Cell-Type-Specific Proteomics: A Neuroscience Perspective
Abstract
:1. Introduction
2. Cell-Type-Specific Isolation Methods
3. Proteome Labeling Methods
4. Mass Spectrometry Methods
5. Future Perspectives
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Appendix A
Technique | Advantages | Disadvantages | Ref. | Cell Source | # Cells/Tissue Quantity Isolated | Protein Quantity for MS Analysis | # Proteins Identified from MS Analysis |
---|---|---|---|---|---|---|---|
Fluorescence-activated cell sorting (FACS) |
|
| [151] | Human neuronal nuclei | 1 g starting tissue, >5 × 106 nuclei | 25 µg | 1755 |
[52] | Mouse inner ear hair cells | 199,894 cells | 3 µg | 6333 | |||
[51] | Mouse glutamatergic synapses | 485 synapses | 8 µg | 2044 total, 163 enriched | |||
[25] | HeLa cells | 1 cell | N/A | 670 | |||
Laser-capture microdissection (LCM) |
|
| [53] | Human cortical neurons from AD patients | 4000–80,000 neurons | N/A | 202 (4k neurons), 1773 (80k neurons) |
[54] | Human substantia nigra | 550,000 µm2 neuromelanin (NM) granules | 200 ng | 1000 | |||
[57] | Human neurons and blood brain barrier (BBB) structures | 2500 neurons and 4000 BBB units | N/A | 365 (Neurons), 539 (BBB) | |||
[26] | Rat cortical cells | 2–6, 10–18, and 30–50 cells | N/A | 180 (2–6 cells), 695 (10–18 cells), 1827 (30–50 cells) | |||
[152] | Human pancreatic islets | 18 islets | N/A | 3219 | |||
[55] | FFPE fetal human brain tissue | 36 samples (4 compartments, 8–15 mm2/compartment) | 10 µg | 3041 | |||
Induced pluripotent stem cells (iPSCs) |
|
| [70] | iPSCs | 108 cells | N/A | 7952 |
[69] | N/A | 4 µg | 9510 | ||||
[72] | N/A | 40 µg | 673 | ||||
[73] | 6 × 104 cells | 240 µg | 2217 | ||||
[74] | N/A | 100 µg | 1855 | ||||
[55] | 2 × 107 cells | 10 µg | 2875 | ||||
BioOrthogonal Non-Canonical Amino Acid Tagging (BONCAT) |
|
| [84] | HEK293T cells | N/A | 1.95–2.1 mg input | 195 |
[153] | HEK293T cells | N/A | N/A | 138 | |||
[85] | Excitatory hippocampal neurons, cerebellar Purkinje cells | 130–200 k neurons (Purkinje) | N/A | 2384 (hippocampal), 1687 (Purkinje) | |||
Stochastic Orthogonal Recoding of Translation (SORT) |
|
| [87] | Fly germ cells | 500 ovaries | 7 mg | 299 |
[89] | Mouse striatal medium spiny neurons (MSNs) | N/A | N/A | 1780 | |||
Antibody-assisted cell-type-specific puromycylation |
|
| [94] | A431 cells | N/A | N/A | >1200 |
[95] | HEK293T cells | 2 × 107 cells | N/A | 1165 enriched | |||
| | | | | | ||
BioID |
|
| [97] | HEK293T cells | 4 × 107 cells | N/A | 122 |
[154] | Toxoplasma gondii parasite | N/A | N/A | 19 | |||
[98] | Mouse cortical and hippocampal neurons | N/A | N/A | 121 (ePSD), 181 (iPSD) | |||
BioID2 |
|
| [99] | HEK293T cells | 4 × 107 cells | 100 µg | 260 |
TurboID |
|
| [100] | HEK293T cells | N/A | 3 mg input | 314 (mito), 186 (ER), 1455 (nuclear) |
| |||||||
Engineered ascorbate peroxidase (APEX) |
|
| [101] | HEK293T cells | 7–8 million cells | 4 mg input | 495 |
[155] | Drosophila melanogaster | N/A | N/A | 389 | |||
[102] | C. elegans L4 larvae | 30,000 larval cells | 450–500 µg input | 3180 | |||
Matrix-assisted laser desorption/ionization MS imaging (MALDI-MSI) |
|
| [107] | APP23 transgenic mouse tissue | 50 µm resolution | N/A | 5 Aβ peptides |
| [116] | Rat spinal cord | 20 µm tissue sections | N/A | 27 peptides | ||
[117] | Mouse pituitary gland | 1.5 mm × 2.5 mm tissue sections | N/A | 10 neuropeptides | |||
[118] | Rat dorsal root ganglia | >1000 cells | N/A | 26 peptides | |||
Secondary ion mass spectrometry (SIMS) |
|
| [121] | Benign prostatic hyperplasia (BPH), HeLa, and human cheek cells | 25–30 µm diameter tissue (BPH: 180 × 180 µm2, HeLa: 88 × 108 µm2, cheek cells: 150 × 175 µm2) | N/A | <10 biomolecule ions |
[116] | Rat spinal cord | 2.3 µm spatial resolution | N/A | 18 biomolecule ions | |||
[120] | Aplysia californica neurons | 0.39–2.3 µm resolution | N/A | 3 biomolecule ions | |||
Mass cytometry |
|
| [122] | Human leukemia cells (monoblastic M5 AML, monocytic M5 AML) and model cell lines (KG1a, Ramos) | 15,000–20,000 cells | N/A | 20 target antigens |
[123] | Human breast tumor cells | N/A | N/A | 10 target antigens | |||
[125] | Human bone marrow aspirates | 480,000 cells | N/A | 28 target antigens | |||
[124] | Human glioma, melanoma, and tonsil tissue cells | N/A | N/A | 8 target antigens | |||
Capillary electrophoresis microflow electrospray ionization mass spectrometry (CE-µESI-MS) |
|
| [143] | Aplysia californica neurons | 1 neuron | N/A | >300 metabolites |
[127] | Aplysia californica neurons | 25 B1 and B2 buccal neurons | N/A | >300 metabolites | |||
[130] | Xenopus laevis 16-cell embryo | 15 blastomeres | N/A | 40 metabolites | |||
[131] | Xenopus laevis 8-cell embryo | D1 blastomere | N/A | 55 small molecules | |||
[132] | Xenopus laevis 16-cell embryo | 1 blastomere | 16 ng | 438 | |||
[133] | Xenopus laevis 16-cell embryo | 1 blastomere | 20 ng | 500–800 | |||
[129] | Xenopus laevis 8–32-cell embryo | 1 blastomere | N/A | 230 molecular features | |||
Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) |
|
| [144] | Mouse embryonic stem cells | 1 cell | >1000 proteins | |
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Wilson, R.S.; Nairn, A.C. Cell-Type-Specific Proteomics: A Neuroscience Perspective. Proteomes 2018, 6, 51. https://doi.org/10.3390/proteomes6040051
Wilson RS, Nairn AC. Cell-Type-Specific Proteomics: A Neuroscience Perspective. Proteomes. 2018; 6(4):51. https://doi.org/10.3390/proteomes6040051
Chicago/Turabian StyleWilson, Rashaun S., and Angus C. Nairn. 2018. "Cell-Type-Specific Proteomics: A Neuroscience Perspective" Proteomes 6, no. 4: 51. https://doi.org/10.3390/proteomes6040051
APA StyleWilson, R. S., & Nairn, A. C. (2018). Cell-Type-Specific Proteomics: A Neuroscience Perspective. Proteomes, 6(4), 51. https://doi.org/10.3390/proteomes6040051