PGx: Putting Peptides to BED

Journal of Proteome Research

Volumn 15, Issue 3, 2016, Pages 795-799

  Askenazi, Manor ^a   Ruggles, Kelly V ^b   Fenyö, David ^b  

^a Biomedical Hosting LLC   (United States)

^b NEW YORK UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

proteogenomic mapping; proteogenomics; proteomics

Indexed keywords

PEPTIDE; TUMOR PROTEIN;

ARTICLE; DATA ANALYSIS SOFTWARE; GENOMICS; HUMAN; MASS SPECTROMETRY; NEXT GENERATION SEQUENCING; PEPTIDE MAPPING; PGX TOOL; PRIORITY JOURNAL; PROTEOMICS; GENE EXPRESSION PROFILING; GENETICS; PROCEDURES; PROTEIN DATABASE; SEQUENCE ANALYSIS;

DATABASES, PROTEIN; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; MASS SPECTROMETRY; NEOPLASM PROTEINS; PEPTIDE MAPPING; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN;

EID: 84960413025     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00870     Document Type: Article

References (28)

1. Nesvizhskii, A. I. Proteogenomics: concepts, applications and computational strategies Nat. Methods 2014, 11 (11) 1114-1125 10.1038/nmeth.3144
2. Risk, B. A.; Spitzer, W. J.; Giddings, M. C. Peppy: proteogenomic search software J. Proteome Res. 2013, 12 (6) 3019-3025 10.1021/pr400208w
3. Sanders, W. S.; Wang, N.; Bridges, S. M.; Malone, B. M.; Dandass, Y. S.; McCarthy, F. M.; Nanduri, B.; Lawrence, M. L.; Burgess, S. C. The proteogenomic mapping tool BMC Bioinf. 2011, 12, 115 10.1186/1471-2105-12-115
4. Ferro, M.; Tardif, M.; Reguer, E.; Cahuzac, R.; Bruley, C.; Vermat, T.; Nugues, E.; Vigouroux, M.; Vandenbrouck, Y.; Garin, J. et al. PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences J. Proteome Res. 2008, 7 (5) 1873-1883 10.1021/pr070415k
5. Kim, S.; Gupta, N.; Bandeira, N.; Pevzner, P. A. Spectral Dictionaries Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra Mol. Cell. Proteomics 2009, 8 (1) 53-69 10.1074/mcp.M800103-MCP200
6. Jeong, K.; Kim, S.; Bandeira, N.; Pevzner, P. A. Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra Mol. Cell. Proteomics 2011, 10 (6) M110.002220 10.1074/mcp.M110.002220
7. Menschaert, G.; Vandekerckhove, T. T. M.; Baggerman, G.; Landuyt, B.; Sweedler, J. V.; Schoofs, L.; Luyten, W.; Van Criekinge, W. A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome J. Proteome Res. 2010, 9 (2) 990-996 10.1021/pr900885k
8. Zickmann, F.; Renard, B. Y. MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms. Bioinforma Bioinformatics 2015, 31 (12) i106-i115 10.1093/bioinformatics/btv236
9. Ghali, F.; Krishna, R.; Perkins, S.; Collins, A.; Xia, D.; Wastling, J.; Jones, A. R. ProteoAnnotator-open source proteogenomics annotation software supporting PSI standards Proteomics 2014, 14 (23-24) 2731-2741 10.1002/pmic.201400265
10. Pang, C. N. I.; Tay, A. P.; Aya, C.; Twine, N. A.; Harkness, L.; Hart-Smith, G.; Chia, S. Z.; Chen, Z.; Deshpande, N. P.; Kaakoush, N. O. et al. Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing J. Proteome Res. 2014, 13 (1) 84-98 10.1021/pr400820p
11. Jagtap, P. D.; Johnson, J. E.; Onsongo, G.; Sadler, F. W.; Murray, K.; Wang, Y.; Shenykman, G. M.; Bandhakavi, S.; Smith, L. M.; Griffin, T. J. Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework J. Proteome Res. 2014, 13 (12) 5898-5908 10.1021/pr500812t
