Data-independent acquisition (DIA) mode of mass spectrometry, such as
the SWATH-MS technology, enables accurate and consistent measurement of
proteins, which is crucial for comparative proteomics studies. However,
there is lack of free and easy to implement data analysis protocols that
can handle the different data processing steps from raw spectrum files
to peptide intensity matrix and its downstream analysis. Here, we
provide a data analysis protocol, named diatools, covering all these
steps from spectral library building to differential expression analysis
of DIA proteomics data. The data analysis tools used in this protocol
are open source and the protocol is distributed at Docker Hub as a
complete software environment that supports Linux, Windows, and macOS
operating systems.