Proteogenomics from a bioinformatics angle: A growing field

Mass Spectrometry Reviews

Volumn 36, Issue 5, 2017, Pages 584-599

  Menschaert, Gerben ^a   Fenyö, David ^b  

^a GHENT UNIVERSITY   (Belgium)

^b NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

bioinformatics; gene annotation; mass spectrometry; next generation sequencing; proteoform; proteogenomics; ribosome profiling

Indexed keywords

BIOINFORMATICS; GENES; MACROMOLECULES; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PEPTIDES; SPECTROMETRY; THROUGHPUT;

GENE ANNOTATION; NEXT-GENERATION SEQUENCING; PROTEOFORM; PROTEOGENOMICS; RIBOSOME PROFILING;

PROTEINS;

ANTIBODY; PEPTIDE; VENOM;

ANIMAL; BIOLOGY; FACTUAL DATABASE; GENETICS; GENOMICS; MASS SPECTROMETRY; PEPTIDE MAPPING; PROCEDURES; PROTEOMICS; SEQUENCE ANALYSIS; SOFTWARE;

ANIMALS; ANTIBODIES; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; GENOMICS; MASS SPECTROMETRY; PEPTIDE MAPPING; PEPTIDES; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; VENOMS;

EID: 84950327482     PISSN: 02777037     EISSN: 10982787     Source Type: Journal    
DOI: 10.1002/mas.21483     Document Type: Review

References (170)

