Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-Injection Multi-Omics Analysis by Direct Infusion Mass Spectrometry

ABSTRACT: Combined multi-omics analysis of proteomics, metabolomics, and lipidomics requires separate liquid chromatography mass spectrometry (LC-MS), which limit throughput and increase costs, hindering the application of mass spectrometry-based multi-omics to large-scale analyses. Here, we present simultaneous multi-omics analysis by direct infusion (SMAD), an integrated platform leveraging ion mobility mass spectrometry and self-developed software tools to enable single injection multi-omics analysis without liquid chromatography. SMAD allows quantification of over 9,000 metabolite m/z features and over 1,300 proteins from the same sample in less than five minutes. We validated the efficiency and reliability of SMAD with three case studies. (1) mouse macrophages after M1/M2 polarization and senescence, (2) a pilot drug screen in human cells, and (3) large-scale high-throughput drug screening of mammalian cells in 96-well plates. Finally, relationships between proteomic and metabolomic data are discovered by machine learning and validated.

INSTRUMENT(S): Orbitrap Fusion Lumos, Orbitrap Astral, Orbitrap Ascend

ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090)

SUBMITTER: jesse meyer

PROVIDER: MSV000098413 | MassIVE | Wed Jul 02 12:00:00 BST 2025

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Quartet Methylomics

Project description:The Quartet Project aims to provide resources for QC of multiple types of omic technologies and the effective integration of diverse datasets from various scenarios. Large quantities of multi-omics materials, datasets, and best practices for their QC utilities were developed for whole process QC of large-scale, multi-center, and longitudinal multi-omics profiling.

2023-09-04 | GSE241900 | GEO

E-MTAB-6597

Project description:A multi-omics approach to decipher the complexity of drug resistance in diffuse large B-cell lymphoma

2025-01-23 | E-MTAB-6597 | ExpressionAtlas

Longitudinal multi-omics analysis of Bordetella pertussis Tohama I fermentation

Project description:A longitudinal multi-omics analysis was carried out over a 26-hour small-scale fermentation of B. pertussis. Fermentations were performed in batch mode and under culture conditions intended to mimic industrial processes.

2023-02-21 | GSE212531 | GEO

proteomic survey of lung development and nmyc function in the lung

Project description:protein profiling of mouse lung organogenesis from embryonic day E13.5 until adulthood by gel-free two-dimensional liquid chromatography coupled to large-scale tandem mass spectrometry (MudPIT). protein expression in Nmyc loss of function mutant with a comparison to wildtype at E18 Keywords: protein, proteomics, Mudpit, lung, development, nuclear, cytosol, mitochondria, mouse

2007-04-24 | GSE6108 | GEO

Pharmacogenomic characterisation of a large collection of primary cell lines identifies novel therapeutic options for pleural mesothelioma

Project description:Background: Pleural mesothelioma (PM) urgently requires novel effective treatments. Drug repurposing is a relevant strategy to discover new therapeutic options among well-known drugs used in clinical practice. This study aimed to identify new therapies in the context of molecular heterogeneity of PM. Methods: We performed a multi-omics study of the largest cohort of patient-derived primary PM cell lines (n=58) to date, using whole exome sequencing, RNA sequencing and methylome analysis. We also conducted a large-scale drug screening of over 1300 compounds on a subset of cell lines (n=11), as well as an extension screen (n=48) for selected drugs of interest. The best candidates were validated using 3D culture and mouse models. Results: We demonstrated that the molecular landscape of the cell lines cohort recapitulates the main findings in tumours and revealed new specific features of PM. The large-scale drug screening and subsequent validations highlighted notably strong sensitivity to entinostat and fluvastatin. Importantly, both compounds displayed same efficacy in 2D and 3D culture models and single treatment prolonged survival in vivo similarly or even better than standard chemotherapy. Strikingly, combining entinostat treatment with anti-PD1 led to cures in some mice and immunized them against tumour cells. Conclusions: Among several candidates, we identified entinostat, notably in combination with immune checkpoint inhibitor, and to a lesser extent fluvastatin, as promising therapeutic options for patients. We believe our study provides a valuable resource that could contribute to advances in the field and warrants further clinical investigation.

2025-04-08 | GSE279871 | GEO

The Quartet Data Portal: integration of community-wide resources for multiomics quality control (Proteomics)

Project description:The Project aims to provide resources for QC of multiple types of omic technologies and effective integration of diverse datasets from various scenarios. Large quantities of multi-omics materials, datasets, and best practice for their QC utilities were developed for whole process QC of large scale, multi-center, and longitudinal multi-omics profiling.

2023-09-01 | PXD045065 |

Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (b23-mouse-brain)

Project description:Single-cell three-dimensional (3D) genome techniques have advanced our understanding of cell-type-specific chromatin structures in complex tissues, yet current methodologies are limited in cell throughput. Here we introduce a high-throughput single-cell Hi-C approach (dscHi-C) and its transcriptome co-assay (dscHi-C-multiome) using droplet microfluidics. Using dicHi-C, we investigated chromatin structural changes during mouse brain aging by profiling 32,777 single cells across three developmental stages (3 month, 12 month and 23 month), yielding a median of 78,220 unique contacts. Our results show that genes with significant structural changes are enriched in pathways related to metabolic process and morphology change in neurons, and innate immune response in glial cells, highlighting the role of 3D genome organization in physiological brain ageing. Furthermore, our multi-omics joint assay, dscHi-C-multiome, enables precise cell type identification in the adult mouse brain and uncovers the intricate relationship between genome architecture and gene expression. Collectively, we developed the sensitive, high-throughput dscHi-C and its multi-omics derivative, dscHi-C-multiome, demonstrating their potential for large-scale cell atlas studies in development and disease.

2025-01-10 | GSE285809 | GEO

Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (dscHi-C multiome)

2025-01-10 | GSE285233 | GEO

Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (b12-mouse-brain)

2025-01-10 | GSE285232 | GEO

Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (b3-mouse-brain)

2025-01-10 | GSE285811 | GEO