Deep proteome and transcriptome mapping of a human cancer cell line

Molecular Systems Biology

Volumn 7, Issue , 2011, Pages

  Nagaraj, Nagarjuna ^a   Wisniewski, Jacek R ^a   Geiger, Tamar ^a   Cox, Juergen ^a   Kircher, Martin ^b   Kelso, Janet ^b   Pääbo, Svante ^b   Mann, Matthias ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^b MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

Author keywords

mass spectrometry; proteomics; RNA Seq; systems biology; transcriptomics

Indexed keywords

PROTEOME; TRANSCRIPTOME;

AMINO ACID SEQUENCE; ARTICLE; GENE DOSAGE; GENE MAPPING; HELA CELL; HUMAN; HUMAN CELL; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; RNA SEQUENCE; BIOLOGICAL MODEL; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; PROTEOMICS; TUMOR CELL LINE;

BASE SEQUENCE; CELL LINE, TUMOR; GENE EXPRESSION PROFILING; HELA CELLS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MASS SPECTROMETRY; MODELS, BIOLOGICAL; PROTEOME; PROTEOMICS; TRANSCRIPTOME;

EID: 80855128254     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2011.81     Document Type: Article

References (35)

1. Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422: 198-207 (Pubitemid 36362757)
2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29 (Pubitemid 30257031)
3. Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, Lander ES (2007) Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 104: 19428-19433
4. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26: 1367-1372
5. Cox J, Mann M (2011) Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem 80: 273-299
6. Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 10: 1794-1805
7. de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Frohlich F, Walther TC, Mann M (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455: 1251-1254
8. de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C (2009) Global signatures of protein and mRNA expression levels. Mol Biosyst 5: 1512-1526
9. Graumann J, Hubner NC, Kim JB, Ko K, Moser M, Kumar C, Cox J, Scholer H, Mann M (2008) Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5111 proteins. Mol Cell Proteomics 7: 672-683 (Pubitemid 351597479)
10. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28: 503-510
11. Haas BJ, Zody MC (2010) Advancing RNA-Seq analysis. Nat Biotechnol 28: 421-423
12. Hebenstreit D, Fang M, Gu M, Charoensawan V, van Oudenaarden A, Teichmann SA (2011) RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol Syst Biol 7: 497
13. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E et al (2002) The Ensembl genome database project. Nucleic Acids Res 30: 38-41 (Pubitemid 34679498)
14. Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K et al (2009) Ensembl 2009. Nucleic Acids Res 37: D690-D697
15. Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P (2006) Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature 443: 594-597 (Pubitemid 44527297)
16. Kircher M, Stenzel U, Kelso J (2009) Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol 10: R83
17. Lundberg E, Fagerberg L, Klevebring D, Matic I, Geiger T, Cox J, Algenas C, Lundeberg J, Mann M, Uhlen M (2010) Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol 6: 450
18. Maier T, Guell M, Serrano L (2009) Correlation of mRNA and protein in complex biological samples. FEBS Lett 583: 3966-3973
19. Mallick P, Kuster B (2010) Proteomics: a pragmatic perspective. Nat Biotechnol 28: 695-709
20. Malmstrom J, Beck M, Schmidt A, Lange V, Deutsch EW, Aebersold R (2009) Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 460: 762-765
21. Mann M, Kelleher NL (2008) Precision proteomics: the case for high resolution and high mass accuracy. Proc Natl Acad Sci USA 105: 18132-18138
22. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628 (Pubitemid 351911867)
23. Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M (2007) Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods 4: 709-712 (Pubitemid 47338163)
24. Olsen JV, Schwartz JC, Griep-Raming J, Nielsen ML, Damoc E, Denisov E, Lange O, Remes P, Taylor D, Splendore M, Wouters ER, Senko M, Makarov A, Mann M, Horning S (2009) A dual pressure linear ion trap orbitrap instrument with very high sequencing speed. Mol Cell Proteomics 8: 2759-2769
25. Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138: 795-806
26. Ramskold D, Wang ET, Burge CB, Sandberg R (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5: e1000598
27. Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using Stage Tips. Nat Protoc 2: 1896-1906 (Pubitemid 47308128)
28. Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M (2011) Global quantification of mammalian gene expression control. Nature 473: 337-342
29. Silva JC, Gorenstein MV, Li GZ, Vissers JP, Geromanos SJ (2006) Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol Cell Proteomics 5: 144-156 (Pubitemid 43169347)
30. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111
31. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515
32. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63
33. Wisniewski JR, Zougman A, Mann M (2009a) Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J Proteome Res 8: 5674-5678
34. Wisniewski JR, Zougman A, Nagaraj N, Mann M (2009b) Universal sample preparation method for proteome analysis. Nat Methods 6: 359-362
35. Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M (2011) A protein epitope signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines. Mol Cell Proteomics (e-pub ahead of print 30 September 2011; doi:10.1074/mcp.O111.009613)