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Confidently detect lipid and metabolite species from single cells
In cancer biology, neuroscience, and immunology, where cell-to-cell heterogeneity profoundly influences behavior, signaling, and disease outcomes, single-cell analysis is particularly valuable. However, despite its transformative potential, since each mammalian cell only contains a few picograms of total lipid mass and few metabolites, distributed across diverse lipid classes and isomeric species, single-cell metabolomics and lipidomics can be challenging.
To accurately characterize molecules, Thermo Scientific mass spectrometers deliver ultra-high sensitivity, sub-ppm mass accuracy, and exceptional resolution. Furthermore, the Thermo Scientific Vanquish Neo UHPLC System operates with reproducibility at nanoliter flow rates to ensure minimal sample loss. To enable confident detection and annotation of hundreds of lipid and metabolite species from single cells, the combination of nano-LC and Thermo Scientific Orbitrap Mass Spectrometers, with their high-resolution and accurate mass (HRAM) capabilities, uniquely satisfies requirements.
Single-cell metabolomics workflows
To accommodate the decrease in sample volume, while increasing the overall workflow sensitivity, low input single cell workflows require highly sensitive LC-MS methods. Single-cell metabolomics workflows implement nanoflow LC-MS methods that meet the same expectations of traditional analytical workflows but with the sensitivity necessary to meet single and low input requirements.
High throughput single-cell polarity switching workflow
For maximum coverage in a single injection, the Thermo Scientific Stellar Mass Spectrometer and Thermo Scientific Orbitrap Excedion Pro Hybrid Mass Spectrometer polarity switching single-cell workflow provides sensitivity, quantitative accuracy, and precision. The workflow provides an unbiased approach for identifying diverse lipids and metabolites from phenotypically distinct cells extracted from complex samples, while requiring minimum sample preparation.
LC-MS configuration and the software needed for data analysis after cell isolation and extraction
Improved lipid coverage and annotation with polarity switching- analysis of a single PANC-1 cell
In the top left corner, we visualize greater than 10 scans per peak for accurate MS1 level quantitation and unknown identification. In the bottom left, the lipid coverage from positive mode alone to +/- switching shows improvement with over 25% more lipids identified. In the top right, two co-eluting compounds at 6 minutes could be detected and fragmented in positive and negative mode, allowing for the greatest single cell coverage and annotation. Representative lipid MS/MS spectra highlight the sensitivity of this method to generate high quality fragmentation data for unknown annotation.
Single-cell and low input workflow
For maximum MS/MS coverage of individual cells in a single polarity, the single-cell workflow, which includes the Thermo Scientific Orbitrap Astral Zoom Mass spectrometer, provides coverage, sensitivity, quantitative accuracy, and precision. The workflow requires minimal sample preparation and provides an unbiased approach for identifying diverse lipids and metabolites from phenotypically distinct cells extracted from complex samples.
After cell isolation and extraction, this workflow shows the LC-MS configuration and the software needed for data analysis.
Parallelization of two HRAM analyzers
Due to the parallelization of the Thermo Scientific Orbitrap Analyzer and Thermo Scientific Astral Analyzer, when using the Thermo Scientific Orbitrap Astral Mass Spectrometer a standard 30-minute data dependent lipidomics run collects 13 times more MS2 scans with higher resolutions and sensitivity than a single injection, in positive mode, where the Orbitrap collects both MS1 and MS/MS data. In addition, the Astral Analyzer records the MS/MS at higher acquisition rates and resolutions while maintaining excellent quality.
What customers say about Orbitrap mass spectrometers
"Orbitrap is the mass spectrometer of choice for untargeted single cell analysis due to the incredible mass resolution, calibration stability and sensitivity that can be achieved, helping us to confidently annotate analytes in single cells.
An additional feature that is helpful in achieving broad metabolite coverage, as well as annotation confidence is polarity switching, which is a feature of Orbitrap analyzers. We are excited about our new purchases and grateful for the amazing customer support that Thermo Fisher Scientific have provided us!"
Melanie Bailey
EPSRC and Professorial Research Fellow Director BBSRC SEISMIC facility
Solutions/products
Our workflows are optimized to generate maximum insight, removing guesswork from choosing the appropriate configuration for your experiments. We offer complete solutions plus a full range of resources to assist you throughout the entire workflow.
Educational resources
Access educational resources to support your single-cell metabolomics analysis.
For Research Use Only. Not for use in diagnostic procedures.