Quantitative Aspects of the Human Cell Proteome
Abstract
:1. Introduction
2. Quantification
2.1. Panoramic Quantification
2.2. Aspects of Cell Size
2.3. Aspects of Proteome Variation
2.4. Aspects of Sensitivity
2.5. Aspects of Cancer
2.6. Analysis of Proteomics Datasets
3. Conclusions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
MS | Mass spectrometry |
ESI LC-MS/MS | Liquid chromatography–electrospray ionization tandem mass spectrometry |
2DE | Two-dimensional gel electrophoresis |
Sec2DE | Sectional two-dimensional gel electrophoresis |
emPAI | Exponentially modified Protein Abundance Index |
iBAQ | intensity Based Absolute Quantification |
SNP | Single-Nucleotide Polymorphism |
TMT | Tandem Mass Tag |
TS | Tissue Specificity |
References
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Cell Type | Average Volume (μm3) | BNID [30] ¹ |
---|---|---|
Platelet | 10 | [33] |
Sperm cell | 30 | 109,891 |
Red blood cell | 100 | 107,600 |
Lymphocyte | 130 | 111,439 |
Neutrophil | 300 | 108,241 |
Beta cell | 1000 | 109,227 |
Enterocyte | 1400 | 111,216 |
Fibroblast | 2000 | 108,244 |
HeLa, cervix | 3000 | 103,725 |
Hepatocyte | 3400 | [32] |
Osteoblast | 4000 | 108,088 |
Cardiomyocyte | 15,000 | 108,243 |
Fat cell | 600,000 | 107,668 |
Oocyte | 4,000,000 | 101,664 |
Sample | Equation | Number | Reference |
---|---|---|---|
Glio (2DE spots) | y = 13.185x−1.085 R2 = 0.9261 | 1000 | [51] |
Glio (sec2DE) | y = 13.653x−0.889 R2 = 0.9845 | 24,000 | [51] |
HepG2 (2DE spots) | y = 17.459x−1 R2 = 0.9776 | 1300 | [27] |
HepG2 (sec2DE) | y = 9.99x−0.984 R2 = 0.9758 | 20,000 | [27] |
Liver (sec2DE) | y = 11.549x−0.98 R2 = 0.8952 | 15,000 | [53] |
Liver (2DE spots) | y = 13.452x−1.16 R2 = 0.9113 | 700 | [53] |
MCF7 (2DE spots) | y = 14.487x−1.06 R2 = 0.9792 | 700 | [59] |
Sample | Equation | Number | Reference |
---|---|---|---|
Liver | y = 7.0162x−1.056 R2 = 0.9398 | 16,000 | [45] |
Fetal liver | y = 11.951x−0.943 R2 = 0.9484 | 16,000 | [45] |
Liver | y = 10.955x−0.958 R2 = 0.9007 | 5000 | [43] |
Liver | y = 7.2197x−1.047 R2 = 0.8961 | 5500 | [43] |
Adrenal | y = 7.2765x−1.003 R2 = 0.8627 | 7000 | [43] |
Adult Adrenal | y = 6.6905x−1.051 R2 = 0.9225 | 15,000 | [45] |
Adult Colon | y = 13.745x−0.915 R2 = 0.9766 | 15,000 | [45] |
Colon | y = 11.996x−0.944 R2 = 0.976 | 5000 | [43] |
Adult Esophagus | y = 15.288x−0.876 R2 = 0.9544 | 9000 | [45] |
Frontal Cortex | y = 12.544x−0.953 R2 = 0.9297 | 16,000 | [45] |
Adult gallbladder | y = 14.781x−0.911 R2 = 0.9727 | 10,000 | [45] |
Adult Pancreas | y = 12.281x−0.948 R2 = 0.9537 | 17,000 | [45] |
Pancreas | y = 12.537x−0.894 R2 = 0.8619 | 7000 | [43] |
