Data-Independent Acquisition Peptidomics

In recent years, data-independent acquisition (DIA) has emerged as a powerful analysis method in biological mass spectrometry (MS). Compared to the previously predominant data-dependent acquisition (DDA), it offers a way to achieve greater reproducibility, sensitivity, and dynamic range in MS measurements. To make DIA accessible to non-expert users, a multifunctional, automated high-throughput pipeline DIAproteomics was implemented in the computational workflow framework "Nextflow" ( https://nextflow.io ). This allows high-throughput processing of proteomics and peptidomics DIA datasets on diverse computing infrastructures. This chapter provides a short summary and usage protocol guide for the most important modes of operation of this pipeline regarding the analysis of peptidomics datasets using the command line. In brief, DIAproteomics is a wrapper around the OpenSwathWorkflow and relies on either existing or ad-hoc generated spectral libraries from matching DDA runs. The OpenSwathWorkflow extracts chromatograms from the DIA runs and performs chromatographic peak-picking. Further downstream of the pipeline, these peaks are scored, aligned, and statistically evaluated for qualitative and quantitative differences across conditions depending on the user's interest. DIAproteomics is open-source and available under a permissive license. We encourage the scientific community to use or modify the pipeline to meet their specific requirements.