- plexDIA Websites: plexDIA.slavovlab.net | scp.slavovlab.net/plexDIA
- Perspective article: Preprint | J. Proteome Res. Article
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.
DIA-NN and Dinosaur outputs are required to run the code. Please visit MassIVE MSV000090650 or this Data Directory and download the following files:
- "pD_HYE_MS1_Report.tsv" to run the code to generate figures for the translated vs not-translated quantitation.
- "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.
- "deltaRT_10222022.txt" and "deltaRT_top10_11022022.txt" that contain source data for Figure 3.
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