Proteogenomics and systems biology: quest for the ultimate missing parts

References

• Auffray C, Noble D. Origins of systems biology in William Harvey’s masterpiece on the movement of the heart and the bood in animals. Int. J. Mol. Sci.10(4), 1658–1669 (2009).
   PubMed Web of Science ®Google Scholar
• Noble D. The Music of Life: Biology Beyond the Genome. Oxford University Press, Oxford, UK (2006).
   Google Scholar
• Strange K. The end of “naive reductionism”: rise of systems biology or renaissance of physiology? Am. J. Physiol. Cell. Physiol.288(5), C968–C974 (2005).
   PubMed Web of Science ®Google Scholar
• Kyrpides NC. Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nat. Biotechnol.27(7), 627–632 (2009).
   PubMed Web of Science ®Google Scholar
• Armengaud J, Dedieu A, Solques O, Pellequer JL, Quemeneur E. Deciphering structure and topology of conserved COG2042 orphan proteins. BMC Struct. Biol.5, 3 (2005).
   PubMedGoogle Scholar
• Brückner A, Polge C, Lentze N, Auerbach D, Schlattner U. Yeast two-hybrid, a powerful tool for systems biology. Int. J. Mol. Sci.10(6), 2763–2788 (2009).
   PubMed Web of Science ®Google Scholar
• Mousson F, Kolkman A, Pijnappel WW, Timmers HT, Heck AJ. Quantitative proteomics reveals regulation of dynamic components within TATA-binding protein (TBP) transcription complexes. Mol. Cell. Proteomics7(5), 845–852 (2008).
   PubMed Web of Science ®Google Scholar
• Barglow KT, Cravatt BF. Activity-based protein profiling for the functional annotation of enzymes. Nat. Methods4(10), 822–827 (2007).
   PubMed Web of Science ®Google Scholar
• Beloqui A, Guazzaroni ME, Pazos F et al. Reactome array: forging a link between metabolome and genome. Science326, 252–257 (2009).
   PubMed Web of Science ®Google Scholar
• Gstaiger M, Aebersold R. Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat. Rev. Genet.10(9), 617–627 (2009).
   PubMed Web of Science ®Google Scholar
• Clamp M, Fry B, Kamal M et al. Distinguishing protein-coding and noncoding genes in the human genome. Proc. Natl Acad. Sci. USA104(49), 19428–19433 (2007).
   PubMed Web of Science ®Google Scholar
• Derrien T, Thézé J, Vaysse A et al. Revisiting the missing protein-coding gene catalog of the domestic dog. BMC Genomics10, 62 (2009).
   PubMedGoogle Scholar
• Porcel BM, Delfour O, Castelli V et al. Numerous novel annotations of the human genome sequence supported by a 5´-end-enriched cDNA collection. Genome Res.14(3), 463–471 (2004).
   PubMed Web of Science ®Google Scholar
• Gallien S, Perrodou E, Carapito C et al. Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol. Genome Res.19, 128–135 (2009).
   PubMed Web of Science ®Google Scholar
• Gupta N, Benhamida J, Bhargava V et al. Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res.18(7), 1133–1142 (2008).
   PubMed Web of Science ®Google Scholar
• Gogarten JP, Hilario E. Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements. BMC Evol. Biol.6, 94 (2006).
   PubMed Web of Science ®Google Scholar
• Liu XQ. Protein-splicing intein: genetic mobility, origin, and evolution. Annu. Rev. Genet.34, 61–76 (2000).
   PubMed Web of Science ®Google Scholar
• Dassa B, London N, Stoddard BL, Schueler-Furman O, Pietrokovski S. Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family. Nucleic Acids Res.37(8), 2560–2573 (2009).
   PubMed Web of Science ®Google Scholar
• Comeau AM, Hatfull GF, Krisch HM, Lindell D, Mann NH, Prangishvili D. Exploring the prokaryotic virosphere. Res. Microbiol.159(5), 306–313 (2008).
