Predictive Phenomics Host-Pathogen Limited Proteolysis Proteomics Analysis Workflow

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.