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Lipid Landscape of the Human Retina and Supporting Tissues Revealed by High Resolution Imaging Mass Spectrometry [article]

David MG Anderson, Jeffrey D Messinger, Nathan H Patterson, Emilio S Rivera, Ankita Kotnala, Jeffrey M Spraggins, Richard M Caprioli, Christine A Curcio, Kevin L Schey
2020 bioRxiv   pre-print
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

Angela R. S. Kruse, Jeffrey M. Spraggins
2022 Frontiers in Physiology  
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

Karin A. Zemski Berry, Joseph A. Hankin, Robert M. Barkley, Jeffrey M. Spraggins, Richard M. Caprioli, Robert C. Murphy
2011 Chemical Reviews  
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]

Christopher J. Good, Elizabeth K. Neumann, Casey E. Butrico, James E. Cassat, Richard M. Caprioli, Jeffrey M. Spraggins
2021 bioRxiv   pre-print
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]

Elizabeth K Neumann, Emilio S Rivera, Nathan Heath Patterson, Mark deCaestecker, Agnes B Fogo, Richard M. Caprioli, Jeffrey M. Spraggins
2020 bioRxiv   pre-print
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

Raf Van de Plas, Junhai Yang, Jeffrey Spraggins, Richard M Caprioli
2015 Nature Methods  
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]

Emma Guiberson, Andy Weiss, Daniel J Ryan, Andrew J Monteith, Kavya Sharman, Danielle B Gutierrez, William Joseph Perry, Richard M Caprioli, Eric P Skaar, Jeffrey M. Spraggins
2020 bioRxiv   pre-print
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]

Leonoor E.M. Tideman, Lukasz G. Migas, Katerina V. Djambazova, Nathan Heath Patterson, Richard M. Caprioli, Jeffrey M. Spraggins, Raf Van de Plas
2020 bioRxiv   pre-print
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

André Kleinridders, Heather A. Ferris, Michelle L. Reyzer, Michaela Rath, Marion Soto, M. Lisa Manier, Jeffrey Spraggins, Zhihong Yang, Robert C. Stanton, Richard M. Caprioli, C. Ronald Kahn
2018 Molecular Metabolism  
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]

Nathan Heath Patterson, Elizabeth K Neumann, Kavya Sharman, Jamie L Allen, Raymond C Harris, Agnes B Fogo, Mark P deCaestecker, Richard M. Caprioli, Raf Van de Plas, Jeffrey M. Spraggins
2021 bioRxiv   pre-print
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
more » ... 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.
doi:10.1101/2021.07.16.452703 fatcat:xwaq4psjsfam3e7bzc5mbgght4

Multi-Contrast Computed Tomography Healthy Kidney Atlas [article]

Ho Hin Lee, Yucheng Tang, Kaiwen Xu, Shunxing Bao, Agnes B. Fogo, Raymond Harris, Mark P. de Caestecker, Mattias Heinrich, Jeffrey M. Spraggins, Yuankai Huo, Bennett A. Landman
2020 arXiv   pre-print
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

Kerri J. Grove, Paul A. Voziyan, Jeffrey M. Spraggins, Suwan Wang, Paisit Paueksakon, Raymond C. Harris, Billy G. Hudson, Richard M. Caprioli
2014 Journal of Lipid Research  
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]

Leah L. Godwin, Yingnan Ju, Naveksha Sood, Yashvardhan Jain, Ellen M Quardokus, Andreas Bueckle, Teri Longacre, Aaron Marks Horning, Yiing Lin, Edward D. Esplin, John W. Hickey, Michael P. Snyder (+3 others)
2021 bioRxiv   pre-print
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]

Katy Borner, Andreas Bueckle, Bruce W. Herr, Leonard E Cross, Ellen M. Quardokus, Elizabeth G. Record, Yingnan Ju, Jonathan C. Silverstein, Kristen Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen (+3 others)
2021 bioRxiv   pre-print
., 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

David M. G. Anderson, Jeffrey M. Spraggins, Kristie L. Rose, Kevin L. Schey
2015 Journal of the American Society for Mass Spectrometry  
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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