Prostate | y = 12.246x−0.939 R2 = 0.973 | 4000 ¹ (11,000) | [44] |
Adult Prostate | y = 14.466x−0.916 R2 = 0.9773 | 17,000 | [45] |
Adult Rectum | y = 11.495x−0.932 R2 = 0.9755 | 17,000 | [45] |
Adult Retina | y = 5.8187x−1.079 R2 = 0.9095 | 19,000 | [45] |
Spinal Cord | y = 11.821x−0.946 R2 = 0.9288 | 15,000 | [45] |
Adult Testis | y = 8.169x−1.045 R2 = 0.8192 | 20,000 | [45] |
Testis | y = 11.105x−0.882 R2 = 0.8996 | 9000 | [44] |
Fetal Testis | y = 5.439x−1.092 R2 = 0.9224 | 15,000 | [45] |
Placenta | y = 9.3737x−0.998 R2 = 0.9267 | 11,000 | [45] |
Kidney | y = 5.9506x−1.075 R2 = 0.9228 | 12,000 | [45] |
Heart | y = 15.719x−0.927 R2 = 0.9755 | 1500 | [44] |
Heart | y = 9.1228x−1.019 R2 = 0.9233 | 5000 | [43] |
Heart | y = 12.319x−0.893 R2 = 0.9824 | 13,000 | [45] |
Aorta | y = 12.254x−1.009 R2 = 0.9655 | 1200 | [61] |
Aortic valve | y = 17.85x−0.698 R2 = 0.8931 | 6800 | [61] |
Stomach | y = 10.254x−1.017 R2 = 0.8661 | 5000 | [43] |
Stomach | y = 15.361x−0.905 R2 = 0.9698 | 4000 | [44] |
Thyroid | y = 9.698x−1.023 R2 = 0.9185 | 5000 | [43] |
Muscle | y = 11.563x−0.974 R2 = 0.9422 | 3500 | [43] |
Muscle | y = 13.174x−0.994 R2 = 0.9409 | 9000 | [44] |
Brain | y = 10.672x−0.985 R2 = 0.8955 | 6000 | [43] |
Fetal brain | y = 8.584x−0.981 R2 = 0.9314 | 15,000 | [45] |
Lung | y = 9.2953x−1.001 R2 = 0.9583 | 12,500 | [45] |
Lung | y = 8.5254x−1.023 R2 = 0.6913 | 6000 | [43] |
Ovary | y = 7.3857x−1.053 R2 = 0.931 | 19,000 | [45] |
Fetal ovary | y = 7.4986x−1.045 R2 = 0.9368 | 17,000 | [45] |
Ovary | y = 9.8454x−0.929 R2 = 0.9009 | 6800 | [43] |
Platelets | y = 13.949x−0.949 R2 = 0.9909 | 3600 | [52] |
Platelets | y = 7.3257x−1.127 R2 = 0.9575 | 11,300 | [45] |
Uterus | y = 7.7271x−1.059 R2 = 0.9477 | 6000 | [43] |
B cells | y = 6.5677x−1.051 R2 = 0.9319 | 17,000 | [45] |
CD4 Cells | y = 7.5448x−1.051 R2 = 0.9533 | 14,000 | [45] |
NK Cells | y = 7.8551x−1.029 R2 = 0.9616 | 16,000 | [45] |
HeLa | y = 6.9393x−0.963 R2 = 0.9312 | 6000 ¹ (7000) | [48] |
HeLa | y = 13.715x−0.931 R2 = 0.9453 | 4700 ¹ (10,200) | [49] |
HeLa | y = 12.004x−0.931 R2 = 0.9187 | 6200 ¹ (14,000) | [50] |
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Naryzhny, S. Quantitative Aspects of the Human Cell Proteome. Int. J. Mol. Sci. 2023, 24, 8524. https://doi.org/10.3390/ijms24108524
Naryzhny S. Quantitative Aspects of the Human Cell Proteome. International Journal of Molecular Sciences. 2023; 24(10):8524. https://doi.org/10.3390/ijms24108524
Chicago/Turabian StyleNaryzhny, Stanislav. 2023. "Quantitative Aspects of the Human Cell Proteome" International Journal of Molecular Sciences 24, no. 10: 8524. https://doi.org/10.3390/ijms24108524