IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v9y2018i1d10.1038_s41467-018-03311-y.html
   My bibliography  Save this article

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow

Author

Listed:
  • Yafeng Zhu

    (Karolinska Institutet)

  • Lukas M. Orre

    (Karolinska Institutet)

  • Henrik J. Johansson

    (Karolinska Institutet)

  • Mikael Huss

    (Stockholm University)

  • Jorrit Boekel

    (Karolinska Institutet)

  • Mattias Vesterlund

    (Karolinska Institutet)

  • Alejandro Fernandez-Woodbridge

    (Karolinska Institutet)

  • Rui M. M. Branca

    (Karolinska Institutet)

  • Janne Lehtiö

    (Karolinska Institutet)

Abstract

Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for genome annotation and potential application as neoantigens in cancer immunotherapy. We here present integrated proteogenomics analysis workflow (IPAW), which combines peptide discovery, curation, and validation. IPAW includes the SpectrumAI tool for automated inspection of MS/MS spectra, eliminating false identifications of single-residue substitution peptides. We employ IPAW to analyze two proteomics data sets acquired from A431 cells and five normal human tissues using extended (pH range, 3–10) high-resolution isoelectric focusing (HiRIEF) pre-fractionation and TMT-based peptide quantitation. The IPAW results provide evidence for the translation of pseudogenes, lncRNAs, short ORFs, alternative ORFs, N-terminal extensions, and intronic sequences. Moreover, our quantitative analysis indicates that protein production from certain pseudogenes and lncRNAs is tissue specific.

Suggested Citation

  • Yafeng Zhu & Lukas M. Orre & Henrik J. Johansson & Mikael Huss & Jorrit Boekel & Mattias Vesterlund & Alejandro Fernandez-Woodbridge & Rui M. M. Branca & Janne Lehtiö, 2018. "Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03311-y
    DOI: 10.1038/s41467-018-03311-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-018-03311-y
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-018-03311-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Eduardo Vieira de Souza & Angie L. Bookout & Christopher A. Barnes & Brendan Miller & Pablo Machado & Luiz A. Basso & Cristiano V. Bizarro & Alan Saghatelian, 2024. "Rp3: Ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Heta Desai & Katrina H. Andrews & Kristina V. Bergersen & Samuel Ofori & Fengchao Yu & Flowreen Shikwana & Mark A. Arbing & Lisa M. Boatner & Miranda Villanueva & Nicholas Ung & Elaine F. Reed & Alexe, 2024. "Chemoproteogenomic stratification of the missense variant cysteinome," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
    3. Ioanna Tzani & Marina Castro-Rivadeneyra & Paul Kelly & Lisa Strasser & Lin Zhang & Martin Clynes & Barry L. Karger & Niall Barron & Jonathan Bones & Colin Clarke, 2024. "Detection of host cell microprotein impurities in antibody drug products," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03311-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.