1. Alfaro JA, Sinha A, Kislinger T, Boutros PC. 2014. Onco-proteogenomics: Cancer proteomics joins forces with genomics. Nat Methods 11:1107–1113.
2. Aman JW, Imperial JS, Ueberheide B, Zhang MM, Aguilar M, Taylor D, Watkins M, Yoshikami D, Showers-Corneli P, Safavi-Hemami H, Biggs J, Teichert RW, Olivera BM. 2015. Insights into the origins of fish hunting in venomous cone snails from studies of Conus tessulatus. Proc Natl Acad Sci USA 112:5087–5092.
3. Amberger J, Bocchini CA, Scott AF, Hamosh A. 2009. Mckusick's online mendelian inheritance in man (OMIM). Nucl Acids Res 37:D793–D796.
4. Armengaud J, Hartmann EM, Bland C. 2013. Proteogenomics for environmental microbiology. Proteomics 13:2731–2742.
5. Armengaud J, Trapp J, Pible O, Geffard O, Chaumot A, Hartmann EM. 2014. Non-model organisms, a species endangered by proteogenomics. J Proteomics 105:5–18.
6. Aspden JL, Eyre-Walker YC, Phillips RJ, Amin U, Mumtaz MA, Brocard M, Couso JP. 2014. Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq. eLife 3:e035288.
7. Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S. 2008. Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320:938–941.
8. Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ, Mann M. 2015. Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation. Mol Cell Proteomics 14:658–673.
9. Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. 2014. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J 33:981–993.
10. Biass D, Violette A, Hulo N, Lisacek F, Favreau P, Stocklin R. 2015. Uncovering intense protein diversification in a cone snail venom gland using an integrative venomics approach. J Proteome Res 14:628–638.
11. Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R. 2009. QuickGO: A web-based tool for Gene Ontology searching. Bioinformatics 25:3045–3046.
12. Boekel J, Chilton JM, Cooke IR, Horvatovich PL, Jagtap PD, Kall L, Lehtio J, Lukasse P, Moerland PD, Griffin TJ. 2015. Multi-omic data analysis using Galaxy. Nat Biotechnol 33:137–139.
13. Brahma RK, McCleary RJ, Kini RM, Doley R. 2015. Venom gland transcriptomics for identifying, cataloging, and characterizing venom proteins in snakes. Toxicon 93:1–10.
14. Branca RM, Orre LM, Johansson HJ, Granholm V, Huss M, Perez-Bercoff A, Forshed J, Kall L, Lehtio J. 2014. HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nat Methods 11:59–62.
15. Brosch M, Saunders GI, Frankish A, Collins MO, Yu L, Wright J, Verstraten R, Adams DJ, Harrow J, Choudhary JS, Hubbard T. 2011. Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome. Genome Res 21:756–767.
16. Brouwer RW, van Hijum SA, Kuipers OP. 2009. MINOMICS: Visualizing prokaryote transcriptomics and proteomics data in a genomic context. Bioinformatics 25:139–140.
17. Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R. 2007. A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol 25:576–583.
18. Capriotti AL, Caruso G, Cavaliere C, Foglia P, Piovesana S, Samperi R, Lagana A. 2013. Proteome investigation of the non-model plant pomegranate (Punica granatum L.). Anal Bioanal Chem 405:9301–9309.
19. Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpizar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R. 2015. An open-source computational and data resource to analyze digital maps of immunopeptidomes. eLife 4:e07661.
20. Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. 2008. Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci USA 105:21034–21038.
21. Castellana NE, Pham V, Arnott D, Lill JR, Bafna V. 2010. Template proteogenomics: Sequencing whole proteins using an imperfect database. Mol Cell Proteomics 9:1260–1270.
22. Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V. 2014. An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. Mol Cell Proteomics 13:157–167.
23. Chaiyarit S, Singhto N, Chen YJ, Cheng CY, Chiangjong W, Kanlaya R, Lam HH, Peerapen P, Sung TY, Tipthara P, Pandey A, Poon TC, Chen YJ, Sirdeshmukh R, Chung MC, Thongboonkerd V. 2014. Chromosome-centric Human Proteome Project (C-HPP): Chromosome 12. J Proteome Res 13:3160–3165.
