TODO: Add preprint
Chambers, M. C., Maclean, B., Burke, R., Amodei, D., Ruderman, D. L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T. A., Brusniak, M.-Y., Paulse, C., Creasy, D., … Mallick, P. (2012). A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology, 30(10), 918–920. https://doi.org/10.1038/nbt.2377
Searle, B. C., Pino, L. K., Egertson, J. D., Ting, Y. S., Lawrence, R. T., MacLean, B. X., Villen, J., & MacCoss, M. J. (2018). Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-07454-w
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 (Oxford, England), 30(17), 2524–2526. https://doi.org/10.1093/bioinformatics/btu305
Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. https://doi.org/10.1038/nbt.3820
Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276–278. https://doi.org/10.1038/s41587-020-0439-x