Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric
Abstract
:1. Introduction
2. Materials and Methods
2.1. Obtaining Data
2.2. Compiling the Absolute Copy Numbers
2.3. Visualization of Copy Number Distribution in R/Shiny
3. Results
3.1. Generational Improvements in Proteomics Hardware for Data Dependent Analysis
3.2. Use of Absolute Copy Number for Optimization of Chromatographic Conditions
3.3. Rapid Proteomics Methods
3.4. Absolute Sensitivity in Single-Shot Proteomics Today
3.5. Match between Runs
3.6. Single-Cell Proteomics
3.7. Additional Methods
4. Conclusions
Supplementary Materials
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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File Description | Number of Proteins | Mean Log Copy Number |
---|---|---|
HeLa HF 2018 (23 h) [11] | 14,179 | 4.2 |
SomaScan 1300 [19] | 1308 | 4.47 |
QE Classic 200 ng 120 min [20] | 2016 | 5.72 |
QE HF 200 ng 120 min [20] | 3487 | 5.4 |
Lumos HCD-IT 60 min [21] | 4435 | 5.25 |
Lumos HCD-IT 90 min | 4770 | 5.21 |
Lumos HCD-IT 120 min | 5098 | 5.17 |
Lumos HCD-IT 240 min | 5604 | 5.09 |
Velos OT-IT 30 min (PRIDE PXD011070) | 1171 | 5.98 |
TIMSTOF Pro pasefDDA 120 min [22] | 5970 | 5.04 |
Exploris 480 FAIMS 21 min [23] | 3182 | 5.32 |
pasefDIA 120 min [24] | 7699 | 4.77 |
QE HF BoxCar 1 ug 60 min (MBR) [25] | 6479 | 5.16 |
QE HF BoxCar 1 ug 60 min (MS/MS) [25] | 2505 | 5.77 |
Exploris 480 Single-Cell TMT 20× Carrier [26] | 769 | 6.15 |
Exploris 480 Single-Cell LFQ [26] | 608 | 6.17 |
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Orsburn, B.C. Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric. Proteomes 2021, 9, 34. https://doi.org/10.3390/proteomes9030034
Orsburn BC. Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric. Proteomes. 2021; 9(3):34. https://doi.org/10.3390/proteomes9030034
Chicago/Turabian StyleOrsburn, Benjamin C. 2021. "Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric" Proteomes 9, no. 3: 34. https://doi.org/10.3390/proteomes9030034