Whole human genome proteogenomic mapping for ENCODE cell line data: Identifying protein-coding regions

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Khatun, Jainab ^a   Yu, Yanbao ^b   Wrobel, John A ^b   Risk, Brian A ^a   Gunawardena, Harsha P ^b   Secrest, Ashley ^a   Spitzer, Wendy J ^a   Xie, Ling ^b   Wang, Li ^b   Chen, Xian ^b   Giddings, Morgan C ^a,b  

^a BOISE STATE UNIVERSITY   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

Genome annotation; Genomics; MS MS spectra; Proteogenomic mapping; Proteomics

Indexed keywords

ARTICLE; CANCER CELL CULTURE; COMPUTER MODEL; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; EXON; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE LOCUS; GENE MAPPING; GENETIC CODE; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; HUMAN GENOME; PROMOTER REGION; PROTEIN ANALYSIS; PROTEOGENOMIC MAPPING; TANDEM MASS SPECTROMETRY;

CELL LINE; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENOME, HUMAN; HUMANS; MASS SPECTROMETRY; MOLECULAR SEQUENCE ANNOTATION; OPEN READING FRAMES; SEQUENCE ANALYSIS, DNA;

EID: 84874380007     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-141     Document Type: Article

References (47)

1. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816. 10.1038/nature05874, 2212820, 17571346.
2. Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 2011, 9. 10.1371/journal.pbio.1001046.
3. Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An Encyclopedia of Human DNA Elements (NCP000). Nature 2012, 489(7414):57-74. 10.1038/nature11247, 3439153, 22955616.
4. Arthur JW, Wilkins MR. Using proteomics to mine genome sequences. J Proteome Res 2004, 3:393-402. 10.1021/pr034056e, 15253419.
5. Chaerkady R, Kelkar DS, Muthusamy B, Kandasamy K, Dwivedi SB, Sahasrabuddhe NA, Kim MS, Renuse S, Pinto SM, Sharma R. A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. Genome Res 2011, 21(11):1872-1881. 10.1101/gr.127951.111, 3205572, 21795387.
6. Choudhary JS, Blackstock WP, Creasy DM, Cottrell JS. Interrogating the human genome using uninterpreted mass spectrometry data. Proteomics 2001, 1:651-667. 10.1002/1615-9861(200104)1:5<651::AID-PROT651>3.0.CO;2-N, 11678035.
7. Giddings MC, Shah AA, Gesteland R, Moore B. Genome-based peptide fingerprint scanning. Proc Natl Acad Sci USA 2003, 100:20-25. 10.1073/pnas.0136893100, 140871, 12518051.
8. Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 2004, 4:59-77. 10.1002/pmic.200300511, 14730672.
9. Brosch M, Saunders GI, Frankish A, Collins MO, Yu L, Wright J, Verstraten R, Adams DJ, Harrow J, Choudhary JS, Hubbard T. Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and " resurrected" pseudogenes in the mouse genome. Genome Res 2011, 21:756-767. 10.1101/gr.114272.110, 3083093, 21460061.
10. Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. Discovery and revision of Arabidopsis genes by proteogenomics. ProcNat Acad Sci U S A 2008, 105:21034-21038.
11. Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol 2006, 7:R35. 10.1186/gb-2006-7-4-r35, 1557991, 16646984.
12. Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, Yadav AK, Shrivastava P, Marimuthu A, Anand S, Sundaram H. Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteomics 2011, MCP 10(12):M111 011627.
13. Kuster B, Mortensen P, Andersen JS, Mann M. Mass spectrometry allows direct identification of proteins in large genomes. Proteomics 2001, 1:641-650. 10.1002/1615-9861(200104)1:5<641::AID-PROT641>3.0.CO;2-R, 11678034.
14. Menon R, Zhang Q, Zhang Y, Fermin D, Bardeesy N, DePinho RA, Lu C, Hanash SM, Omenn GS, States DJ. Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Cancer Res 2009, 69:300-309. 10.1158/0008-5472.CAN-08-2145, 2613545, 19118015.
15. Merrihew GE, Davis C, Ewing B, Williams G, Kall L, Frewen BE, Noble WS, Green P, Thomas JH, MacCoss MJ. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res 2008, 18:1660-1669. 10.1101/gr.077644.108, 2556273, 18653799.
16. Oyama M, Kozuka-Hata H, Suzuki Y, Semba K, Yamamoto T, Sugano S. Diversity of translation start sites may define increased complexity of the human short ORFeome. Mol Cell Proteomics 2007, 6:1000-1006. 10.1074/mcp.M600297-MCP200, 17317662.
17. Tanner S, Shen Z, Ng J, Florea L, Guigo R, Briggs SP, Bafna V. Improving gene annotation using peptide mass spectrometry. Genome Res 2007, 17:231-239. 10.1101/gr.5646507, 1781355, 17189379.
18. Washburn MP, Wolters D, Yates JR. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19:242-247. 10.1038/85686, 11231557.
19. Bafna V, Edwards N. SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. Bioinformatics 2001, 17(Suppl 1):S13-21. 10.1093/bioinformatics/17.suppl_1.S13, 11472988.
