (18) Jarvis, M. F.; Williams, M. ...
Scale bar 200 µm. C) Medullary region of the kidney with many tubules present. Scale bar 200 µm. ...
doi:10.1101/2020.12.04.412429
fatcat:jobw2xblrzgibmppepm2xq6aui
Image fusion of mass spectrometry and microscopy: a multimodality paradigm for molecular tissue mapping
2015
Nature Methods
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Prediction of the ion distribution of m/z 762.5 in mouse brain at 10 μm resolution from 100 μm IMS and 10 μm microscopy measurements (sharpening). ...
Measured ion images acquired in mouse brain for m/z 646.4 and m/z 788.5 at 10 μm spatial resolution (a) are fused with an H&E-stained microscopy image measured at 0.33 μm resolution (b). ...
doi:10.1038/nmeth.3296
pmid:25707028
pmcid:PMC4382398
fatcat:qwqtqaxptfcx7mly7lfqx7lx6y
Spatially-targeted proteomics of the host-pathogen interface during staphylococcal abscess formation
[article]
2020
bioRxiv
pre-print
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Carbamidomethylation was set as a fixed modification and 580 acetyl (protein N-term) and oxidation (M) were set as variable modifications. Minimal peptide length was 581 7 amino acids. ...
Tissues were then cryosectioned at 10 µm thickness (Leica 529 Microsystems, Buffalo Grove, IL) and thaw mounted onto custom fiducial microscope slides (Delta 530 Technology, Loveland, CO). ...
doi:10.1101/2020.09.01.267773
fatcat:6tijwgd73rc2vjngehpz2fp2cu
Automated Biomarker Candidate Discovery in Imaging Mass Spectrometry Data Through Spatially Localized Shapley Additive Explanations
[article]
2020
bioRxiv
pre-print
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M. Spraggins et al. "High-Performance Molecular Imaging with MALDI Trapped Ion-Mobility Time-of-Flight (timsTOF) Mass Spectrometry". In: Analytical Chemistry . ...
Although the global SHAP scores of m/z . and m/z . are higher than that of m/z . ...
Tissue imaging data ( , pixels) were collected at µm spatial resolution, using shots per pixel and % laser power. Data were collected in positive ionization mode from m/z to , . ...
doi:10.1101/2020.12.23.424201
fatcat:po2nrupr3jbkpjgrlqafvshj2u
Regional differences in brain glucose metabolism determined by imaging mass spectrometry
2018
Molecular Metabolism
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The following transitions were monitored: ATP: MS 3 m/z 506 / m/z 408 / m/z 273 þ 214; ADP: MS 3 m/z 426 / m/z 328 / m/z 134; Glucose-1,6-bisphosphate: MS 3 m/z 339 / m/z 241 / [m/z 79 þ 97] þ m/z 121 ...
þ 139; Fructose-1,6bisphosphate: MS 3 m/z 339 / m/z 241 / [m/z 79 þ 97] þ m/z 151. ...
doi:10.1016/j.molmet.2018.03.013
pmid:29681509
pmcid:PMC6001904
fatcat:iy7v2rjqpvgl5hncidbbdeh4ie
Autofluorescence microscopy as a label-free tool for renal histology and glomerular segmentation
[article]
2021
bioRxiv
pre-print
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Functional tissue units (FTUs) composed of multiple cells like the glomerulus in the kidney nephron play important roles in health and disease. Histological staining is often used for annotation or segmentation of FTUs, but chemical stains can introduce artefacts through experimental factors that influence analysis. Secondly, many molecular -omics techniques are incompatible with common histological stains. To enable FTU segmentation and annotation in human kidney without the need for
doi:10.1101/2021.07.16.452703
fatcat:xwaq4psjsfam3e7bzc5mbgght4
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... al staining, we detail here the use of widefield autofluorescence (AF) microscopy as a simple, label-free modality that provides detailed renal morphology comparable to periodic acid-Schiff (PAS) stained tissue in both formalin-fixed paraffin-embedded (FFPE) and fresh frozen samples and with no tissue processing beyond sectioning. We demonstrate automated deep learning-based glomerular unit recognition and segmentation on PAS and AF images of the same tissue section from 9 fresh frozen samples and 9 FFPE samples. All training comparisons were carried out using registered AF microscopy and PAS stained whole slide images originating from the same section, and the recognition models were built with the exact same training and test examples. Measures of recognition performance, such as the Dice-Sorensen coefficient, the true positive rate, and the positive predictive value differed less than 2% between standard PAS and AF microscopy for both preservation methods. These results demonstrate that AF is a potentially powerful tool to study human kidney tissue, that it can serve as a label-free source for automated and manual annotation of tissue structures.