24. Choudhary JS, Blackstock WP, Creasy DM, Cottrell JS. 2001. Interrogating the human genome using uninterpreted mass spectrometry data. Proteomics 1:651–667.
25. Conlon KP, Basrur V, Rolland D, Wolfe T, Nesvizhskii AI, MacCoss MJ, Lim MS, Elenitoba-Johnson KS. 2013. Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer. Mol Cell Proteomics 12:2714–2723.
26. Consortium EP. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74.
27. Craig R, Beavis RC. 2004. TANDEM: Matching proteins with tandem mass spectra. Bioinformatics 20:1466–1467.
28. Craig R, Cortens JP, Beavis RC. 2004. Open source system for analyzing, validating, and storing protein identification data. J Proteome Res 3:1234–1242.
29. Crappe J, Van Criekinge W, Trooskens G, Hayakawa E, Luyten W, Baggerman G, Menschaert G. 2013. Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs. BMC Genomics 14:648.
30. Crappe J, Ndah E, Koch A, Steyaert S, Gawron D, De Keulenaer S, De Meester E, De Meyer T, Van Criekinge W, Van Damme P, Menschaert G. 2015. PROTEOFORMER: Deep proteome coverage through ribosome profiling and MS integration. Nucl Acids Res 43:e29.
31. Dasari S, Chambers MC, Slebos RJ, Zimmerman LJ, Ham AJ, Tabb DL. 2010. TagRecon: High-throughput mutation identification through sequence tagging. J Proteome Res 9:1716–1726.
32. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498.
33. Degroeve S, Martens L. 2013. MS2PIP: A tool for MS/MS peak intensity prediction. Bioinformatics 29:3199–3203.
34. Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. 2010. A guided tour of the Trans-Proteomic Pipeline. Proteomics 10:1150–1159.
35. de Souza GA, Arntzen MO, Wiker HG. 2010. MSMSpdbb: Providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes. Bioinformatics 26:698–699.
36. de Souza GA, Arntzen MO, Fortuin S, Schurch AC, Malen H, McEvoy CR, van Soolingen D, Thiede B, Warren RM, Wiker HG. 2011. Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database. Mol Cell Proteomics 10:M110 002527.
37. Diament BJ, Noble WS. 2011. Faster SEQUEST searching for peptide identification from tandem mass spectra. J Proteome Res 10:3871–3879.
38. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. 2013. STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21.
39. Dorfer V, Pichler P, Stranzl T, Stadlmann J, Taus T, Winkler S, Mechtler K. 2014. MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra. J Proteome Res 13:3679–3684.
40. Dutertre S, Jin AH, Kaas Q, Jones A, Alewood PF, Lewis RJ. 2013. Deep venomics reveals the mechanism for expanded peptide diversity in cone snail venom. Mol Cell Proteomics 12:312–329.
41. Edwards NJ. 2007. Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. Mol Syst Biol 3:102.
42. Eng JK, Jahan TA, Hoopmann MR. 2013. Comet: An open-source MS/MS sequence database search tool. Proteomics 13:22–24.
43. Evans VC, Barker G, Heesom KJ, Fan J, Bessant C, Matthews DA. 2012. De novo derivation of proteomes from transcriptomes for transcript and protein identification. Nat Methods 9:1207–1211.
44. Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ. 2006. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol 7:R35.
45. Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ. 2008. PepLine: A software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences. J Proteome Res 7:1873–1883.
46. Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ. 2014. Ensembl 2014. Nucl Acids Res 42:D749–D755.
47. Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, Kok CY, Jia M, De T, Teague JW, Stratton MR, McDermott U, Campbell PJ. 2015. COSMIC: Exploring the world's knowledge of somatic mutations in human cancer. Nucl Acids Res 43:D805–D811.
48. Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. 2013. STRING v9. 1: Protein-protein interaction networks, with increased coverage and integration. Nucl Acids Res 41:D808–D815.
49. Frank A, Pevzner P. 2005. PepNovo: De novo peptide sequencing via probabilistic network modeling. Anal Chem 77:964–973.
50. Frenkel-Morgenstern M, Gorohovski A, Vucenovic D, Maestre L, Valencia A. 2015. ChiTaRS 2. 1-an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts. Nucl Acids Res 43:D68–D75.