20. Craig R, Beavis RC. A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun Mass Spectrom 2003, 17:2310-2316. 10.1002/rcm.1198, 14558131.
21. Eng JK, McCormack AL, Yates JRI. An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database. J Am Soc Mass Spectrom 1994, 5:976-989.
22. Khatun J, Hamlett E, Giddings MC. Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification. Bioinformatics 2008, 24:674-681. 10.1093/bioinformatics/btn011, 2699941, 18187442.
23. Tabb DL, Fernando CG, Chambers MC. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res 2007, 6:654-661. 10.1021/pr0604054, 2525619, 17269722.
24. Wan YH, Yang A, Chen T. PepHMM: a hidden Markov model based scoring function for mass spectrometry database search. Anal Chem 2006, 78:432-437. 10.1021/ac051319a, 16408924.
25. Zhang Z, Sun S, Zhu X, Chang S, Liu X, Yu C, Bu D, Chen R. A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data. BMC Bioinformatics 2006, 7:222. 10.1186/1471-2105-7-222, 1463009, 16638152.
26. Fischer B, Roth V, Roos F, Grossmann J, Baginsky S, Widmayer P, Gruissem W, Buhmann JM. NovoHMM: a hidden Markov model for de novo peptide sequencing. Anal Chem 2005, 77:7265-7273. 10.1021/ac0508853, 16285674.
27. Taylor JA, Johnson RS. Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem 2001, 73:2594-2604. 10.1021/ac001196o, 11403305.
28. Oyama M, Itagaki C, Hata H, Suzuki Y, Izumi T, Natsume T, Isobe T, Sugano S. Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. Genome Res 2004, 14:2048-2052. 10.1101/gr.2384604, 528919, 15489325.
29. Bitton DA, Smith DL, Connolly Y, Scutt PJ, Miller CJ. An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome. PLoS One 2010, 5:e8949. 10.1371/journal.pone.0008949, 2812506, 20126623.
30. Renuse S, Chaerkady R, Pandey A. Proteogenomics. Proteomics 2011, 11:620-630. 10.1002/pmic.201000615, 21246734.
31. Tran JC, Doucette AA. Gel-eluted liquid fraction entrapment electrophoresis: an electrophoretic method for broad molecular weight range proteome separation. Anal Chem 2008, 80:1568-1573. 10.1021/ac702197w, 18229945.
32. Wisniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods 2009, 6:359-362. 10.1038/nmeth.1322, 19377485.
33. Yu Y, Xie L, Gunawardena PH, Khatun J, Maier C, Leerkes M, Giddings M, Chen X. GOFAST: An integrated approach for efficient and comprehensive membrane proteome analysis. Anal Chem 2012, 84:9008-9014.
34. Vogel C, Marcotte EM. Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data. Nat Protocols 2008, 3:1444-1451.
35. Yamashita R, Suzuki Y, Nakai K, Sugano S. Small open reading frames in 5′ untranslated regions of mRnas. Comptes Rendus Biologies 2003, 326:987-991. 10.1016/j.crvi.2003.09.028, 14744105.
36. Morris DR, Geballe AP. Upstream open reading frames as regulators of mRNA translation. Mol Cell Biol 2000, 20:8635-8642. 10.1128/MCB.20.23.8635-8642.2000, 86464, 11073965.
37. Kochetov AV, Ahmad S, Ivanisenko V, Volkova OA, Kolchanov NA, Sarai A. uORFs, reinitiation and alternative translation start sites in human mRNAs. FEBS Lett 2008, 582:1293-1297. 10.1016/j.febslet.2008.03.014, 18358843.
38. Ge X, Jung YC, Wu Q, Kibbe WA, Wang SM. Annotating nonspecific SAGE tags with microarray data. Genomics 2006, 87:173-180. 10.1016/j.ygeno.2005.08.014, 16314072.
39. Balázs B, Hui J, Jainab K, Emily W, Brian R, Will G, Anshul K, Gunawardena HP, Yanbao Y, Ling X. Long non-coding RNAs are rarely translated in two human cell lines. Genome research 2010, 22(9):646-1657.
40. Omenn GS, Yocum AK, Menon R. Alternative splice variants, a new class of protein cancer biomarker candidates: findings in pancreatic cancer and breast cancer with systems biology implications. Dis Markers 2010, 28:241-251.
41. Menon R, Omenn GS. Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers. Cancer Res 2010, 70:3440-3449. 10.1158/0008-5472.CAN-09-2631, 2866518, 20388783.
42. Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 2010, 464:999-1005. 10.1038/nature08989, 2872544, 20393555.
43. Song XC, Fu G, Yang X, Jiang Z, Wang Y, Zhou GW. Protein expression profiling of breast cancer cells by dissociable antibody microarray (DAMA) staining. Mol Cell Proteomics 2008, 7:163-169.
44. Cox B, Emili A. Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics. Nat Protocols 2006, 1:1872-1878.
45. Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protocols 2006, 1:2856-2860.
46. Fenyo D, Beavis RC. A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem 2003, 75:768-774. 10.1021/ac0258709, 12622365.
47. Kall L, Storey JD, MacCoss MJ, Noble WS. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res 2008, 7:29-34. 10.1021/pr700600n, 18067246.