QuantPipe: A User-Friendly Pipeline Software Tool for DIA Data Analysis Based on the OpenSWATH-PyProphet-TRIC Workflow

Targeted analysis of data-independent
acquisition (DIA) mass spectrometry
data requires elegant software tools and strict statistical control.
OpenSWATH-PyProphet-TRIC is a widely used DIA data analysis workflow.
The OpenSWATH-PyProphet-TRIC workflow is typically executed by running
command lines. Here, we present QuantPipe, which is a graphic interface
software tool based on the OpenSWATH-PyProphet-TRIC workflow. In addition
to OpenSWATH-PyProphet-TRIC functions, QuantPipe can convert the spectral
library to the assay library and output peptides and protein intensities.
We demonstrated that QuantPipe can be used to analyze SWATH-MS data
from TripleTOF 5600 and TripleTOF 6600, phospho-SWATH-MS data, DIA
data from Orbitrap instrument, and diaPASEF data from TimsTOF Pro
instrument. The executable files, user manual, and source code of
QuantPipe are freely available at https://github.com/tachengxmu/QuantPipe/releases.