Open AccessDeep proteome and transcriptome mapping of a human cancer cell line
Author(s) -
Nagaraj Nagarjuna,
Wisniewski Jacek R,
Geiger Tamar,
Cox Juergen,
Kircher Martin,
Kelso Janet,
Pääbo Svante,
Mann Matthias
Publication year - 2011
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb.2011.81
Subject(s) - proteome , transcriptome , biology , proteomics , human proteome project , computational biology , gene , hela , cell , genetics , gene expression
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.