The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
Open accessAbstract
Replicate mass spectrometry (MS) measurements and the use of multiple analytical methods can greatly expand the comprehensiveness of shotgun proteomic profiling of biological samples. However, the inherent biases and variations in such data create computational and statistical challenges for quantitative comparative analysis. We developed and tested a normalized, label-free quantitative method termed the normalized spectral index (SIN), which combines three MS abundance features: peptide count, spectral count and fragment-ion (tandem MS or MS/MS) intensity. SIN largely eliminated variances between replicate MS measurements, permitting quantitative reproducibility and highly significant quantification of thousands of proteins detected in replicate MS measurements of the same and distinct samples. It accurately predicts protein abundance more often than the five other methods we tested. Comparative immunoblotting and densitometry further validate our method. Comparative quantification of complex data sets from multiple shotgun proteomics measurements is relevant for systems biology and biomarker discovery.
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STATISTICAL METHODS FOR ASSESSING AGREEMENT BETWEEN TWO METHODS OF CLINICAL MEASUREMENT
Martin Bland, J., & Altman, D. (1986) · The Lancet · doi:10.1016/s0140-6736(86)90837-8 · Cited by 47,965
Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., et al. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400129-mcp200 · Cited by 4,401
Absolute Quantification of Proteins by LCMSE
Silva, J. C., Gorenstein, M. V., Li, G.-Z., Vissers, J. P. C., & Geromanos, S. J. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500230-mcp200 · Cited by 1,529
Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics
Choi, H., Fermin, D., & Nesvizhskii, A. I. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800203-mcp200 · Cited by 364
Cited by
Nanoparticle Size and Surface Chemistry Determine Serum Protein Adsorption and Macrophage Uptake
Walkey, C. D., Olsen, J. B., Guo, H., Emili, A., & Chan, W. C. W. (2012) · Journal of the American Chemical Society · doi:10.1021/ja2084338 · Cited by 1,926
Walkey, C. D., & Chan, W. C. W. (2012) · Chem. Soc. Rev. · doi:10.1039/c1cs15233e · Cited by 1,758
Protein Analysis by Shotgun/Bottom-up Proteomics
Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491
Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present
Bantscheff, M., Lemeer, S., Savitski, M. M., & Kuster, B. (2012) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-012-6203-4 · Cited by 801
SAINT: probabilistic scoring of affinity purification–mass spectrometry data
Choi, H., Larsen, B., Lin, Z.-Y., Breitkreutz, A., Mellacheruvu, D., Fermin, D., Qin, Z. S., Tyers, M., Gingras, A.-C., & Nesvizhskii, A. I. (2011) · Nature Methods · doi:10.1038/nmeth.1541 · Cited by 800
Metadata
- Authors
- Griffin, N. M., Yu, J., Long, F., Oh, P., Shore, S., Li, Y., Koziol, J. A., & Schnitzer, J. E.
- Venue
- Nature Biotechnology
- Published
- 2010-01
- Volume
- 28
- Issue
- 1
- Pages
- 83-89
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2039380477
- Cited by
- 402
- References
- 4
- FWCI
- 13.93
- Type
- journal article
- Language
- en
- Open access
- green
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