The Viral Experiment LiP Analysis Workflow is an adaptable user-friendly computational notebook for analyzing host-pathogen proteomic datasets using Limited Proteolysis (LiP) standardized experimental sampling methods. This analysis workflow is a supplement to the published dataset collection "Human Host Cellular Response to HCoV-229E Infection Multi-Omics (ACS-JM-DP2)" evaluating the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-229E) infection. See Related works and Technical info note below for more information. Reference Input Files Host Sequence Annotation Collection (.FASTA) - Homo sapiens (Human) [UniProt Proteome ID: UP000005640] (version: 20,383 gene entries) Processed Datasets (.txt) - A549, MRC5, and primary HAE cell MaxQuant (v.1.6.17.0) peptide and proteinGroups processed raw dataset results files Funding Acknowledgments The source code described here was funded by the Predictive Phenomics Science & Technology Initiative, conducted under the Laboratory Directed Research and Development Program, at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy Office of Science under Contract No. DE-AC05-76RL0183.

Requirements for Reuse User must specify the search software used to generate the input file in addition to the path of the input and output files. Current workflow only supports reference input files generated by MaxQuant and MSFragger search software outputs. User must provide a sequence collection annotation file (.FASTA) and corresponding parameters.