ArticleJournal of molecular and cellular cardiology2021
Computation-assisted targeted proteomics of alternative splicing protein isoforms in the human heart.
Article in Journal of molecular and cellular cardiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 17 citations in OpenAlex.
- Transcriptome Reprogramming in Heart Failure: The Hidden Splicing Code.Current cardiology reports · 2026Review
- Ponatinib confers adult human cardiomyocyte toxicity via inhibition of AKT signaling.Physiological reports · 2026Article
- Natural language processing of biomedical text to map and prioritize protein-disease associations in HFpEF.Computers in biology and medicine · 2026Article
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- Predominant mutated non-canonical tumor-specific antigens identified by proteogenomics demonstrate immunogenicity and tumor suppression in CRC.Cell genomics · 2026Article
- IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection.Journal of the American Society for Mass Spectrometry · 2024Article
- Enhanced Sample Multiplexing-Based Targeted Proteomics with Intelligent Data Acquisition.Journal of the American Society for Mass Spectrometry · 2024Article
- Expression and splicing mediate distinct biological signals.BMC biology · 2023Article
- Proteogenomics reveals sex-biased aging genes and coordinated splicing in cardiac aging.American journal of physiology. Heart and circulatory physiology · 2022Article
- The World of Protein Interactions: Defining the Caveolin 3 Cardiac Interactome.Circulation research · 2021Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Alternative splicing is prevalent in the heart and implicated in many cardiovascular diseases, but not every alternative transcript is translated and detecting non-canonical isoforms at the protein level remains challenging. Here we show the use of a computation-assisted targeted proteomics workflow to detect protein alternative isoforms in the human heart. We build on a recent strategy to integrate deep RNA-seq and large-scale mass spectrometry data to identify candidate translated isoform peptides. A machine learning approach is then applied to predict their fragmentation patterns and design protein isoform-specific parallel reaction monitoring detection (PRM) assays. As proof-of-principle, we built PRM assays for 29 non-canonical isoform peptides and detected 22 peptides in a human heart lysate. The predictions-aided PRM assays closely mirrored synthetic peptide standards for non-canonical sequences. This approach may be useful for validating non-canonical protein identification and discovering functionally relevant isoforms in the heart.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.