51. Fresno M, Jimenez A, Vazquez D. 1977. Inhibition of translation in eukaryotic systems by harringtonine. Eur J Biochem 72:323–330.
52. Fridy PC, Li Y, Keegan S, Thompson MK, Nudelman I, Scheid JF, Oeffinger M, Nussenzweig MC, Fenyo D, Chait BT, Rout MP. 2014. A robust pipeline for rapid production of versatile nanobody repertoires. Nat Methods 11:1253–1260.
53. Gao X, Wan J, Liu B, Ma M, Shen B, Qian SB. 2015. Quantitative profiling of initiating ribosomes in vivo. Nat Methods 12:147–153.
54. Gawron D, Gevaert K, Van Damme P. 2014. The proteome under translational control. Proteomics 14:2647–2662.
55. Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH. 2004. Open mass spectrometry search algorithm. J Proteome Res 3:958–964.
56. Ghali F, Krishna RF, Perkins SF, Collins AF, Xia D, Wastling J, Jones AR. 2014. ProteoAnnotator-open source proteogenomics annotation software supporting PSI standards. Proteomics 14:2731–2741.
57. Goecks J, Nekrutenko A, Taylor J, Galaxy T. 2010. Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11:R86.
58. Gonnelli G, Stock M, Verwaeren J, Maddelein D, De Baets B, Martens L, Degroeve S. 2015. A decoy-free approach to the identification of peptides. J Proteome Res 14:1792–1798.
59. Goode RJ, Yu S, Kannan A, Christiansen JH, Beitz A, Hancock WS, Nice E, Smith AI. 2013. The proteome browser web portal. J Proteome Res 12:172–178.
60. Granados DP, Sriranganadane D, Daouda T, Zieger A, Laumont CM, Caron-Lizotte O, Boucher G, Hardy MP, Gendron P, Cote C, Lemieux S, Thibault P, Perreault C. 2014. Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides. Nat Commun 5:3600.
61. Granados DP, Sriranganadane D, Daouda T, Zieger A, Laumont CM, Caron-Lizotte O, Boucher G, Hardy MP, Gendron P, Cote C, Lemieux S, Thibault P, Perreault C. 2010. UTRdb and UTRsite (RELEASE 2010): A collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucl Acids Res 38:D75–D80.
62. Gubin MM, Artyomov MN, Mardis ER, Schreiber RD. 2015. Tumor neoantigens: Building a framework for personalized cancer immunotherapy. J Clin Invest 125:3413–3421.
63. Han Y, Ma B, Zhang K. 2005. SPIDER: Software for protein identification from sequence tags with de novo sequencing error. J Bioinform Comput Biol 3:697–716.
64. Hartmann EM, Armengaud J. 2014. N-terminomics and proteogenomics, getting off to a good start. Proteomics 14:2637–2646.
65. Hartmann EM, Durighello E, Pible O, Nogales B, Beltrametti F, Bosch R, Christie-Oleza JA, Armengaud J. 2014. Proteomics meets blue biotechnology: A wealth of novelties and opportunities. Mar Genomics 17:35–42.
66. He T, Du P, Li Y. 2007. DbRES: A web-oriented database for annotated RNA editing sites. Nucl Acids Res 35:D141–D144.
67. Huang da W, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57.
68. Hunter AA, Macgregor AB, Szabo TO, Wellington CA, Bellgard MI. 2012. Yabi: An online research environment for grid, high performance and cloud computing. Source Code Biol Med 7:1.
69. Immel F, Renaut J, Masfaraud JF. 2012. Physiological response and differential leaf proteome pattern in the European invasive Asteraceae Solidago canadensis colonizing a former cokery soil. J Proteomics 75:1129–1143.
70. Ingolia NT, Lareau LF, Weissman JS. 2011. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147:789–802.
71. Ingolia NT, Brar GA, Stern-Ginossar N, Harris MS, Talhouarne GJ, Jackson SE, Wills MR, Weissman JS. 2014. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep 8:1365–1379.
72. Jaffe JD, Berg HC, Church GM. 2004. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 4:59–77.
73. Jagtap P, Bandhakavi S, Higgins L, McGowan T, Sa R, Stone MD, Chilton J, Arriaga EA, Seymour SL, Griffin TJ. 2012. Workflow for analysis of high mass accuracy salivary data set using MaxQuant and ProteinPilot search algorithm. Proteomics 12:1726–1730.
74. Jagtap P, Goslinga J, Kooren JA, McGowan T, Wroblewski MS, Seymour SL, Griffin TJ. 2013. A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies. Proteomics 13:1352–1357.
75. Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, Shenykman GM, Bandhakavi S, Smith LM, Griffin TJ. 2014. Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. J Proteome Res 13:5898–5908.
