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Strategies for increasing the depth and throughput of protein analysis by plexDIA

View ORCID ProfileJason Derks, View ORCID ProfileNikolai Slavov
doi: https://doi.org/10.1101/2022.11.05.515287
Jason Derks
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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  • ORCID record for Jason Derks
Nikolai Slavov
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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  • For correspondence: nslavov@northeastern.edu
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Abstract

Accurate protein quantification is key to identifying protein markers, regulatory relationships between proteins, and pathophysiological mechanisms. Realizing this potential requires sensitive and deep protein analysis of a large number of samples. Toward this goal, proteomics throughput can be increased by parallelizing the analysis of both precursors and samples using multiplexed data independent acquisition (DIA) implemented by the plexDIA framework. Here we demonstrate the improved precisions of RT estimates within plexDIA and how this enables more accurate protein quantification. plexDIA has demonstrated multiplicative gains in throughput, and these gains may be substantially amplified by improving the multiplexing reagents, data acquisition and interpretation. We discuss future directions for advancing plexDIA, which include engineering optimized mass-tags for high-plexDIA and developing algorithms that utilize the regular structures of plexDIA data to improve sensitivity, proteome coverage and quantitative accuracy. These advances in plexDIA will increase the throughput of functional proteomic assays, including quantifying protein conformations, turnover dynamics, modifications states and activities. The sensitivity of these assays will extend to single-cell analysis, thus enabling functional single-cell protein analysis.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Data, code & protocols: scp.slavovlab.net/plexDIA

  • https://scp.slavovlab.net/plexDIA

  • https://plexDIA.slavovlab.net/

Copyright 
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-NC-ND 4.0 International license.
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Posted November 05, 2022.
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Strategies for increasing the depth and throughput of protein analysis by plexDIA
Jason Derks, Nikolai Slavov
bioRxiv 2022.11.05.515287; doi: https://doi.org/10.1101/2022.11.05.515287
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Strategies for increasing the depth and throughput of protein analysis by plexDIA
Jason Derks, Nikolai Slavov
bioRxiv 2022.11.05.515287; doi: https://doi.org/10.1101/2022.11.05.515287

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