Deep proteome and transcriptome mapping of a human cancer cell line

• Published in: Molecular systems biology Vol. 7; no. 1; pp. 548 - n/a
• Main Authors: Nagaraj, Nagarjuna, Wisniewski, Jacek R, Geiger, Tamar, Cox, Juergen, Kircher, Martin, Kelso, Janet, Pääbo, Svante, Mann, Matthias
• Format: Journal Article
• Language: English
• Published: Chichester, UK John Wiley & Sons, Ltd 08.11.2011; EMBO Press; Nature Publishing Group
• Subjects: Base Sequence; Cancer; Cell Line, Tumor; Coding; Gene expression; Gene Expression Profiling - methods; HeLa Cells; High-Throughput Nucleotide Sequencing - methods; Humans; Liquid chromatography; Mass spectrometry; Mass Spectrometry - methods; Mass spectroscopy; Models, Biological; Peptides; Proteins; Proteome - genetics; Proteome - metabolism; Proteomics; Proteomics - methods; RNA‐Seq; systems biology; Transcriptome; transcriptomics; United States > US
• ISSN: 1744-4292; 1744-4292
• DOI: 10.1038/msb.2011.81

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. More than 10 000 proteins were identified by high‐resolution mass spectrometry in a human cancer cell line. The data cover most of the functional proteome as judged by RNA‐seq data and it reveals the expression range of different protein classes.