   PubMed Web of Science ®Google Scholar
• La Scola B, Desnues C, Pagnier I et al. The virophage as a unique parasite of the giant mimivirus. Nature455(7209), 100–104 (2008).
   PubMed Web of Science ®Google Scholar
• Raoult D, Audic S, Robert C et al. The 1.2-megabase genome sequence of Mimivirus. Science306(5700), 1344–1350 (2004).
   PubMed Web of Science ®Google Scholar
• Yates JR 3rd, Eng JK, McCormack AL. Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal. Chem.67(18), 3202–3210 (1995).
   PubMed Web of Science ®Google Scholar
• Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics4(1), 59–77 (2004).
   PubMed Web of Science ®Google Scholar
• Jaffe JD, Stange-Thomann N, Smith C et al. The complete genome and proteome of Mycoplasma mobile. Genome Res.14(8), 1447–1461 (2004).
   PubMed Web of Science ®Google Scholar
• Ansong C, Purvine SO, Adkins JN, Lipton MS, Smith RD. Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Brief Funct. Genomic Proteomic7(1), 50–62.
   PubMedGoogle Scholar
• Banfield JF, Verberkmoes NC, Hettich RL, Thelen MP. Proteogenomic approaches for the molecular characterization of natural microbial communities. Omics9(4), 301–333 (2008).
   Google Scholar
• Gupta N, Tanner S, Jaitly N et al. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res.17(9), 1362–1377 (2007).
   PubMed Web of Science ®Google Scholar
• Wilkins MJ, Verberkmoes NC, Williams KH et al. Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl. Environ. Microbiol.28, 28 (2009).
   Google Scholar
• Yuan J, Zhu L, Liu X et al. A proteome reference map and proteomic analysis of Bifidobacterium longum NCC2705. Mol. Cell. Proteomics5(6), 1105–1118 (2006).
   PubMed Web of Science ®Google Scholar
• de Groot A, Dulermo R, Ortet P et al. Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. PLoS Genet.5(3), e1000434 (2009).
   PubMedGoogle Scholar
• Lipton MS, Pasa-Tolic’ L, Anderson GA et al. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc. Natl Acad. Sci. USA99(17), 11049–11054 (2002).
   PubMed Web of Science ®Google Scholar
• Zhang W, Culley DE, Gritsenko MA et al. LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris. Biochem. Biophys. Res. Commun.349(4), 1412–1419 (2006).
   PubMed Web of Science ®Google Scholar
• Lopez-Campistrous A, Semchuk P, Burke L et al. Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth. Mol. Cell. Proteomics4(8), 1205–1209 (2005).
   PubMed Web of Science ®Google Scholar
• Maillet I, Berndt P, Malo C et al. From the genome sequence to the proteome and back: evaluation of E. coli genome annotation with a 2-D gel-based proteomics approach. Proteomics7(7), 1097–1106 (2007).
   PubMed Web of Science ®Google Scholar
• Kolker E, Purvine S, Galperin MY et al. Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J. Bacteriol.185(15), 4593–4602 (2003).
   PubMed Web of Science ®Google Scholar
• Link AJ, Hays LG, Carmack EB, Yates JR 3rd. Identifying the major proteome components of Haemophilus influenzae type-strain NCTC 8143. Electrophoresis18(8), 1314–1334 (1997).
   PubMed Web of Science ®Google Scholar
• Chaves DF, Ferrer PP, de Souza EM, Gruz LM, Monteiro RA, de Oliveira Pedrosa F. A two-dimensional proteome reference map of Herbaspirillum seropedicae proteins. Proteomics7(20), 3759–3763 (2007).
   PubMed Web of Science ®Google Scholar
• Dandekar T, Huynen M, Regula JT et al. Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Res.28(17), 3278–3288 (2000).
   PubMed Web of Science ®Google Scholar
• Deshayes C, Perrodou E, Gallien S et al. Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors? Genome Biol.8(2), R20 (2007).
