quantms: quantms (and its predecessor proteomicsLFQ ) is a cloud-based workflow that uses OpenMS 39 tools to enable quantitative analysis of LFQ data-dependent (LFQ-DDA) and independent acquisition (LFQ-DIA) and TMT data (). In the present work, we used the LFQ-DDA sub-workflow of the pipeline on the three datasets to do the peptide quantification benchmarking. The sub-workflow performs the peptide identifications using Comet and MSGF+ and the feature detection using the OpenMS proteomicsLFQ 39 algorithm.