Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome

Carol L. Nilsson, Ekaterina Mostovenko, Cheryl F. Lichti, Kelly Ruggles, David Fenyö, Kate R. Rosenbloom, William S. Hancock, Young Ki Paik, Gilbert S. Omenn, Joshua LaBaer, Roger A. Kroes, Matthias Uhlén, Sophia Hober, Ákos Végvári, Per E. Andrén, Erik P. Sulman, Frederick F. Lang, Manuel Fuentes, Elisabet Carlsohn, Mark R. Emmett & 4 others Joseph R. Moskal, Frode S. Berven, Thomas E. Fehniger, György Marko-Varga

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

We describe the utility of integrated strategies that employ both translation of ENCODE data and major proteomic technology pillars to improve the identification of the missing proteins', novel proteoforms, and PTMs. On one hand, databases in combination with bioinformatic tools are efficiently utilized to establish microarray-based transcript analysis and supply rapid protein identifications in clinical samples. On the other hand, sequence libraries are the foundation of targeted protein identification and quantification using mass spectrometric and immunoaffinity techniques. The results from combining proteoENCODEdb searches with experimental mass spectral data indicate that some alternative splicing 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.

Original languageEnglish (US)
Pages (from-to)603-608
Number of pages6
JournalJournal of Proteome Research
Volume14
Issue number2
DOIs
StatePublished - Feb 6 2015

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Proteome
Proteins
Pulse time modulation
Alternative Splicing
Bioinformatics
Microarrays
Computational Biology
Proteomics
Libraries
Biomedical Research
Databases
Technology

Keywords

  • Chromosome-centric Human Protein Project
  • ENCODE
  • glioma stem cell
  • microassays
  • missing proteins
  • protein sequence mass spectrometry

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Nilsson, C. L., Mostovenko, E., Lichti, C. F., Ruggles, K., Fenyö, D., Rosenbloom, K. R., ... Marko-Varga, G. (2015). Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome. Journal of Proteome Research, 14(2), 603-608. https://doi.org/10.1021/pr500564q

Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome. / Nilsson, Carol L.; Mostovenko, Ekaterina; Lichti, Cheryl F.; Ruggles, Kelly; Fenyö, David; Rosenbloom, Kate R.; Hancock, William S.; Paik, Young Ki; Omenn, Gilbert S.; LaBaer, Joshua; Kroes, Roger A.; Uhlén, Matthias; Hober, Sophia; Végvári, Ákos; Andrén, Per E.; Sulman, Erik P.; Lang, Frederick F.; Fuentes, Manuel; Carlsohn, Elisabet; Emmett, Mark R.; Moskal, Joseph R.; Berven, Frode S.; Fehniger, Thomas E.; Marko-Varga, György.

In: Journal of Proteome Research, Vol. 14, No. 2, 06.02.2015, p. 603-608.

Research output: Contribution to journalArticle

Nilsson, CL, Mostovenko, E, Lichti, CF, Ruggles, K, Fenyö, D, Rosenbloom, KR, Hancock, WS, Paik, YK, Omenn, GS, LaBaer, J, Kroes, RA, Uhlén, M, Hober, S, Végvári, Á, Andrén, PE, Sulman, EP, Lang, FF, Fuentes, M, Carlsohn, E, Emmett, MR, Moskal, JR, Berven, FS, Fehniger, TE & Marko-Varga, G 2015, 'Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome', Journal of Proteome Research, vol. 14, no. 2, pp. 603-608. https://doi.org/10.1021/pr500564q
Nilsson CL, Mostovenko E, Lichti CF, Ruggles K, Fenyö D, Rosenbloom KR et al. Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome. Journal of Proteome Research. 2015 Feb 6;14(2):603-608. https://doi.org/10.1021/pr500564q
Nilsson, Carol L. ; Mostovenko, Ekaterina ; Lichti, Cheryl F. ; Ruggles, Kelly ; Fenyö, David ; Rosenbloom, Kate R. ; Hancock, William S. ; Paik, Young Ki ; Omenn, Gilbert S. ; LaBaer, Joshua ; Kroes, Roger A. ; Uhlén, Matthias ; Hober, Sophia ; Végvári, Ákos ; Andrén, Per E. ; Sulman, Erik P. ; Lang, Frederick F. ; Fuentes, Manuel ; Carlsohn, Elisabet ; Emmett, Mark R. ; Moskal, Joseph R. ; Berven, Frode S. ; Fehniger, Thomas E. ; Marko-Varga, György. / Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome. In: Journal of Proteome Research. 2015 ; Vol. 14, No. 2. pp. 603-608.
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