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MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
Abstract
Summary: MSstats is an R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. Version 2.0 of MSstats supports label-free and label-based experimental workflows and data-dependent, targeted and data-independent spectral acquisition. It takes as input identified and quantified spectral peaks, and outputs a list of differentially abundant peptides or proteins, or summaries of peptide or protein relative abundance. MSstats relies on a flexible family of linear mixed models. Availability and implementation: The code, the documentation and example datasets are available open-source at www.msstats.org under the Artistic-2.0 license. The package can be downloaded from www.msstats.org or from Bioconductor www.bioconductor.org and used in an R command line workflow. The package can also be accessed as an external tool in Skyline (Broudy et al., 2014) and used via graphical user interface. Contact: ovitek@purdue.edu
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Cited by
Bruderer, R., Bernhardt, O. M., Gandhi, T., Miladinović, S. M., Cheng, L.-Y., Messner, S., Ehrenberger, T., Zanotelli, V., Butscheid, Y., Escher, C., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.044305 · Cited by 1,238
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Liao, Y.-C., Fernandopulle, M. S., Wang, G., Choi, H., Hao, L., Drerup, C. M., Patel, R., Qamar, S., Nixon-Abell, J., Shen, Y., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.050 · Cited by 550
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Metadata
- Authors
- Choi, M., Chang, C.-Y., Clough, T., Broudy, D., Killeen, T., MacLean, B., & Vitek, O.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-05-02
- Volume
- 30
- Issue
- 17
- Pages
- 2524-2526
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2114165700
- Cited by
- 1,035
- References
- 0
- FWCI
- 19.59
- Type
- journal article
- Language
- en
- Open access
- closed
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- Choi, M., Chang, C.-Y., Clough, T., Broudy, D., Killeen, T., MacLean, B., & Vitek, O. (2014). MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics. https://doi.org/10.1093/bioinformatics/btu305
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