Table 1.
Single Cell Proteomic Methodologies
| Technique | Proteomic Depth (Number of proteins) | Cellular Isolation Mechanism | Published Applications | Advantages | Limitations |
|---|---|---|---|---|---|
| Mass Cytometry (CYTOF) | 40–50 / cell.[203] | Mass cytometry uses rare metal isotope conjugated antibodies.[203] | Cultured mammalian cells.[221] Human microglia from fresh & cryopreserved brain.[27] |
Compatible with frozen brain tissue.[27] Detection of intracellular and extracellular proteins.[27] |
Dependent on well-validated antibodies and targets. Inability to sort cells for other applications. |
| Nanodroplet Processing in One pot for Trace Samples (NanoPOTS) | ~1500–3000 from ~10–100 cultured cells.[205] ~2,000 proteins / 100 μm diameter brain section. [208,222] |
Flow cytometry of cultured cells.[205,223] Laser Capture Microdissection from brain tissue. |
Cultured mammalian cells [223] & rodent brain.[208,222] | Spatial resolution of proteomic signatures in rodent brain. Compatible with chemical multiplexing. [224] |
Nanoliter-scale volumes limit compatibility with automated LC-MS. [206] |
| Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS / SCoPE2) |
>1,000 / cell. [202] | Acoustic sonication.[202] | Cultured mammalian cells.[202,209] | Obviate dependence on chemical lysing. Accurate quantification of protein changes across single cells.[211] |
Lower accuracy of comparing abundances of different proteins. [211] Limited capability in quantifying lower-abundance proteins.[211] |
| Single cell integrated Proteomics Chip (SciProChip) | >1,400 / cell. [225] | Size-based digital microfluidic isolation.[226] | Cultured mammalian cells. [225] | High label-free sensitivity.[225] Integrated isolation, lysis, counting, imaging, and processing.[225] |
Size-based isolation alone limits analyses of sub-populations of cells.[225] Sample loss with manual peptide transfer to autosampler.[225] |
| Parallel Accumulation-Serial Fragmentation (PASEF) | >2,000 / cell. [215] | Flow cytometry of cultured cells.[215] | Cultured mammalian cells.[215] | High label-free sensitivity.[215] Fast Scanning Speed.[227] |
Limited throughput of 20–40 single cells / day. [227] |