4.6 Article

Identification of Non-Canonical Translation Products in C. elegans Using Tandem Mass Spectrometry

期刊

FRONTIERS IN GENETICS
卷 12, 期 -, 页码 -

出版社

FRONTIERS MEDIA SA
DOI: 10.3389/fgene.2021.728900

关键词

C; elegans; altORFs; LC-MS; MS; mass spectrometry; timsTOF; MSFragger; PEAKS; sORFs

资金

  1. FWO [G052217N]
  2. KU Leuven [C16/19/003]

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Transcriptome and ribosome sequencing have identified numerous non-canonical transcripts in C. elegans, leading to the discovery of a large number of non-canonical proteins and splice variants through tandem mass spectrometry. Diverse proteomic and peptidomic strategies have also helped in detecting additional novel non-canonical proteins, providing a valuable resource for further research.
Transcriptome and ribosome sequencing have revealed the existence of many non-canonical transcripts, mainly containing splice variants, ncRNA, sORFs and altORFs. However, identification and characterization of products that may be translated out of these remains a challenge. Addressing this, we here report on 552 non-canonical proteins and splice variants in the model organism C. elegans using tandem mass spectrometry. Aided by sequencing-based prediction, we generated a custom proteome database tailored to search for non-canonical translation products of C. elegans. Using this database, we mined available mass spectrometric resources of C. elegans, from which 51 novel, non-canonical proteins could be identified. Furthermore, we utilized diverse proteomic and peptidomic strategies to detect 40 novel non-canonical proteins in C. elegans by LC-TIMS-MS/MS, of which 6 were common with our meta-analysis of existing resources. Together, this permits us to provide a resource with detailed annotation of 467 splice variants and 85 novel proteins mapped onto UTRs, non-coding regions and alternative open reading frames of the C. elegans genome.

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