Automating Large-Scale Experiment Scheduling and Planning with the WorkListGenerator

As proteomics capabilities have grown increasingly robust, biological experiments and hypotheses investigating hundreds or thousands of samples are now possible. With an increase in project scale, both experimental design and metadata management become major bottlenecks. Of particular importance in this data management process is the generation of instrument scheduling files for both LC and MS instruments, especially the randomization of the run ordering to prevent batch artifacts that would confound the experimental hypothesis. Although best practices for blocking and randomization exist, this is frequently done by hand─a tedious and error-prone task. We present a software tool, WorkListGenerator, that captures core project metadata in a structured format, performs block randomization, and produces instrument worklists for LC-MS. The tool is flexible to various experimental designs common in single-cell proteomics and other large-scale studies and is available as an open-source command-line tool at https://github.com/RTKlab-BYU/worklist_generation.