The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Role of spectral counting in quantitative proteomics
Abstract
Spectral count, defined as the total number of spectra identified for a protein, has gained acceptance as a practical, label-free, semiquantitative measure of protein abundance in proteomic studies. In this review, we discuss issues affecting the performance of spectral counting relative to other label-free methods, as well as its limitations. Possible consequences of modifications, which are commonly applied to raw spectral counts to improve abundance estimations, are considered. The use of spectral counting for different types of quantitation studies is explored and critiqued. Different statistical methods and underlying frameworks that have been applied to spectral count analysis are described and compared, and problem areas that undermine confident statistical analysis are considered. Finally, the issue of accurate estimation of false-discovery rates is addressed and identified as a major current challenge in quantitative proteomics.
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Citations
Cites
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Cited by
Ramos, A. D., Andersen, R. E., Liu, S. J., Nowakowski, T. J., Hong, S. J., Gertz, C. C., Salinas, R. D., Zarabi, H., Kriegstein, A. R., & Lim, D. A. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.02.007 · Cited by 359
Alzheimer’s disease: Ablating single master site abolishes tau hyperphosphorylation
Stefanoska, K., Gajwani, M., Tan, A. R. P., Ahel, H. I., Asih, P. R., Volkerling, A., Poljak, A., & Ittner, A. (2022) · Science Advances · doi:10.1126/sciadv.abl8809 · Cited by 128
Mass Spectrometric Analysis of Histone Proteoforms
Yuan, Z.-F., Arnaudo, A. M., & Garcia, B. A. (2014) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-071213-015959 · Cited by 64
Enabling proteomic studies with RNA-seq: the proteome of tomato pollen as a test case
Lopez‐Casado, G., Covey, P. A., Bedinger, P. A., Mueller, L. A., Thannhauser, T. W., Zhang, S., Fei, Z., Giovannoni, J. J., & Rose, J. K. C. (2012) · PROTEOMICS · doi:10.1002/pmic.201100164 · Cited by 64
Applications and challenges of forensic proteomics
Merkley, E. D., Wunschel, D. S., Wahl, K. L., & Jarman, K. H. (2019) · Forensic Science International · doi:10.1016/j.forsciint.2019.01.022 · Cited by 64
Metadata
- Authors
- Lundgren, D. H., Hwang, S.-I., Wu, L., & Han, D. K.
- Venue
- Expert Review of Proteomics
- Publisher
- Informa UK Limited
- Published
- 2010-02
- Volume
- 7
- Issue
- 1
- Pages
- 39-53
- ISSN
- 1478-9450 (ISSN-L)
- 1744-8387
- OpenAlex
- W2167728354
- Cited by
- 428
- References
- 11
- FWCI
- 17.69
- Type
- journal article
- Language
- en
- Open access
- closed
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