Fast visual exploration of mass spectrometry images with interactive dynamic spectral similarity pseudocoloring

Wüllems, Karsten; Zurowietz, Annika; Zurowietz, Martin; Schneider, R.S.; Bednarz, Hanna; Niehaus, Karsten; Nattkemper, Tim Wilhelm

doi:10.1038/s41598-021-84049-4

Cited by 3 publications

(1 citation statement)

References 31 publications

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“…The MALDI-MSI data featured, respectively, 3,108 features in positive and 2,133 in negative ionization modes with 4 animals per Treatment x Development condition (i.e., PND 7, 14, 21, and 50 days for both CTL and PL). Individual data were (1) log-transformed to account for log-normal distribution by peak, (2) standardized to z-scores to give same weight to all peaks independently of abundance and (3) 5% winsorized to minimize the influence of individual outliers ( 58 ). Principal component analysis (PCA) of these data was performed to simultaneously visualize the correlation structure of features (biplot loadings) and the multivariate discrimination between conditions (biplot scores, average of 4 animals) ( 59 ).…”

Section: Methodsmentioning

confidence: 99%

Early Life to Adult Brain Lipidome Dynamic: A Temporospatial Study Investigating Dietary Polar Lipid Supplementation Efficacy

et al. 2022

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The lipid composition of the brain is well regulated during development, and the specific temporospatial distribution of various lipid species is essential for the development of optimal neural functions. Dietary lipids are the main source of brain lipids and thus contribute to the brain lipidome. Human milk is the only source of a dietary lipids for exclusively breastfed infant. Notably, it contains milk fat globule membrane (MFGM) enriched in polar lipids (PL). While early life is a key for early brain development, the interplay between dietary intake of polar lipids and spatial dynamics of lipid distribution during brain development is poorly understood. Here, we carried out an exploratory study to assess the early postnatal temporal profiling of brain lipidome between postnatal day (PND) 7 and PND 50 using matrix-assisted laser desorption ionization as a mass spectrometry imaging (MALDI-MSI) in an in vivo preclinical model. We also assessed the effect of chronic supplementation with PL extracted from alpha-lactalbumin-enriched whey protein concentrate (WPC) containing 10% lipids, including major lipid classes found in the brain (37% phospholipids and 15% sphingomyelin). MALDI-MSI of the spatial and temporal accretion of lipid species during brain development showed that the brain lipidome is changing heterogeneously along time during brain development. In addition, increases in 400+ PL supplement-dependent lipids were observed. PL supplementation had significant spatial and temporal effect on specific fatty esters, glycerophosphocholines, glycerophosphoethanolamines, and phosphosphingolipids. Interestingly, the average levels of these lipids per brain area tended to be constant in various brain structures across the age groups, paralleling the general brain growth. In contrast, other lipids, such as cytidine diphosphate diacylglycerol, diacylglycerophosphates, phosphocholines, specific ether-phosphoethanolamines, phosphosphingolipids, glycerophosphoinositols, and glycerophosphoserines showed clear age-dependent changes uncoupled from the general brain growth. These results suggest that the dietary PL supplementation may preferentially provide the building blocks for the general brain growth during development. Our findings add to the understanding of brain-nutrient relations, their temporospatial dynamics, and potential impact on neurodevelopment.

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Section: Methodsmentioning

confidence: 99%

Early Life to Adult Brain Lipidome Dynamic: A Temporospatial Study Investigating Dietary Polar Lipid Supplementation Efficacy

et al. 2022

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msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis

Spangenberg,

Bessler,

Widera

et al. 2024

Preprint

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Multimodal imaging by matrix-assisted laser desorption ionisation mass spectrometry imaging (MALDI MSI) and immunofluorescence microscopy holds great potential for understanding pathological mechanisms by mapping molecular signatures from the tissue microenvironment to specific cell populations. However, existing open-source software solutions for analysis of MALDI MSI data are incomplete, require programming skills and contain laborious manual steps, hindering broadly applicable, reproducible, and high-throughput analysis to generate impactful biological discoveries across interdisciplinary research fields. Here we present msiFlow, an accessible open-source, platform-independent and vendor-neutral software for end-to-end, high-throughput, transparent and reproducible analysis of multimodal imaging data. msiFlow integrates all necessary steps from import and pre-processing of raw MALDI MSI data to visual analysis output, as well as registration, along with state-of-the-art and newly developed algorithms, into automated workflows. Using msiFlow, we unravel the molecular heterogeneity of leukocytes in infected tissues by spatial regulation of ether-linked phospholipids containing arachidonic acid. We anticipate that msiFlow will facilitate the broad applicability of MSI in the emerging field of multimodal imaging to uncover context-dependent cellular regulations in disease states.

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The software for interactive evaluation of mass spectrometric imaging heterogeneity

et al. 2022

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Mass spectrometry imaging is a promising tool complement to the histology study for evaluation of presence of different tissue types in the sample. To make this method faster, more accurate and precise we have presented earlier the cosine similarity measure maps (CSMM). The method provides the spatial distribution of cosine similarity measure metrics between chosen MSI pixel and the rest of the image. In cases when samples under test are heterogeneous and not guaranteed to have clear clusters with distinct borders, it is interesting to analyze the heterogeneity, area borders and their sensitivity to reference CSMM pixel selection. Here we present the software for interactive building of CSMM for different parameters, their visual analysis and saving such CSMM in publication-ready quality without additional programming. Source code, example datasets, binaries, and other information are available at https://github.com/EvgenyZhvansky/Interactive_CSMM.

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Fast visual exploration of mass spectrometry images with interactive dynamic spectral similarity pseudocoloring

Cited by 3 publications

References 31 publications

Early Life to Adult Brain Lipidome Dynamic: A Temporospatial Study Investigating Dietary Polar Lipid Supplementation Efficacy

Early Life to Adult Brain Lipidome Dynamic: A Temporospatial Study Investigating Dietary Polar Lipid Supplementation Efficacy

msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis

The software for interactive evaluation of mass spectrometric imaging heterogeneity

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