Alexandrov Team
Projects
METASPACE
Cloud Platform for Spatial Metabolomics
Spatial Metabolomics SoftwareMETASPACE is a cloud platform for spatial metabolomics. At its core is an high-performance engine for metabolite annotation. It also serves as a knowledge base by providing access to over 10,000 public datasets. It offers multiple other features for data analysis, visualization, sharing & publication.
Go to METASPACE Read publication in Nature Methods
SpaceM
Method for Single-Cell Metabolomics
Single-Cell MetabolomicsSpaceM is a method for single-cell metabolomics which integrates microscopy & imaging mass spectrometry. SpaceM can be used for any cell type cultured or plated on glass. It uses MALDI-imaging mass spectrometry for detecting metabolites, lipids, or drugs, and can detect 100+ small molecules or 500+ lipids from single cells. It integrates data using computational methods & software.
Read publication in Nature Methods
METASPACE-ML
Machine Learning-Based Metabolite Annotation
Spatial MetabolomicsMETASPACE-ML is a machine learning-based tool that improves metabolite identification in imaging mass spectrometry, offering higher precision, throughput, and sensitivity compared to its rule-based predecessor.
Read preprint
Detectability of Metabolites & Lipids
Inter-Lab Study
Spatial Metabolomics SoftwareWe compared 24 MALDI-imaging protocols and 10 imaging mass spectrometry technologies in their ability to detect 172 small molecules and lipids. We present the results and data through a new interactive web application integrated with METASPACE. This resource can guide selection of the best protocol, in particular for newcomers in the field of spatial metabolomics.
Open web-app on METASPACE Read preprint
S2isomer
Metabolite Enrichment Robust to Isomers & Isobars
Spatial Metabolomics SoftwareS2IsoMEr is an R package that addresses isomeric/isobaric ambiguities, enabling accurate overrepresentation and metabolite set enrichment analysis for spatial and single-cell metabolomics datasets.
Read preprint Open GitHub repository
13C-SpaceM
Spatial & Single-Cell Isotope Tracing
Single-Cell Metabolomics13C-SpaceM is a method for highly-sensitive spatial single-cell isotope tracing of lipid metabolism. The key idea of the method resembles saponification (separation of fatty acids from lipids) but is performed for each pixel analyzed by the imaging mass spec, in the gas phase, on-the-fly, while molecules are flying through a mass spectrometer. This “gas-phase saponification” method boosts sensitivity & data quality, is perfectly suited for single-cell & spatial analyses of lipid metabolism, and can be used in the framework of SpaceM.
Read publication in Nature Metabolism Read Twittorial
`ili
Software for 3D Molecular Cartography
Software`ili is an open-source visualization software for 3D molecular cartography. The approach was developed by the Dorrestein lab at UC San Diego, with the software developed by our team. The software can be used for mapping molecular data onto surfaces where it was collected, as well as for 3D volume mapping (as developed in the NIH LungMAP2 project).
Go to `ili Read publication in Nature Protocols
pyimzML
Parser for imzML files
Spatial Metabolomics SoftwarepyimzML is a parser for the imzML format used primarily in imaging mass spectrometry datasets
Open GitHub repository
METASPACE Converter
Convert METASPACE datasets to AnnData and SpatialData
Spatial Metabolomics Single-Cell Metabolomics SoftwareMETASPACE Converter is a Python package to download and convert datasets from METASPACE to common formats for single-cell and spatial omics analysis
Open GitHub repository