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A Guide to the Quantitative Proteomic Profiles of the Cancer Cell Line Encyclopedia

View ORCID ProfileDavid P. Nusinow, Steven P. Gygi
doi: https://doi.org/10.1101/2020.02.03.932384
David P. Nusinow
Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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  • For correspondence: david_nusinow@hms.harvard.edu
Steven P. Gygi
Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Abstract

We recently reported the quantitative proteomics of 375 samples as part of the Cancer Cell Line Encyclopedia (Nusinow et al., 2020). Mass spectrometry-based proteomics data is broadly unfamiliar to most biologists in our experience, resulting in questions from analysts about how to use the data. From the proteomics community there was interest about how we normalized the data, as the scope of this project was so much larger than what has been commonly available. This paper serves as a guide to the data set to answer these questions and acts as a supplement to the main manuscript. The first part addresses users of the data, describing the experimental design, interpretation of the values, and dealing with standard issues in proteomics like multiple protein isoforms per gene and missing values. The second part of the manuscript details how we arrived at the normalization procedure reported in the paper, including the diagnostics used to assess multiple normalization schemes.

Footnotes

  • https://www.cell.com/cell/fulltext/S0092-8674(19)31385-6

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 03, 2020.
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A Guide to the Quantitative Proteomic Profiles of the Cancer Cell Line Encyclopedia
David P. Nusinow, Steven P. Gygi
bioRxiv 2020.02.03.932384; doi: https://doi.org/10.1101/2020.02.03.932384
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A Guide to the Quantitative Proteomic Profiles of the Cancer Cell Line Encyclopedia
David P. Nusinow, Steven P. Gygi
bioRxiv 2020.02.03.932384; doi: https://doi.org/10.1101/2020.02.03.932384

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