2023
DOI: 10.1038/s41592-023-02007-6
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Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome

Florian A. Rosenberger,
Marvin Thielert,
Maximilian T. Strauss
et al.

Abstract: Single-cell proteomics by mass spectrometry is emerging as a powerful and unbiased method for the characterization of biological heterogeneity. So far, it has been limited to cultured cells, whereas an expansion of the method to complex tissues would greatly enhance biological insights. Here we describe single-cell Deep Visual Proteomics (scDVP), a technology that integrates high-content imaging, laser microdissection and multiplexed mass spectrometry. scDVP resolves the context-dependent, spatial proteome of … Show more

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Cited by 42 publications
(24 citation statements)
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“…Cells were counted using the Countess TM 3 FL Automated Cell Counter (SN: AMQAF2000, Invitrogen) and strained using a 5-mL cell strainer tube (SN: 352235, Falcon®) to a final concentration of 200 cells/µL for optimal cell dispensing on the cellenONE®. For the proteome perturbation experiment, HEK-293T cells were seeded in a 6-well plate (Costar® 6-well plates, 3506, Corning Incorporated) at a density of 3 x 10 5 cells/well. THP-1 cells were seeded in a T25 flask at a density of 4 x 10 5 cells/mL in Gibco RPMI media supplemented with 10% Fetal Bovine Serum, Penicillin-Streptomycin and Glutamax.…”
Section: Methodsmentioning
confidence: 99%
See 2 more Smart Citations
“…Cells were counted using the Countess TM 3 FL Automated Cell Counter (SN: AMQAF2000, Invitrogen) and strained using a 5-mL cell strainer tube (SN: 352235, Falcon®) to a final concentration of 200 cells/µL for optimal cell dispensing on the cellenONE®. For the proteome perturbation experiment, HEK-293T cells were seeded in a 6-well plate (Costar® 6-well plates, 3506, Corning Incorporated) at a density of 3 x 10 5 cells/well. THP-1 cells were seeded in a T25 flask at a density of 4 x 10 5 cells/mL in Gibco RPMI media supplemented with 10% Fetal Bovine Serum, Penicillin-Streptomycin and Glutamax.…”
Section: Methodsmentioning
confidence: 99%
“…For the proteome perturbation experiment, HEK-293T cells were seeded in a 6-well plate (Costar® 6-well plates, 3506, Corning Incorporated) at a density of 3 x 10 5 cells/well. THP-1 cells were seeded in a T25 flask at a density of 4 x 10 5 cells/mL in Gibco RPMI media supplemented with 10% Fetal Bovine Serum, Penicillin-Streptomycin and Glutamax. After 8-hours, media was supplemented with LPS (final conc.…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…Tissue volumes were estimated using commercially available biopsy punches based on needs (0.35 mm, 0.5 mm, 0.75 mm, 1 mm, 1.5 mm, 2 mm, 3 mm; Integra Miltex, the United States). Specifically, the formula to calculate the volume is: volume (nL) = π × (D/2F) 2 × h × 10 - 6 , where D is the diameter (µm) of the punch, F is the expansion factor calculated as the square root of the ratio of the tissue area after expansion to the area before expansion, and h is the thickness (µm) of the slice. The detection range calibration curves were estimated using Local Polynomial Regression Fitting estimation (loess) using the number of identified peptides and proteins.…”
Section: Methodsmentioning
confidence: 99%
“…Follow-up work based on further improved sample preparation and LC-MS workflows recently led to the first single-cell (i.e. slice of a single cell) proteome measurements from frozen and formalin-fixed (FFPE) tissues (8, 9). In FFPE tissue, we reproducibly quantified up to 2,000 proteins from single excised hepatocyte contours (∼5,000 µm 3 in volume) based on an optimized sample preparation protocol and label-free based diaPASEF acquisition (10) on the Bruker timsTOF SCP instrument (11).…”
Section: Introductionmentioning
confidence: 99%