Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance
Abstract
:1. Introduction
2. Materials and Methods
2.1. Yeast Cultures
2.2. Total Protein Extraction and In-Gel Digestion
2.3. Preparation of the UPS2 Samples
2.4. Sample Preparation for Method Validation
2.5. Mass Spectrometry Analysis
2.6. Protein Identification
2.7. Protein Quantification
2.8. Data Analysis
3. Results and Discussion
3.1. Implementation of the UPS2-Based Strategy in Yeast
3.2. Performance of the Quantification Methods with the UPS2 Proteins
3.3. Performance of the Semi-Absolute Quantification Techniques with the UPS2 Proteins
3.4. Performance of the Semi-Absolute Quantification Techniques with External Proteins
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Quantification Methods | Linearity (r2) | CV among Proteins (%) | CV among Replicates (%) | |
---|---|---|---|---|
SC-based | PAI | 0.89 | 48.8 | 10.2 |
emPAI | 0.61 | 161.4 | 59.1 | |
SAF | 0.90 | 48.0 | 10.2 | |
NSAF | 0.90 | 48.0 | 10.9 | |
XIC-based | SUMnorm | 0.96 | 52.9 | 10.0 |
TOP3 | 0.91 | 62.6 | 10.5 | |
iBAQ | 0.96 | 51.3 | 10.0 |
Quantification Methods | Purified Proteins | Spiked UPS2 Proteins | ||
---|---|---|---|---|
UPS2 | TPA | UPS2 | TPA | |
iBAQ | 0.15 | 0.65 | 0.69 | 0.96 |
SUMnorm | 0.16 | 0.89 | 0.74 | 0.95 |
TOP3 | 0.21 | 0.53 | 1.09 | 0.96 |
NSAF | 0.21 | 0.16 | 1.21 | 0.92 |
SAF | 0.22 | 0.16 | 1.19 | 0.92 |
PAI | 0.17 | 0.15 | 1.17 | 0.92 |
emPAI | 0.12 | 3.67 | 84.83 | 0.99 |
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Millán-Oropeza, A.; Blein-Nicolas, M.; Monnet, V.; Zivy, M.; Henry, C. Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance. Proteomes 2022, 10, 2. https://doi.org/10.3390/proteomes10010002
Millán-Oropeza A, Blein-Nicolas M, Monnet V, Zivy M, Henry C. Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance. Proteomes. 2022; 10(1):2. https://doi.org/10.3390/proteomes10010002
Chicago/Turabian StyleMillán-Oropeza, Aarón, Mélisande Blein-Nicolas, Véronique Monnet, Michel Zivy, and Céline Henry. 2022. "Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance" Proteomes 10, no. 1: 2. https://doi.org/10.3390/proteomes10010002
APA StyleMillán-Oropeza, A., Blein-Nicolas, M., Monnet, V., Zivy, M., & Henry, C. (2022). Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance. Proteomes, 10(1), 2. https://doi.org/10.3390/proteomes10010002