   PubMedGoogle Scholar
• Jungblut PR, Müller EC, Mattow J, Kaufmann SH. Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics. Infect. Immun.69(9), 5905–5907 (2001).
   PubMed Web of Science ®Google Scholar
• Elias DA, Monroe ME, Marshall MJ et al. Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics. Proteomics5(12), 3120–3130 (2005).
   PubMed Web of Science ®Google Scholar
• Elias DA, Monroe ME, Smith RD, Fredrickson JK, Lipton MS. Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1. J. Microbiol. Methods66(2), 223–233 (2006).
   PubMed Web of Science ®Google Scholar
• Gupta RS, Mok A. Phylogenomics and signature proteins for the α proteobacteria and its main groups. BMC Microbiol.7, 106 (2007).
   PubMedGoogle Scholar
• Kolker E, Picone AF, Galperin MY et al. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc. Natl Acad. Sci. USA102(6), 2099–2104 (2005).
   PubMed Web of Science ®Google Scholar
• Romine MF, Elias DA, Monroe ME et al. Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis. Omics8(3), 239–254 (2004).
   PubMed Web of Science ®Google Scholar
• Wei C, Peng J, Xiong Z, Yang J, Wang J, Jin Q. Subproteomic tools to increase genome annotation complexity. Proteomics8(20), 4209–4213 (2008).
   PubMed Web of Science ®Google Scholar
• Ishino Y, Okada H, Ikeuchi M, Taniguchi H. Mass spectrometry-based prokaryote gene annotation. Proteomics7(22), 4053–4065 (2007).
   PubMed Web of Science ®Google Scholar
• Yamazaki S, Yamazaki J, Nishijima K et al. Proteome analysis of an aerobic hyperthermophilic crenarchaeon, Aeropyrum pernix K1. Mol. Cell. Proteomics5(5), 811–823.
   PubMed Web of Science ®Google Scholar
• Goo YA, Yi EC, Baliga NS et al. Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Mol. Cell. Proteomics2(8), 506–524 (2003).
   PubMed Web of Science ®Google Scholar
• Tebbe A, Klein C, Bisle B et al. Analysis of the cytosolic proteome of Halobacterium salinarum and its implication for genome annotation. Proteomics5(1), 168–179 (2005).
   PubMed Web of Science ®Google Scholar
• Giometti CS et al. Global analysis of a ‘simple’ proteome: Methanococcus jannaschii. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.782(1–2), 227–243 (2002).
   PubMed Web of Science ®Google Scholar
• Konstantinidis K, Tebbe A, Klein C et al. Genome-wide proteomics of Natronomonas pharaonis. J. Proteome Res.6(1), 185–193 (2007).
   PubMed Web of Science ®Google Scholar
• Zivanovic Y, Armengaud J, Lagorce A et al. Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the archaea. Genome Biol.10(6), R70 (2009).
   PubMedGoogle Scholar
• Shevchenko A, Jensen ON, Podtelejnikov AV et al. Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proc. Natl Acad. Sci. USA93(25), 14440–14445 (1996).
   PubMed Web of Science ®Google Scholar
• Oshiro G, Wodicka LM, Washburn MP, Yates JR 3rd, Lockhart DJ, Winzeler EA. Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res.12(8), 1210–1220 (2002).
   PubMed Web of Science ®Google Scholar
• Wright JC, Sugden D, Francis-McIntyre S et al. Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger. BMC Genomics10, 61 (2009).
   PubMedGoogle Scholar
• Bindschedler LV, Burgis TA, Mills DJ, Ho JT, Cramer R, Spanu PD. In planta proteomics and proteogenomics of the biotrophic barley fungal pathogen Blumeria graminis f. sp. hordei. Mol. Cell. Proteomics8(10), 2368–2381 (2009).
