SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra

Journal of Proteome Research

Volumn 15, Issue 1, 2016, Pages 144-151

  Kolmogorov, Mikhail ^a   Liu, Xiaowen ^b   Pevzner, Pavel A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

genome annotation; protein identification; proteogenomics; top down mass spectrometry

Indexed keywords

PROTEOME; ARCHAEAL PROTEIN; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENOME; COMPUTER PROGRAM; GENOMICS; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEOMICS; PYROCOCCUS FURIOSUS; QUALITY CONTROL; TANDEM MASS SPECTROMETRY; AMINO ACID SEQUENCE; ARCHAEAL GENE; BACTERIAL GENE; CHEMISTRY; GENETICS; MOLECULAR GENETICS; PROCEDURES; SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; STANDARD; STANDARDS;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; BACTERIAL PROTEINS; GENES, ARCHAEAL; GENES, BACTERIAL; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; PROTEOME; PROTEOMICS; PYROCOCCUS FURIOSUS; REFERENCE STANDARDS; SALMONELLA TYPHIMURIUM;

EID: 84953258062     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00610     Document Type: Article

References (31)

1. Yates, J. r.; Eng, J.; McCormack, A. Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases Anal. Chem. 1995, 67, 3202-3202 10.1021/ac00114a016
2. Jaffe, H.; Vinade, L.; Dosemeci, A. Identification of novel phosphorylation sites on postsynaptic density proteins Biochem. Biophys. Res. Commun. 2004, 321, 210-218 10.1016/j.bbrc.2004.06.122
3. Fermin, D.; Allen, B. B.; Blackwell, T. W.; Menon, R.; Adamski, M.; Xu, Y.; Ulintz, P.; Omenn, G. S.; States, D. J. 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
4. Gupta, N.; Tanner, S.; Jaitly, N.; Adkins, J. N.; Lipton, M.; Edwards, R.; Romine, M.; Osterman, A.; Bafna, V.; Smith, R. D.; Pevzner, P. A. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation Genome Res. 2007, 17, 1362-1377 10.1101/gr.6427907
5. Gupta, N.; Benhamida, J.; Bhargava, V.; Goodman, D.; Kain, E.; Kerman, I.; Nguyen, N.; Ollikainen, N.; Rodriguez, J.; Wang, J.; Lipton, M. S.; Romine, M.; Bafna, V.; Smith, R. D.; Pevzner, P. A. Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes Genome Res. 2008, 18, 1133-1142 10.1101/gr.074344.107
6. Castellana, N. E.; Payne, S. H.; Shen, Z.; Stanke, M.; Bafna, V.; Briggs, S. P. Discovery and revision of Arabidopsis genes by proteogenomics Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 21034-21038 10.1073/pnas.0811066106
7. Woo, S.; Cha, S. W.; Na, S.; Guest, C.; Liu, T.; Smith, R. D.; Rodland, K. D.; Payne, S. P.; Bafna, V. Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data Proteomics 2014, 14, 2719-2730 10.1002/pmic.201400206
8. Li, H.; Menon, R.; Omenn, G.; Guan, Y. Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence Proteomics 2014, 14, 2709-2718 10.1002/pmic.201400170
9. Kucharova, V.; Wiker, H. G. Proteogenomics in microbiology: Taking the right turn at the junction of genomics and proteomics Proteomics 2014, 14, 2360-2675 10.1002/pmic.201400168
10. Stern-Ginossar, N.; Weisburd, B.; Michalski, A.; Le, V. T. K.; Hein, M. Y.; Huang, S.-X.; Ma, M.; Shen, B.; Qian, S.-B.; Hengel, H.; Mann, M.; Ingolia, N. T.; Weissman, J. S. Decoding Human Cytomegalovirus Science 2012, 338, 1088-1093 10.1126/science.1227919
11. Koch, A.; Gawron, D.; Steyaert, S.; Ndah, E.; Crappé, J.; De Keulenaer, S.; De Meester, E.; Ma, M.; Shen, B.; Gevaert, K.; Van Criekinge, W. V.; Van Damme, P.; Menschaert, G. A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites Proteomics 2014, 14, 2688-2698 10.1002/pmic.201400180
12. Veenstra, T. D.; Conrads, T. P.; Issaq, H. J. What to do with "one-hit wonders"? Electrophoresis 2004, 25, 1278-1279 10.1002/elps.200490007
