plexDIA Perspective

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

• plexDIA Websites: plexDIA.slavovlab.net   |   scp.slavovlab.net/plexDIA
• Perspective article: Preprint   |   J. Proteome Res. Article

 

Requirements

This application has been tested on R >= 3.5.0, OSX 10.14 / Windows 7/8/10. R can be downloaded from the main R Project page or downloaded with the RStudio Application.

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Reproducing the data analysis

DIA-NN and Dinosaur outputs are required to run the code. Please visit MassIVE MSV000090650 or this Data Directory and download the following files:

1. "pD_HYE_MS1_Report.tsv" to run the code to generate figures for the translated vs not-translated quantitation.
2. "eJD1443_45_Report.tsv", "eJD1443.features.tsv", "eJD1444.features.tsv", and "eJD1445.features.tsv" to run the code to generate figures for the RT-deviations within and between runs.
3. "deltaRT_10222022.txt" and "deltaRT_top10_11022022.txt" that contain source data for Figure 3.

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Jason Derks, Nikolai Slavov, Strategies for increasing the depth and throughput of protein analysis by plexDIA, J. Proteome Res., doi: 10.1021/acs.jproteome.2c00721; Preprint at bioRxiv 2022.11.05.515287; doi: 10.1101/2022.11.05.515287