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microbial-isolate-lip-analysis

Microbial Isolate Limited Proteolysis (LiP) Analysis Workflow

https://github.com/pnnl-predictive-phenomics/microbial-isolate-lip-analysis

Science Score: 49.0%

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Keywords

proteomics-data-analysis
Last synced: 6 months ago · JSON representation

Repository

Microbial Isolate Limited Proteolysis (LiP) Analysis Workflow

Basic Info
  • Host: GitHub
  • Owner: PNNL-Predictive-Phenomics
  • License: gpl-3.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 119 KB
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Topics
proteomics-data-analysis
Created 8 months ago · Last pushed 7 months ago
Metadata Files
Readme License Zenodo

README.md

DOI License <!-- badges: end -->

Microbial Isolate LiP Analysis Workflow

The Microbial Isolate LiP Analysis Workflow is a user-friendly computational notebook (adapted from the "Viral Experiment LiP Analysis Workflow") for analyzing proteomic datasets, from a single microbial isolated organism, using Limited Proteolysis (LiP) and Thermal Proteome Profiling (TPP) standardized experimental sampling methods. This analysis workflow is a supplement to the published dataset collection "S. elongatus PCC 7942 Limited Proteolysis and Thermal Proteome Profiling Structural Proteomics (JM-BH-DP3)" evaluating alterations in solvent accessibility and structural stability adaptation patterns, in response to environmental light perturbations, through structural remodeling of the proteome. See Usage for additional requirements information applicable to source code reuse.

Reference Input Files

  • Sequence Annotation Collection (.FASTA) - Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805) UniProt Proteome ID: UP000889800
  • Processed Datasets (.txt/.tsv) - FragPipe (v.21.1), equipped with MSFragger (v.4.0), peptide and protein processed raw dataset results files

Usage

User must specify the search software used to generate the input file in addition to the path of the input files and output files. This workflow currently only supports reference input files generated by MaxQuant and MSFragger search software outputs.

License

This code is released under a GNU General Public License version 3 (GPL-3.0-only). See our License for detailed information.

Funding

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.

Citation Guidance

Feng, S., Rozum, J. C., Shouaib, A.D. (2025). Predictive Phenomics Microbial Isolate Limited Proteolysis Proteomics Analysis Workflow. Zenodo. https://doi.org/10.5281/zenodo.15881600

Owner

  • Name: pnnl-predictive-phenomics
  • Login: pnnl-predictive-phenomics
  • Kind: organization

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