Multi-Contrast Computed Tomography Healthy Kidney Atlas
[article]
2020
arXiv
pre-print
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2020 pre-print arXiv:2012.12432v1 fatcat:s55k7cezvngn3eznobnnzztfae
ACKNOWLEDGEMENT This research is supported by HuBMAP, NIH Common Fund and National Institute of Diabetes, Digestive and Kidney Diseases U54DK120058 (Spraggins), NSF CAREER 1452485, NIH 2R01EB006136, NIH ...
Fogo, Raymond Harris, Mark P. de Caestecker, Mattias Heinrich, Jeffrey M. Spraggins, Yuankai Huo, Bennett A. ...
The self-similarity metric S is optimizing a distance function D between the image patches extracted from the moving image M. ...
arXiv:2012.12432v2
fatcat:q24uyoiaavbydlznmfxpwaw4dm
Diabetic nephropathy induces alterations in the glomerular and tubule lipid profiles
2014
Journal of Lipid Research
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Spectra were collected in the range of m/z of 400-1500 with 500 shots/spectra. Image resolution was set at 40 µm or 10 µm. ...
Raster steps were taken in 10 µm stage increments and the laser spot size was also 10 µm in diameter as measured on a thin matrix coating. ...
doi:10.1194/jlr.m049189
pmid:24864273
pmcid:PMC4076088
fatcat:beponvxkabgjbjrl747wqd25qq
Robust and generalizable segmentation of human functional tissue units
[article]
2021
bioRxiv
pre-print
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Normal human colonic crypts have a diameter of 73.5±3.4µm and length of 433±25µm 34 . ...
The images have a spatial resolution of 0.5µm, and the average annotation area was calculated in pixels and µm 2 . ...
The average BMI of the dataset (29.61kg/m 2 ) is between that given as the average for females (29.8kg/m 2 ) and males (29.4kg/m 2 ) in the US 83 . ...
doi:10.1101/2021.11.09.467810
fatcat:fyqd3txj3jdornv55o54nqahi4
Tissue Registration and Exploration User Interfaces in support of a Human Reference Atlas
[article]
2021
bioRxiv
pre-print
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., scRNAseq data costs about $1 per cell; sampling a tissue block of 1mm 3 filled with 10μm diameter cells costs about $1 million). ...
Data is shared in JSON-LD with the following 22 fields: donor ID (de-identified), age (or age range), sex, BMI (kg/m 2 ), consortium name, tissue provider name, tissue provider UUID, tissue provider author ...
annotation consisting of 14-segment polyline, the associated 15 points are highlighted in yellow in JSON--note that the first set of coordinates is identical to the last closing the polyline (scale bar: 50µm) ...
doi:10.1101/2021.12.30.474265
fatcat:hst5gbdkjzg3jn3uti2r6jrwdu
High Spatial Resolution Imaging Mass Spectrometry of Human Optic Nerve Lipids and Proteins
2015
Journal of the American Society for Mass Spectrometry
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Ion images display the distributions of (a) SM(d36:2), (M+Na) + , (b) SM(d36:1), (M+Na) + , (c) SM(d34:1), (M+Na) + , (d) Heme b, (e) unidentified m/z 651.5. ...
bundles at m/z 753.6. ...
doi:10.1007/s13361-015-1143-9
pmid:25893273
pmcid:PMC5650057
fatcat:me7lyqnbcfg7xhqdruksce4akq
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