Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry

PROTEOMICS, Journal Year: 2024, Volume and Issue: 24(12-13)

Published: March 4, 2024

Abstract Ion mobility spectrometry‐mass spectrometry (IMS‐MS or IM‐MS) is a powerful analytical technique that combines the gas‐phase separation capabilities of IM with identification and quantification MS. IM‐MS can differentiate molecules indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, contaminant ions). The importance this reflected by staged increase in number applications for characterization across variety fields, from MS‐based omics (proteomics, metabolomics, lipidomics, etc.) to structural glycans, organic matter, proteins, macromolecular complexes. With increasing application there pressing need effective accessible computational tools. This article presents an overview most recent free open‐source software tools specifically tailored analysis interpretation data derived instrumentation. review enumerates these outlines their main algorithmic approaches, while highlighting representative fields. Finally, discussion current limitations expectable improvements presented.

Language: Английский

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Advances in multimodal mass spectrometry for single‐cell analysis and imaging enhancement

FEBS Letters, Journal Year: 2024, Volume and Issue: 598(6), P. 591 - 601

Published: Jan. 19, 2024

Multimodal mass spectrometry (MMS) incorporates an imaging modality with probe‐based (MS) to enable precise, targeted data acquisition and provide additional biological chemical not available by MS alone. Two categories of MMS are covered; in the first, guides probe target individual cells reduce time automatically defining regions interest. In second category, coupled analysis pipeline increase effective spatial resolution using a higher method, correct for tissue deformation, incorporate fine morphological features dataset. Recent methodological computational developments covered along their application single‐cell analyses.

Language: Английский

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High-Specificity Imaging Mass Spectrometry

Annual Review of Analytical Chemistry, Journal Year: 2024, Volume and Issue: 17(1), P. 1 - 24

Published: April 10, 2024

Imaging mass spectrometry (IMS) enables highly multiplexed, untargeted tissue mapping for a broad range of molecular classes, facilitating in situ biological discovery. Yet, challenges persist specificity, which is the ability to discern one molecule from another, and spatial link imaging data specific features. Instrumental developments have dramatically improved IMS resolution, allowing observations be more readily associated with distinct features across scales, ranging larger anatomical regions single cells. High-performance analyzers systems integrating ion mobility technologies are also becoming prevalent, further improving coverage chemical identity. This review provides an overview recent advancements high-specificity that providing critical context imaging, enabling integrated analyses, addressing advanced biomedical research applications.

Language: Английский

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To image or not to image: Use of imaging mass spectrometry in biomedical lipidomics

Progress in Lipid Research, Journal Year: 2025, Volume and Issue: 97, P. 101319 - 101319

Published: Jan. 1, 2025

Language: Английский

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B cell expression of the enzyme PexRAP, an intermediary in ether lipid biosynthesis, promotes antibody responses and germinal center size

Published: Jan. 15, 2025

The qualities of antibody (Ab) responses provided by B lymphocytes and their plasma cell (PC) descendants are crucial facets to vaccines microbes. Metabolic processes products regulate aspects proliferation differentiation into germinal center (GC) PC states as well Ab diversification. However, there is little information about lymphoid cell-intrinsic functions enzymes that mediate ether lipid biosynthesis, including a major class membrane phospholipids. Imaging mass spectrometry (IMS) results had indicated concentrations number these phospholipids were substantially enhanced in GC compared the background average spleens. it was not clear if biosynthesis cells basis for this finding, or whether such contributes physiology responses. Ether can involve enzyme PexRAP, product Dhrs7b gene. Using combinations IMS immunization experiments mouse models with inducible loss-of-function, we now show lineage-intrinsic expression PexRAP promotes magnitude affinity maturation serological response. Moreover, data revealed -dependent increase primary follicles more prominent GC. Mechanistically, impacted via survival associated controlling levels ROS peroxidation. These findings reveal vital role peroxisomal homeostasis humoral immunity.

