title: Deep proteome and transcriptome mapping of a human cancer cell line.
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.
authors: Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
authors: Nagarjuna
authors: N
authors: Nagaraj
authors: Jacek R
authors: JR
authors: Wisniewski
authors: Tamar
authors: T
authors: Geiger
authors: Juergen
authors: J
authors: Cox
authors: Martin
authors: M
authors: Kircher
authors: Janet
authors: J
authors: Kelso
authors: Svante
authors: S
authors: Pääbo
authors: Matthias
authors: M
authors: Mann
mesh_terms: D001483:Base Sequence; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling / Q000379:methods*; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D008954:Models, Biological; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D059467:Transcriptome
chemical_list: D020543:Proteome