13. Ansong, C.; Wu, S.; Meng, D.; Liu, X.; Brewer, H. M.; Deatherage Kaiser, B. L.; Nakayasu, E. S.; Cort, J. R.; Pevzner, P.; Smith, R. D.; Heffron, F.; Adkins, J. N.; Paša-Tolić, L. Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 10153-10158 10.1073/pnas.1221210110
14. TopPIC website. http://proteomics.informatics.iupui.edu/software/toppic/.
15. Liu, X.; Sirotkin, Y.; Shen, Y.; Anderson, G.; Tsai, Y. S.; Ting, Y. S.; Goodlett, D. R.; Smith, R. D.; Bafna, V.; Pevzner, P. A. Protein identification using top-down spectra Mol. Cell. Proteomics 2012, 11, M111.008524 10.1074/mcp.M111.008524
16. Liu, X.; Segar, M. W.; Li, S. C.; Kim, S. Spectral probabilities of top-down tandem mass spectra BMC Genomics 2014, 15, S9 10.1186/1471-2164-15-S1-S9
17. Zamdborg, L.; LeDuc, R. D.; Glowacz, K. J.; Kim, Y.-B.; Viswanathan, V.; Spaulding, I. T.; Early, B. P.; Bluhm, E. J.; Babai, S.; Kelleher, N. L. ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry Nucleic Acids Res. 2007, 35, W701-W706 10.1093/nar/gkm371
18. Liu, X.; Mammana, A.; Bafna, V. Speeding up tandem mass spectral identification using indexes Bioinformatics 2012, 28, 1692-1697 10.1093/bioinformatics/bts244
19. Smith, L. D.; Kelleher, N. L.; Consortium for Top Down Proteomics et al. Proteoform: a single term describing protein complexity Nat. Methods 2013, 10, 186-187 10.1038/nmeth.2369
20. Han, X.; Wang, Y.; Aslanian, A.; Bern, M.; Lavallée-Adam, M., III; Yates, J. R. Sheathless Capillary Electrophoresis-Tandem Mass Spectrometry for Top-Down Characterization of Pyrococcus furiosus Proteins on a Proteome Scale Anal. Chem. 2014, 86, 11006-11012 10.1021/ac503439n
21. Borodovsky, M.; McIninch, J. GENMARK: Parallel gene recognition for both DNA strands Comput. Chem. 1993, 17, 123-133 10.1016/0097-8485(93)85004-V
22. Salzberg, S. L.; Delcher, A. L.; Kasif, S.; White, O. Microbial gene identification using interpolated Markov models Nucleic Acids Res. 1998, 26, 544-548 10.1093/nar/26.2.544
23. Bonissone, S.; Gupta, N.; Romine, M.; Bradshaw, R. A.; Pevzner, P. A. N-terminal Protein Processing: A Comparative Proteogenomic Analysis Mol. Cell. Proteomics 2013, 12, 14-28 10.1074/mcp.M112.019075
24. Williamson, M. P. The structure and function of proline-rich regions in proteins Biochem. J. 1994, 297, 249-260 10.1042/bj2970249
25. Elias, J. E.; Gygi, S. P. Target-Decoy Search Strategy for Mass Spectrometry-Based Proteomics Methods Mol. Biol. 2010, 604, 55-77 10.1007/978-1-60761-444-9-5
26. de Souza, G. A.; Malen, H.; Søfteland, T.; Sælensminde, G.; Prasad, S.; Jonassen, I.; Wiker, H. G. High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example BMC Genomics 2008, 9, 316 10.1186/1471-2164-9-316
27. Bakke, P.; Carney, N.; DeLoache, W.; Gearing, M.; Ingvorsen, K.; Lotz, M.; McNair, J.; Penumetcha, P.; Simpson, S.; Voss, L.; Win, M.; Heyer, L. J.; Campbell, A. M. Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis PLoS One 2009, 4, e6291 10.1371/journal.pone.0006291
28. Nielsen, P.; Krogh, A. Large-scale prokaryotic gene prediction and comparison to genome annotation Bioinformatics 2005, 21, 4322-4329 10.1093/bioinformatics/bti701
29. Jaffe, J. D.; Berg, H. C.; Church, G. M. Proteogenomic mapping as a complementary method to perform genome annotation Proteomics 2004, 4, 59-77 10.1002/pmic.200300511
30. Bland, C.; Hartmann, E. M.; Christie-Oleza, J. A.; Fernandez, B.; Armengaud, J. N-Terminal-oriented Proteogenomics of the Marine Bacterium Roseobacter Denitrificans Och114 using N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) Labeling and Diagonal Chromatography Mol. Cell. Proteomics 2014, 13, 1369-1381 10.1074/mcp.O113.032854
31. Bertaccini, D.; Vaca, S.; Carapito, C.; Arséne-Ploetze, F.; Van Dorsselaer, A.; Schaeffer-Reiss, C. An improved stable isotope N-terminal labeling approach with light/heavy TMPP to automate proteogenomics data validation: dN-TOP J. Proteome Res. 2013, 12, 3063-3070 10.1021/pr4002993