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The SWATHAtlas at the Institute for Systems Biology is a resource for planning your DIA/SWATH™ experiments, depositing published experimental high-quality spectral assay libraries, and exploring the results of deposited datasets.
Below are the list of publications of spectral ion libraries uploaded at SWATHAtlas.
Zhu, T., Zhu T, Zhu Y, Xuan Y, et al. DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery. Genomics Proteomics Bioinformatics. 2020;18(2):104-119.
Weerakoon, H., Potriquet, J., Shah, A.K. et al. A primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics. Sci Data 7, 412 (2020).
Midha, M.K., Kusebauch, U., Shteynberg, D. et al. A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS. Sci Data 7, 389 (2020).
Krasny L., Bland P., Burns J. et al. A mouse SWATH-mass spectrometry reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts. Dis Model Mech. 2020 Jul 14;13(7):dmm044586.
Blattmann, P., Stutz, V., Lizzo, G. et al. Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins. Sci Data 6, 190011 (2019).
Schuster, H., Shao, W., Weiss, T. et al. A tissue-based draft map of the murine MHC class I immunopeptidome. Sci Data 5, 180157 (2018).
Mandal K., Bader S.L., Kumar P. et al. An integrated transcriptomics-guided genome-wide promoter analysis and next-generation proteomics approach to mine factor(s) regulating cellular differentiation. DNA Res. 2017 Apr 1;24(2):143-157.
Michalik S., Depke, M., Murr, A. et al. A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions. Sci Rep 7, 9718 (2017).
Bouchal P., Schubert O.T., Faktor J. et al. Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry. Cell Rep. 2019 Jul 16;28(3):832-843.e7.
Müller D.B., Schubert O.T., Röst H. et al. Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization. Mol Cell Proteomics. 2016 Oct;15(10):3256-3269.
Kusebauch U, Campbell DS, Deutsch EW, et al. Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. Cell. 2016;166(3):766-778.
Caron E., Espona L., Kowalewski D.J. et al. An open-source computational and data resource to analyze digital maps of immunopeptidomes. Elife. 2015;4:e07661. Published 2015 Jul 8.
Schubert O.T., Ludwig C., Kogadeeva M. et al. Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis. Cell Host Microbe. 2015;18(1):96-108.
Rosenberger G., Koh C., Guo T. et al. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Sci Data 1, 140031 (2014).
Picotti P., Clément-Ziza M., Lam H. et al. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature 494, 266–270 (2013).