Co-registration and analysis of multiple imaging mass spectrometry datasets targeting different analytes

Patterson, Nathan Heath; Yang, Eun Jung; Kranjec, Elizabeth-Ann; Chaurand, Pierre

doi:10.1093/bioinformatics/bty780

Cited by 26 publications

(25 citation statements)

References 3 publications

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“…The parameters for the smoothing radius (r), the number of cluster (k), and the shrinking parameter (s) were determined based on the histology and kept constant throughout the sample set. The package RegCombIMS was used to combine the positive and negative IMS datasets from the same section before statistical analysis …”

Section: Methodsmentioning

confidence: 99%

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Mapping the fly Malpighian tubule lipidome by imaging mass spectrometry

2019

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Matrix‐assisted laser/desorption ionization imaging mass spectrometry (MALDI IMS) is an analytical technique for understanding the spatial distribution of biomolecules across a sample surface. Originally employed for mammalian tissues, this technology has been adapted to study specimens as diverse as microbes and cell cultures, food such as strawberries, and invertebrates including the vinegar fly Drosophila melanogaster. As an ideal model organism, Drosophila has brought greater understanding about conserved biological processes, organism development, and diseased states and even informed management practices of agriculturally and environmentally important species. Drosophila displays anatomically separated renal (Malpighian) tubules that are the physiological equivalent to the vertebrate nephron. Insect Malpighian tubules are also responsible for pesticide detoxification. In this article, we first describe an effective workflow and sample preparation method to study the phospholipid distribution of the Malpighian tubules that initially involves the manual microdissection of the tubules in saline buffer followed by a series of washes to remove excess salt and enhances the phospholipid signals prior to matrix deposition and IMS at 25‐μm spatial resolution. We also established a complementary methodology for lipid IMS analysis of whole‐body fly sections using a dual‐polarity data acquisition approach at the same spatial resolution after matrix deposition by sublimation. Both procedures yield rich signal profiles from the major phospholipid classes. The reproducibility and high‐quality results offered by these methodologies enable cohort studies of Drosophila through MALDI IMS.

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Section: Methodsmentioning

confidence: 99%

“…The package RegCombIMS was used to combine the positive and negative IMS datasets from the same section before statistical analysis. 34…”

Section: Ims Data Analysismentioning

confidence: 99%

Mapping the fly Malpighian tubule lipidome by imaging mass spectrometry

2019

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“…The actual idea of a co-registration is much broader, it has been used, e.g., in synthetic aperture radars [61] or mass spectrometry [83].…”

Section: Co-registration In Other Modalitiesmentioning

confidence: 99%

The tempest in a cubic millimeter: Image-based refinements necessitate the reconstruction of 3D microvasculature from a large series of damaged alternately-stained histological sections

Lobachev

2019

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This work presents two methods that facilitate a 3D reconstruction of microscopic blood vessels in the volume slightly larger than 1 mm 3 . The source of the data are histological serial sections, i. e., microscopic images of probes, stained with immunohistochemistry. Odd and even sections have different stainings in our primary data set. Thus, firstly, an approach to register an alternately-stained series is presented. With image filtering and a feature-detection-based registration we obtain a registered stack of 148 serial sections. The series has missing sections, locally damaged sections, artifacts from acquisition. All these hinder correct connectivity of blood vessels. With our second approach we interpolate the missing information while maintaining the connectivity. We achieve this with deformations based on dense optical flow. The presented methodology is applicable to further histological series. A combination of both approaches allows us to reconstruct more than 76 % larger volumes. An important detail was the composition mode of images. Summarizing, we use methods from image processing and computer vision to create large-scale 3D models from immunostained histological serial sections.

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“…No current MALDI matrix preparation provides high sensitivity for all classes of biomolecules within a single IMS experiment. Thus, the MALDI matrix chosen for an IMS experiment will greatly influence the measured intensities of various analyte classes during analysis …”

Section: Introductionmentioning

confidence: 99%

Uncovering matrix effects on lipid analyses in MALDI imaging mass spectrometry experiments

et al. 2020

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The specific matrix used in matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) can have an effect on the molecules ionized from a tissue sample. The sensitivity for distinct classes of biomolecules can vary when employing different MALDI matrices. Here, we compare the intensities of various lipid subclasses measured by Fourier transform ion cyclotron resonance (FT-ICR)

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Co-registration and analysis of multiple imaging mass spectrometry datasets targeting different analytes

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 26 publications

References 3 publications

Mapping the fly Malpighian tubule lipidome by imaging mass spectrometry

Mapping the fly Malpighian tubule lipidome by imaging mass spectrometry

The tempest in a cubic millimeter: Image-based refinements necessitate the reconstruction of 3D microvasculature from a large series of damaged alternately-stained histological sections

Uncovering matrix effects on lipid analyses in MALDI imaging mass spectrometry experiments

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