76. Jeong K, Kim S, Pevzner PA. 2013. UniNovo: A universal tool for de novo peptide sequencing. Bioinformatics 29:1953–1962.
77. Jeong SK, Lee HJ, Na K, Cho JY, Lee MJ, Kwon JY, Kim H, Park YM, Yoo JS, Hancock WS, Paik YK. 2013. GenomewidePDB, a proteomic database exploring the comprehensive protein parts list and transcriptome landscape in human chromosomes. J Proteome Res 12:106–111.
78. Junqueira M, Spirin V, Balbuena TS, Thomas H, Adzhubei I, Sunyaev S, Shevchenko A. 2008. Protein identification pipeline for the homology-driven proteomics. J Proteomics 71:346–356.
79. Kall L, Canterbury JD, Weston J, Noble WS, MacCoss MJ. 2007. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923–925.
80. Kayser JP, Vallet JL, Cerny RL. 2004. Defining parameters for homology-tolerant database searching. J Biomol Tech 15:285–295.
81. Khatun J, Yu Y, Wrobel JA, Risk BA, Gunawardena HP, Secrest A, Spitzer WJ, Xie L, Wang L, Chen X, Giddings MC. 2013. Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions. BMC Genomics 14:141.
82. Kim S, Pevzner PA. 2014. MS-GF+ makes progress towards a universal database search tool for proteomics. Nat Commun 5:5277.
83. Kim P, Yoon S, Kim N, Lee S, Ko M, Lee H, Kang H, Kim J, Lee S. 2010. ChimerDB 2.0—a knowledgebase for fusion genes updated. Nucl Acids Res 38:D81–D85.
84. Kiran AM, O'Mahony JJ, Sanjeev K, Baranov PV. 2013. Darned in 2013: Inclusion of model organisms and linking with Wikipedia. Nucl Acids Res 41:D258–D261.
85. Koch A, Gawron D, Steyaert S, Ndah E, Crappe J, De Keulenaer S, De Meester E, Ma M, Shen B, Gevaert K, Van Criekinge W, Van Damme P, Menschaert G. 2014. A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites. Proteomics 14:2688–2698.
86. Kodama Y, Shumway M, Leinonen R. 2012. International Nucleotide Sequence Database, C. The Sequence Read Archive: Explosive growth of sequencing data. Nucl Acids Res 40:D54–D56.
87. Kong F, Zhu J, Wu J, Peng J, Wang Y, Wang Q, Fu S, Yuan LL, Li T. 2011. DbCRID: A database of chromosomal rearrangements in human diseases. Nucl Acids Res 39:D895–D900.
88. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. Circos: An information aesthetic for comparative genomics. Genome Res 19:1639–1645.
89. Kuhring M, Renard BY. 2012. IPiG: Integrating peptide spectrum matches into genome browser visualizations. PloS ONE 7:e50246.
90. Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D. 2013. Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline. Mol Cell Proteomics 12:3388–3397.
91. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359.
92. Lee S, Liu B, Lee S, Huang SX, Shen B, Qian SB. 2012. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc Natl Acad Sci USA 109:E2424–E2432.
93. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760.
94. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079.
95. Li J, Duncan DT, Zhang B. 2010. CanProVar: A human cancer proteome variation database. Hum Mutat 31:219–228.
96. Li HD, Menon R, Omenn GS, Guan Y. 2014. Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence. Proteomics 14:2709–2718.
97. Lindenbaum P, Le Scouarnec S, Portero V, Redon R. 2011. Knime4Bio: A set of custom nodes for the interpretation of next-generation sequencing data with KNIME. Bioinformatics 27:3200–3201.
98. Liska AJ, Sunyaev S, Shilov IN, Schaeffer DA, Shevchenko A. 2005. Error-tolerant EST database searches by tandem mass spectrometry and multiTag software. Proteomics 5:4118–4122.
99. Liu S, Im H, Bairoch A, Cristofanilli M, Chen R, Deutsch EW, Dalton S, Fenyo D, Fanayan S, Gates C, Gaudet P, Hincapie M, Hanash S, Kim H, Jeong SK, Lundberg E, Mias G, Menon R, Mu Z, Nice E, Paik YK, Uhlen M, Wells L, Wu SL, Yan F, Zhang F, Zhang Y, Snyder M, Omenn GS, Beavis RC, Hancock WS. 2013. A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. J Proteome Res 12:45–57.
100. Luge T, Kube M, Freiwald A, Meierhofer D, Seemuller E, Sauer S. 2014. Transcriptomics assisted proteomic analysis of Nicotiana occidentalis infected by Candidatus Phytoplasma mali strain AT. Proteomics 14:1882–1889.
