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; Joseph R. Moskal; Frode S. Berven; Thomas E. Fehniger; György Marko-Varga

doi:10.1021/pr500564q

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. EmmettJoseph R. Moskal, Frode S. Berven, Thomas E. Fehniger, György Marko-Varga

Division of Immunobiology

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

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 language	English
Pages (from-to)	603-608
Number of pages	6
Journal	Journal of Proteome Research
Volume	14
Issue number	2
DOIs	https://doi.org/10.1021/pr500564q
State	Published - Feb 6 2015

Keywords

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

Access to Document

10.1021/pr500564q

Cite this

Nilsson, C. L., Mostovenko, E., Lichti, C. F., Ruggles, K., Fenyö, D., Rosenbloom, K. R., Hancock, W. S., Paik, Y. K., Omenn, G. S., Labaer, J., Kroes, R. A., Uhlén, M., Hober, S., Végvári, Á., Andrén, P. E., Sulman, E. P., Lang, F. F., Fuentes, M., Carlsohn, E., ... 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

@article{557e9f6fabde403aac7c2cc2e86eb82c,

title = "Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome",

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.",

keywords = "Chromosome-centric Human Protein Project, ENCODE, glioma stem cell, microassays, missing proteins, protein sequence mass spectrometry",

author = "Nilsson, {Carol L.} and Ekaterina Mostovenko and Lichti, {Cheryl F.} and Kelly Ruggles and David Feny{\"o} and Rosenbloom, {Kate R.} and Hancock, {William S.} and Paik, {Young Ki} and Omenn, {Gilbert S.} and Joshua Labaer and Kroes, {Roger A.} and Matthias Uhl{\'e}n and Sophia Hober and {\'A}kos V{\'e}gv{\'a}ri and Andr{\'e}n, {Per E.} and Sulman, {Erik P.} and Lang, {Frederick F.} and Manuel Fuentes and Elisabet Carlsohn and Emmett, {Mark R.} and Moskal, {Joseph R.} and Berven, {Frode S.} and Fehniger, {Thomas E.} and Gy{\"o}rgy Marko-Varga",

note = "Publisher Copyright: {\textcopyright} 2015 American Chemical Society.",

year = "2015",

month = feb,

day = "6",

doi = "10.1021/pr500564q",

language = "English",

volume = "14",

pages = "603--608",

journal = "Journal of Proteome Research",

issn = "1535-3893",

number = "2",

}

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

TY - JOUR

T1 - Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome

AU - Nilsson, Carol L.

AU - Mostovenko, Ekaterina

AU - Lichti, Cheryl F.

AU - Ruggles, Kelly

AU - Fenyö, David

AU - Rosenbloom, Kate R.

AU - Hancock, William S.

AU - Paik, Young Ki

AU - Omenn, Gilbert S.

AU - Labaer, Joshua

AU - Kroes, Roger A.

AU - Uhlén, Matthias

AU - Hober, Sophia

AU - Végvári, Ákos

AU - Andrén, Per E.

AU - Sulman, Erik P.

AU - Lang, Frederick F.

AU - Fuentes, Manuel

AU - Carlsohn, Elisabet

AU - Emmett, Mark R.

AU - Moskal, Joseph R.

AU - Berven, Frode S.

AU - Fehniger, Thomas E.

AU - Marko-Varga, György

PY - 2015/2/6

Y1 - 2015/2/6

N2 - 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.

AB - 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.

KW - Chromosome-centric Human Protein Project

KW - ENCODE

KW - glioma stem cell

KW - microassays

KW - missing proteins

KW - protein sequence mass spectrometry

UR - http://www.scopus.com/inward/record.url?scp=84922613073&partnerID=8YFLogxK

U2 - 10.1021/pr500564q

DO - 10.1021/pr500564q

M3 - Article

C2 - 25369122

AN - SCOPUS:84922613073

SN - 1535-3893

VL - 14

SP - 603

EP - 608

JO - Journal of Proteome Research

JF - Journal of Proteome Research

IS - 2

ER -

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

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this