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Updated: Mar 17, 2026

Dynamic Proteomic and miRNA Analysis of Polysomes from Isolated Mouse Heart After Langendorff Perfusion

Dynamic Proteomic and miRNA Analysis of Polysomes from Isolated Mouse Heart After Langendorff Perfusion

Published on: August 29, 2018

Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics.

David Wissel^1,2,3, Gloria M Sheynkman^4,5,6, Mark D Robinson^1,3

¹Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.

Biorxiv : the Preprint Server for Biology

|March 16, 2026

Summary

This summary is machine-generated.

This study introduces a new workflow using long-read RNA sequencing (lrRNA-seq) to create accurate, sample-specific protein databases. This improves mass spectrometry (MS) analysis, enabling the detection of novel protein isoforms and genetic variants.

Keywords:

Long-read RNA-seq Proteogenomics Variant phasing

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Last Updated: Mar 17, 2026

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Published on: August 29, 2018

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Area of Science:

Proteogenomics
Molecular Biology
Bioinformatics

Background:

Mass spectrometry (MS)-based proteogenomics relies on accurate protein databases.
Existing methods often fail to capture the full genetic and transcriptomic diversity within a sample.
Long-read RNA sequencing (lrRNA-seq) offers a way to identify complete transcript structures and genetic variants simultaneously.

Purpose of the Study:

To develop an end-to-end workflow for constructing and searching haplotype-resolved, sample-specific proteomes.
To leverage matched lrRNA-seq and MS data for improved proteogenomics.
To enable the detection of allele-specific protein isoforms and linked variants.

Main Methods:

Benchmarking phasing algorithms on PacBio lrRNA-seq data.
Developing a Snakemake pipeline for variant calling, read-based phasing, transcript discovery, and proteome construction.
Searching sample-specific, haplotype-resolved proteomes against MS data.

Main Results:

Identified high-accuracy and complete phasing methods for lrRNA-seq.
Demonstrated that sample-specific databases detect variant and splice peptides, allele-specific isoforms, and linked variants missed by reference proteomes.
Successfully applied the workflow to cell lines and differentiation time courses.

Conclusions:

lrRNA-seq-based phasing is a feasible and effective approach for proteogenomics.
The developed workflow provides a practical framework for allele-resolved proteome characterization.
This method enhances the characterization of proteomes in dynamic or disease-relevant biological settings.