12. Askenazi, M.; Linial, M. Mass Informatics: From Mass Spectrometry Peaks to Biological Pathways Isr. J. Chem. 2013, 53 (3-4) 157-165 10.1002/ijch.201200076
13. Perkins, D. N.; Pappin, D. J. C.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20 (18) 3551-3567 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2
14. Eng, J. K.; McCormack, A. L.; Yates, J. R., III 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 (11) 976-989 10.1016/1044-0305(94)80016-2
15. Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra Bioinformatics 2004, 20 (9) 1466-1467 10.1093/bioinformatics/bth092
16. Raymond, E. S. The Art of UNIX Programming; Addison-Wesley Professional, 2003.
17. Thorvaldsdóttir, H.; Robinson, J. T.; Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration Briefings Bioinf. 2013, 14 (2) 178-192 10.1093/bib/bbs017
18. Rosenbloom, K. R.; Armstrong, J.; Barber, G. P.; Casper, J.; Clawson, H.; Diekhans, M.; Dreszer, T. R.; Fujita, P. A.; Guruvadoo, L.; Haeussler, M. et al. The UCSC Genome Browser database: 2015 update Nucleic Acids Res. 2015, 43 (D1) D670-D681 10.1093/nar/gku1177
19. Zhou, X.; Maricque, B.; Xie, M.; Li, D.; Sundaram, V.; Martin, E. A.; Koebbe, B. C.; Nielsen, C.; Hirst, M.; Farnham, P. et al. The Human Epigenome Browser at Washington University Nat. Methods 2011, 8 (12) 989-990 10.1038/nmeth.1772
20. Stalker, J.; Gibbins, B.; Meidl, P.; Smith, J.; Spooner, W.; Hotz, H.-R.; Cox, A. V. The Ensembl Web Site: Mechanics of a Genome Browser Genome Res. 2004, 14 (5) 951-955 10.1101/gr.1863004
21. Kim, D.; Pertea, G.; Trapnell, C.; Pimentel, H.; Kelley, R.; Salzberg, S. L. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biol. 2013, 14 (4) R36 10.1186/gb-2013-14-4-r36
22. Quinlan, A. R. BEDTools: The Swiss-Army Tool for Genome Feature Analysis Curr. Protoc. Bioinforma. Ed. Board Andreas Baxevanis Al 2014, 47, 11.12.1-11.12.34 10.1002/0471250953.bi1112s47
23. Li, J.; Su, Z.; Ma, Z.-Q.; Slebos, R. J. C.; Halvey, P.; Tabb, D. L.; Liebler, D. C.; Pao, W.; Zhang, B. A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics Mol. Cell. Proteomics 2011, 10 (5) M110.006536 10.1074/mcp.M110.006536
24. Wang, X.; Zhang, B. customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search Bioinformatics 2013, 29 (24) 3235-3237 10.1093/bioinformatics/btt543
25. Castellana, N. E.; Shen, Z.; He, Y.; Walley, J. W.; Cassidy, C. J.; Briggs, S. P.; Bafna, V. An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes in Zea mays Mol. Cell. Proteomics 2014, 13 (1) 157-167 10.1074/mcp.M113.031260
26. Askenazi, M.; Marto, J. A.; Linial, M. The complete peptide dictionary-A meta-proteomics resource Proteomics 2010, 10 (23) 4306-4310 10.1002/pmic.201000270
27. Pruitt, K. D.; Brown, G. R.; Hiatt, S. M.; Thibaud-Nissen, F.; Astashyn, A.; Ermolaeva, O.; Farrell, C. M.; Hart, J.; Landrum, M. J.; McGarvey, K. M. et al. RefSeq: an update on mammalian reference sequences Nucleic Acids Res. 2014, 42 (1) D756-D763 10.1093/nar/gkt1114
28. Schaefer, C.; Meier, A.; Rost, B.; Bromberg, Y. SNPdbe: constructing an nsSNP functional impacts database Bioinformatics 2012, 28 (4) 601-602 10.1093/bioinformatics/btr705