   PubMed Web of Science ®Google Scholar
• Ferro M, Tardif M, Reguer E et al. PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences. J. Proteome Res.7(5), 1873–1883 (2008).
   PubMed Web of Science ®Google Scholar
• Lasonder E, Ishihama Y, Andersen JS et al. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature419(6906), 537–542 (2002).
   PubMed Web of Science ®Google Scholar
• Xia D, Sanderson SJ, Jones AR et al. The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation. Genome Biol.9(7), R116 (2008).
   PubMedGoogle Scholar
• Baerenfaller K, Grossmann J, Grobei MA et al. Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science320(5878), 938–941 (2008).
   PubMed Web of Science ®Google Scholar
• Kalume DE, Peri S, Reddy R et al. Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics6, 128 (2005).
   PubMedGoogle Scholar
• Merrihew GE, Davis C, Ewing B et al. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res.18(10), 1660–1669 (2008).
   PubMed Web of Science ®Google Scholar
• Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. Discovery and revision of Arabidopsis genes by proteogenomics. Proc. Natl Acad. Sci. USA105(52), 21034–21038 (2008).
   PubMed Web of Science ®Google Scholar
• Oyama M, Itagaki C, Hata H et al. Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. Genome Res.14(10B), 2048–2052 (2004).
   PubMed Web of Science ®Google Scholar
• Tanner S, Shen Z, Ng J et al. Improving gene annotation using peptide mass spectrometry. Genome Res.17(2), 231–239 (2007).
   PubMed Web of Science ®Google Scholar
• Omenn GS, States DJ, Adamski M et al. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics5(13), 3226–3245 (2005).
   PubMed Web of Science ®Google Scholar
• Klein C, Aivaliotis M, Olsen JV et al. The low molecular weight proteome of Halobacterium salinarum. J. Proteome Res.6(4), 1510–1518 (2007).
   PubMed Web of Science ®Google Scholar
• Armengaud J. A perfect genome annotation is within reach with the proteomics and genomics alliance. Curr. Opin. Microbiol.12(3), 292–300 (2009).
   PubMed Web of Science ®Google Scholar
• Leitner A, Lindner W. Chemistry meets proteomics: the use of chemical tagging reactions for MS-based proteomics. Proteomics6(20), 5418–5434 (2006).
   PubMed Web of Science ®Google Scholar
• Gevaert K, Goethals M, Martens L et al. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat. Biotechnol.21(5), 566–569 (2003).
   PubMed Web of Science ®Google Scholar
• Staes A, Van Damme P, Helsens K, Demol H, Vandekerckhove J, Gevaert K. Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics8(7), 1362–1370 (2008).
   PubMed Web of Science ®Google Scholar
• Baudet M, Ortet P, Gaillard JC et al. Proteomic-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. Mol. Cell. Proteomics (2009) (Epub ahead of print).
   PubMedGoogle Scholar
• Dormeyer W, Mohammed S, van Breukelen B, Krijgsveld J, Heck AJR Targeted analysis of protein termini. J. Proteome Res.6(12), 4634–4645 (2007).
   PubMed Web of Science ®Google Scholar
• Goetze S, Qeli E, Mosimann C et al. Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PLoS Biol.7(11), E1000236 (2009).
   PubMed Web of Science ®Google Scholar
• Arnesen T, Van Damme P, Polevoda B et al. Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans. Proc. Natl Acad. Sci. USA106(20), 8157–8162 (2009).
   PubMed Web of Science ®Google Scholar
• Koonin EV. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat. Rev. Microbiol.1(2), 127–136 (2003).
   PubMed Web of Science ®Google Scholar
• Koonin EV, Wolf YI. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res.36(21), 6688–6719 (2008).
   PubMed Web of Science ®Google Scholar
• VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF. Systems biology: functional analysis of natural microbial consortia using community proteomics. Nat. Rev. Microbiol.7(3), 196–205 (2009).
   PubMed Web of Science ®Google Scholar
• Liu H, Sadygov RG, Yates JR 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem.76(14), 4193–4201 (2004).