101. Ma K, Vitek O, Nesvizhskii AI. 2012. A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet. Bioinformatics 13:S1.
102. Ma J, Ward CC, Jungreis I, Slavoff SA, Schwaid AG, Neveu J, Budnik BA, Kellis M, Saghatelian A. 2014. Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue. J Proteome Res 13:1757–1765.
103. Margres MJ, McGivern JJ, Wray KP, Seavy M, Calvin K, Rokyta DR. 2014. Linking the transcriptome and proteome to characterize the venom of the eastern diamondback rattlesnake (Crotalus adamanteus). J Proteomics 96:145–158.
104. Mason ME, Koch JL, Krasowski M, Loo J. 2013. Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia). Proteome Sci 11:2.
105. Menschaert G, Vandekerckhove TT, Baggerman G, Landuyt B, Sweedler JV, Schoofs L, Luyten W, Van Criekinge W. 2010. A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome. J Proteome Res 9:990–996.
106. Menschaert G, Van Criekinge W, Notelaers T, Koch A, Crappe J, Gevaert K, Van Damme P. 2013. Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events. Mol Cell Proteomics 12:1780–1790.
107. Muellenbeck MF, Ueberheide B, Amulic B, Epp A, Fenyo D, Busse CE, Esen M, Theisen M, Mordmuller B, Wardemann H. 2013. Atypical and classical memory B cells produce Plasmodium falciparum neutralizing antibodies. J Exp Med 210:389–399.
108. Muth T, Weilnbock L, Rapp E, Huber CG, Martens L, Vaudel M, Barsnes H. 2014. DeNovoGUI: An open source graphical user interface for de novo sequencing of tandem mass spectra. J Proteome Res 13:1143–1146.
109. Nagaraj SH, Waddell N, Madugundu AK, Wood S, Jones A, Mandyam RA, Nones K, Pearson JV, Grimmond SM. 2015. PGTools: A software suite for proteogenomics data analysis and visualization. J Proteome Res 14: 2255–2266.
110. Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R. 2006. Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics 5:652–670.
111. Nesvizhskii AI. 2014. Proteogenomics: Concepts, applications and computational strategies. Nat Methods 11:1114–1125.
112. Olexiouk V, Crappé J, Verbruggen S, Verhegen K, Martens L, Menschaert G. 2015. sORFs.org: A repository of small ORFs identified by ribosome profiling. Nucleic Acids Res. doi: 10.1093/nar/gkv1175.
113. Omasits U, Ahrens CH, Muller S, Wollscheid B. 2014. Protter: Interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics 30:884–886.
114. Pandey A, Pevzner PA. 2014. Proteogenomic. Proteomics 14:2631–2632.
115. Park H, et al. 2014. Compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses. Proteomics 14:2742–2749.
116. Pawar H, Kulkarni A, Dixit T, Chaphekar D, Patole MS. 2014. A bioinformatics approach to reanalyze the genome annotation of kinetoplastid protozoan parasite Leishmania donovani. Genomics 104:554–561.
117. Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ. 2012. VESPA: Software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data. BMC Genomics 13:131.
118. Picardi E, D'Erchia AM, Montalvo A, Pesole G. 2015. Using REDItools to Detect RNA Editing Events in NGS Datasets. Current protocols in bioinformatics/editoral board, Andreas D. Baxevanis. [et al.] 49, 12 12 11-12 12 15.
119. Pineda SS, Undheim EA, Rupasinghe DB, Ikonomopoulou MP, King GF. 2014. Spider venomics: Implications for drug discovery. Future Med Chem 6:1699–1714.
120. Pinto SM, Manda SS, Kim MS, Taylor K, Selvan LD, Balakrishnan L, Subbannayya T, Yan F, Prasad TS, Gowda H, Lee C, Hancock WS, Pandey A. 2014. Functional annotation of proteome encoded by human chromosome 22. J Proteome Res 13:2749–2760.
121. Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, DiCuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. 2014. RefSeq: An update on mammalian reference sequences. Nucl Acids Res 42:D756–D763.
122. Risk BA, Spitzer WJ, Giddings MC. 2013. Peppy: Proteogenomic search software. J Proteome Res 12:3019–3025.
123. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. 2011. Integrative genomics viewer. Nat Biotechnol 29:24–26.
