Use of ENCODE Resources to Characterize Novel Proteoforms and Missing Proteins in the Human Proteome

Research output: Contribution to journalArticle


We describe integrated strategies that employ both translation of ENCODE data and major proteomic technology pillars to improve the identification of the missing proteins, protein isoforms, and PTMs. The results from proteoENCODEdb searches with experimental mass spectral data indicate that some novel splice forms detected at the transcript level are in fact translated to proteins. Our results provide a step toward the directives of the C-HPP initiative and related biomedical research.


  • Carol Nilsson
  • Ekaterina Mostovenko
  • Cheryl Lichti
  • Kelly Ruggles
  • David Fenyö
  • Kate Rosenbloom
  • William Hancock
  • Young-Ki Paik
  • Gilbert Omenn
  • Joshua LaBaer
  • Roger Kroes
  • Mathias Uhlén
  • Sophia Hober
  • Ákos Végvári
  • Per Andrén
  • Erik Sulman
  • Frederick Lang
  • Manuel Fuentes
  • Elisabet Carlsohn
  • Mark Emmett
  • Joseph Moskal
  • Frode Berven
  • Thomas Fehniger
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Medical Engineering


  • Glioma stem cell, ENCODE, Chromosome-centric Human Protein Project, Protein sequence mass spectrometry, Microassays, Missing proteins
Original languageEnglish
Pages (from-to)603-608
JournalJournal of Proteome Research
Issue number2
Publication statusPublished - 2015
Publication categoryResearch