Language: Английский

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B cell expression of the enzyme PexRAP, an intermediary in ether lipid biosynthesis, promotes antibody responses and germinal center size

Published: Jan. 15, 2025

The qualities of antibody (Ab) responses provided by B lymphocytes and their plasma cell (PC) descendants are crucial facets to vaccines microbes. Metabolic processes products regulate aspects proliferation differentiation into germinal center (GC) PC states as well Ab diversification. However, there is little information about lymphoid cell-intrinsic functions enzymes that mediate ether lipid biosynthesis, including a major class membrane phospholipids. Imaging mass spectrometry (IMS) results had indicated concentrations number these phospholipids were substantially enhanced in GC compared the background average spleens. it was not clear if biosynthesis cells basis for this finding, or whether such contributes physiology responses. Ether can involve enzyme PexRAP, product Dhrs7b gene. Using combinations IMS immunization experiments mouse models with inducible loss-of-function, we now show lineage-intrinsic expression PexRAP promotes magnitude affinity maturation serological response. Moreover, data revealed -dependent increase primary follicles more prominent GC. Mechanistically, impacted via survival associated controlling levels ROS peroxidation. These findings reveal vital role peroxisomal homeostasis humoral immunity.

Language: Английский

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Imaging and spatially resolved mass spectrometry applications in nephrology

Nature Reviews Nephrology, Journal Year: 2025, Volume and Issue: unknown

Published: March 27, 2025

Language: Английский

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Metabolism and metabolomics in senescence, aging, and age-related diseases: a multiscale perspective

Frontiers of Medicine, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 17, 2025

Language: Английский

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Combining imaging mass spectrometry and immunohistochemistry to analyse the lipidome of spinal cord inflammation

Analytical and Bioanalytical Chemistry, Journal Year: 2024, Volume and Issue: 416(8), P. 1923 - 1933

Published: Feb. 7, 2024

Abstract Inflammation is a complex process that accompanies many pathologies. Actually, dysregulation of the inflammatory behind autoimmune diseases. Thus, treatment such pathologies may benefit from in-depth knowledge metabolic changes associated with inflammation. Here, we developed strategy to characterize lipid fingerprint inflammation in mouse model spinal cord injury. Using imaging mass spectrometry (LIMS), scanned sections nine animals injected lysophosphatidylcholine, chemical demyelination. The lesions were demonstrated be highly heterogeneous, and therefore, comparison immunofluorescence experiments carried out same section by LIMS was required accurately identify morphology lesion. Following this protocol, three main areas defined: lesion core, peri-lesion, which front rich infiltrating cells, uninvolved tissue. Segmentation allowed us isolate each area precise way, as analysis using classification models. A clear difference signature observed between epicentre, where damage maximized. This study first step unravel lipidome context diverse pathologies, multiple sclerosis. Graphical abstract

Language: Английский

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RevealingIn SituMolecular Profiles of Glomerular Cell Types and Substructures with Integrated Imaging Mass Spectrometry and Multiplexed Immunofluorescence Microscopy

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 23, 2024

Abstract Glomeruli filter blood through the coordination of podocytes, mesangial cells, fenestrated endothelial and glomerular basement membrane. Cellular changes, such as podocyte loss, are associated with pathologies like diabetic kidney disease (DKD). However, little is known regarding in situ molecular profiles specific cell types how these change disease. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) well-suited for untargeted tissue mapping a wide range classes. Additional modalities can be integrated MALDI IMS to associate biomolecular distributions types. Herein, we demonstrate an workflow combining multiplexed immunofluorescence (MxIF) microscopy. High spatial resolution (5 µm pixel size) was used determine lipid within human glomeruli, revealing intra-glomerular heterogeneity. Mass spectrometric data were linked new methods that enable MxIF microscopy performed on same section following without sacrificing signal quality from either modality. A combination machine-learning approaches assembled, enabling cell-type segmentation identification based followed by mining type or cluster-associated signatures using classification models interpretable machine learning. This allowed automated discovery spatially biomarker candidates substructures Overall, work presented here establishes toolbox probing microenvironments provides framework applies other features organ systems.

Language: Английский

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