Table 3.
Overview of the containers and software versions used in the open data analysis pipeline.
| Step | Name | URL or DockerHub handle | Version |
|---|---|---|---|
| Conversion from raw file to mzML | wiffConverter | sciex/wiffconverter:0.7 | 0.7.0 |
| QC/QA | yamato | https://github.com/PaulBrack/Yamato/releases/download/v1.0.4/release-linux-x64.zip | 1.0.4 |
| Window management | python scripts | https://github.com/PRIDE-reanalysis/DIA-reanalysis | 1.0.0 |
| OpenSWATH | OpenSWATH | openswath/Openswath:0.1.2 | 2.4.0 (git 868546e) |
| PyProphet | 2.0.dev1 (git ddcedac) | ||
| TRIC | msproteomicstools | 0.8.0 (git eeed765) | |
| Post-processing | R | https://github.com/PRIDE-reanalysis/DIA-reanalysis | 4.0.3 |
| MSstats | 3.22.0 | ||
| MyGene.info | 1.24.0, Ensembl 99/GRCh38 |