Deep proteome and transcriptome mapping of a human cancer cell line

Molecular Systems Biology

Nagarjuna Nagaraj²  Jacek R Wisniewski²  Tamar Geiger²  Juergen Cox²  Martin Kircher¹  Janet Kelso¹  Svante Pääbo¹ 

[1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany;Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany

关键词: mass spectrometry;    proteomics;    RNA‐Seq;    systems biology;    transcriptomics;   

DOI  :  10.1038/msb.2011.81

来源: Wiley

【 摘 要 】

Abstract

While the number and identity of proteins expressed in a single human cell type is currently unknown, this fundamental question can be addressed by advanced mass spectrometry (MS)-based proteomics. Online liquid chromatography coupled to high-resolution MS and MS/MS yielded 166 420 peptides with unique amino-acid sequence from HeLa cells. These peptides identified 10 255 different human proteins encoded by 9207 human genes, providing a lower limit on the proteome in this cancer cell line. Deep transcriptome sequencing revealed transcripts for nearly all detected proteins. We calculate copy numbers for the expressed proteins and show that the abundances of >90% of them are within a factor 60 of the median protein expression level. Comparisons of the proteome and the transcriptome, and analysis of protein complex databases and GO categories, suggest that we achieved deep coverage of the functional transcriptome and the proteome of a single cell type.

【 授权许可】

CC BY-NC-SA   
Copyright © 2011 EMBO and Macmillan Publishers Limited

Creative Commons Attribution License, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation without specific permission.