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Alternative RNA Splicing02:18

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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PASS: A Proteomics Alternative Splicing Screening Pipeline.

Peng Wu1,2, Lingling Pu3, Bingnan Deng3

  • 1State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China.

Proteomics
|May 17, 2019
PubMed
Summary
This summary is machine-generated.

A new software, PASS, identifies alternative splicing (AS) events directly from proteomics mass spectrometry (MS) data. This tool aids in understanding proteome complexity and isoforms using proteogenomics.

Keywords:
PASSalternative splicingproteogenomicsproteomics

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Alternative splicing (AS) is extensively studied at the transcriptome level using RNA-sequencing (RNA-seq).
  • The biological significance of AS in generating proteome complexity remains a subject of debate.
  • A robust computational tool is needed to identify AS events directly from proteomic data.

Purpose of the Study:

  • To develop a software tool, PASS, for comprehensive detection of alternative splicing events from proteomics mass spectrometry (MS) data.
  • To enable the identification of novel AS events and isoforms using proteogenomic approaches.

Main Methods:

  • Development of the PASS software, integrating transcript reconstruction from RNA-Seq, novel protein sequence generation, and MS data searching.
  • Compatibility of PASS with proteogenomic workflows for enhanced proteome identification.
  • Workflow includes transcript reconstruction, novel protein sequence generation, MS data searching, proSAM file formatting, and AS detection.

Main Results:

  • PASS successfully identified 407 alternative splicing events in mouse hepatocyte proteome data using MS evidence.
  • These represent the first set of AS events identified directly from proteomic MS data for this sample type.
  • The software facilitates the discovery of novel proteomic isoforms arising from alternative splicing.

Conclusions:

  • The PASS software provides a valuable toolkit for identifying alternative splicing events directly from proteomics data.
  • It is expected to advance the understanding of proteome complexity and the functional implications of alternative splicing.
  • PASS is freely available, promoting wider adoption in proteomic and transcriptomic research.