Published July 8, 2021
| Version v11
Dataset
Open
TEST DATA for Enhanced protein isoform characterization through long-read proteogenomics
Authors/Creators
- 1. University of Wisconsin - Madison
- 2. University of Virginia
- 3. Lifebit Biotech Ltd.
- 4. University of Zurich
- 5. University of Florida
- 6. University of Wisconsin
- 7. Science and Technology Consulting LLC
Description
Test data for The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic analysis relies on accurate reference databases that match the sample; neither a subset nor a superset database is ideal. Long-read RNA sequencing (e.g. PacBio, Oxford Nanopore) provides full-length transcript sequencing, which can be used to predict full-length proteins. Here, we describe a long-read proteogenomics approach for integrating matched long-read RNA-seq and MS-based proteomics data to enhance isoform characterization. We introduce a classification scheme for protein isoforms, discover novel protein isoforms, and present the first protein inference algorithm for the direct incorporation of long-read transcriptome data in protein inference to enable detection of protein isoforms that are intractable to MS detection. We have released an open-source Nextflow pipeline that integrates long-read sequencing in a proteomic workflow for isoform-resolved analysis.
Companion Repositories:
- Long-Read-Proteogenomics Workflow GitHub Repository Release
- Long-Read-Proteogenomics Analysis GitHub Repository Release
Companion Datasets
- Jurkat Samples and Reference Data
- Long-Read-Proteogenomics Workflow Results using Jurkat Sample data
This Repository contains the test data, specifically:
TEST Data for Long-Read-Proteogenomics Workflow GitHub Actions
Files
execution_trace.txt
Files
(785.2 MB)
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