   PubMed Web of Science ®Google Scholar
• Brun V et al. Isotope dilution strategies for absolute quantitative proteomics. J. Proteomics72(5), 740–749 (2009).
   PubMed Web of Science ®Google Scholar
• Mayya V, Han KD. Proteomic applications of protein quantification by isotope-dilution mass spectrometry. Expert Rev. Proteomics3(6), 597–610 (2006).
   PubMed Web of Science ®Google Scholar
• Malmström J, Beck M, Schmidt A, Lange V, Deutsch EW, Aebersold R. Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature460(7256), 762–765 (2009).
   PubMed Web of Science ®Google Scholar
• Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell138(4), 795–806 (2009).
   PubMed Web of Science ®Google Scholar
• Cravatt BF, Wright AT, Kozarich JW. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu. Rev. Biochem.77, 383–414 (2008).
   PubMed Web of Science ®Google Scholar
• Jessani N, Cravatt BF. The development and application of methods for activity-based protein profiling. Curr. Opin. Chem. Biol.8(1), 54–59 (2004).
   PubMed Web of Science ®Google Scholar
• Bantscheff M, Scholten A, Heck AJ. Revealing promiscuous drug-target interactions by chemical proteomics. Drug Discov. Today14(21–22), 1021–1029 (2009).
   PubMed Web of Science ®Google Scholar
• Rix U, Superti-Furga G. Target profiling of small molecules by chemical proteomics. Nat. Chem. Biol.5(9), 616–624 (2009).
   PubMed Web of Science ®Google Scholar
• Koonin EV, Mushegian AR. Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics. Curr. Opin. Genet. Dev.6(6), 757–762 (1996).
   PubMed Web of Science ®Google Scholar
• Perez-Iratxeta C, Palidwor G, Andrade-Navarro MA. Towards completion of the Earth’s proteome. EMBO Rep.8(12), 1135–1141 (2007).
   PubMed Web of Science ®Google Scholar
• Schneiker S, Perlova O, Kaiser O et al. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat. Biotechnol.25(11), 1281–1289 (2007).
   PubMed Web of Science ®Google Scholar
• Chin JW. Modular approaches to expanding the functions of living matter. Nat. Chem. Biol.2(6), 304–311 (2006).
   PubMed Web of Science ®Google Scholar
• Tanouchi Y, Pai A, You L. Decoding biological principles using gene circuits. Mol. Biosyst.5(7), 695–703 (2009).
   PubMedGoogle Scholar
• Callister SJ, McCue LA, Turse JE et al. Comparative bacterial proteomics: analysis of the core genome concept. PLoS ONE3(2), e1542 (2008).
   PubMed Web of Science ®Google Scholar
• Gibson DG, Benders GA, Andrews-Pfannkoch C et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science319, 1215–1220 (2008).
   PubMed Web of Science ®Google Scholar
• Lartigue C, Glass JI, Alperovich N et al. Genome transplantation in bacteria: changing one species to another. Science317(5838), 632–638 (2007).
   PubMed Web of Science ®Google Scholar
• Lartigue C, Vashee S, Algire MA et al. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science325(5948), 1693–1696 (2009).
   PubMed Web of Science ®Google Scholar
• Brancia FL. Recent developments in ion-trap mass spectrometry and related technologies. Expert Rev. Proteomics3(1), 143–151 (2006).
   PubMed Web of Science ®Google Scholar
• Han X, Aslanian A, Yates JR 3rd. Mass spectrometry for proteomics. Curr. Opin. Chem. Biol.12(5), 483–490 (2008).
   PubMed Web of Science ®Google Scholar
• Yates JR, Ruse CI, Nakorchevsky A. Proteomics by mass spectrometry: approaches, advances and applications. Annu. Rev. Biomed. Eng.11, 49–79 (2009).
   PubMed Web of Science ®Google Scholar