124. Safavi-Hemami H, Gajewiak J, Karanth S, Robinson SD, Ueberheide B, Douglass AD, Schlegel A, Imperial JS, Watkins M, Bandyopadhyay PK, Yandell M, Li Q, Purcell AW, Norton RS, Ellgaard L, Olivera BM. 2015. Specialized insulin is used for chemical warfare by fish-hunting cone snails. Proc Natl Acad Sci USA 112:1743–1748.
125. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. 2012. A travel guide to Cytoscape plugins. Nat Methods 9:1069–1076.
126. Sanders WS, Wang N, Bridges SM, Malone BM, Dandass YS, McCarthy FM, Nanduri B, Lawrence ML, Burgess SC. 2011. The proteogenomic mapping tool. Bioinformatics 12:115.
127. Scheid JF, Mouquet H, Ueberheide B, Diskin R, Klein F, Oliveira TY, Pietzsch J, Fenyo D, Abadir A, Velinzon K, Hurley A, Myung S, Boulad F, Poignard P, Burton DR, Pereyra F, Ho DD, Walker BD, Seaman MS, Bjorkman PJ, Chait BT, Nussenzweig MC. 2011. Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding. Science 333:1633–1637.
128. Schneider-Poetsch T, Ju J, Eyler DE, Dang Y, Bhat S, Merrick WC, Green R, Shen B, Liu JO. 2010. Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin. Nat Chem Biol 6:209–217.
129. Schumacher TN, Schreiber RD. 2015. Neoantigens in cancer immunotherapy. Science 348:69–74.
130. Shanmugam AK, Yocum AK, Nesvizhskii AI. 2014. Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS. J Proteome Res 13:4113–4119.
131. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. 2001. DbSNP: The NCBI database of genetic variation. Nucl Acids Res 29:308–311.
132. Shevchenko A, Sunyaev S, Liska A, Bork P, Shevchenko A. 2003. Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes. Methods Mol Biol 211:221–234.
133. Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, Onsongo G, Frey BL, Griffin TJ, Smith LM. 2014. Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations. BMC Genomics 15:703.
134. Silvester N, Alako B, Amid C, Cerdeno-Tarraga A, Cleland I, Gibson R, Goodgame N, Ten Hoopen P, Kay S, Leinonen R, Li W, Liu X, Lopez R, Pakseresht N, Pallreddy S, Plaister S, Radhakrishnan R, Rossello M, Senf A, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. 2015. Content discovery and retrieval services at the European Nucleotide Archive. Nucl Acids Res 43:D23–D29.
135. Slavoff SA, Mitchell AJ, Schwaid AG, Cabili MN, Ma J, Levin JZ, Karger AD, Budnik BA, Rinn JL, Saghatelian A. 2013. Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol 9:59–64.
136. Spivak M, Weston J, Bottou L, Kall L, Noble WS. 2009. Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets. J Proteome Res 8:3737–3745.
137. Staes A, Impens F, Van Damme P, Ruttens B, Goethals M, Demol H, Timmerman E, Vandekerckhove J, Gevaert K. 2011. Selecting protein N-terminal peptides by combined fractional diagonal chromatography. Nat Protoc 6:1130–1141.
138. Steijger T, Abril JF, Engstrom PG, Kokocinski F, Hubbard TJ, Guigo R, Harrow J, Bertone P, Consortium R. 2013. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 10:1177–1184.
139. Sun H, Chen C, Shi M, Wang D, Liu M, Li D, Yang P, Li Y, Xie L. 2014. Integration of mass spectrometry and RNA-Seq data to confirm human ab initio predicted genes and lncRNAs. Proteomics 14:2760–2768.
140. Tabb DL, Fernando CG, Chambers MC. 2007. MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res 6:654–661.
141. Tabb DL, Ma ZQ, Martin DB, Ham AJ, Chambers MC. 2008. DirecTag: Accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res 7:3838–3846.
142. Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V. 2005. InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem 77:4626–4639.
143. Tanner S, Shen Z, Ng J, Florea L, Guigo R, Briggs SP, Bafna V. 2007. Improving gene annotation using peptide mass spectrometry. Genome Res 17:231–239.
144. Thorvaldsdottir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Brief Bioinform 14:178–192.
145. Tovchigrechko A, Venepally P, Payne SH. 2014. PGP: Parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations. Bioinformatics 30:1469–1470.
146. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111.
147. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578.
148. Ucciferri N, Rocchiccioli S. 2014. Proteomics techniques for the detection of translated pseudogenes. Methods Mol Biol 1167:187–195.
149. Ueberheide BM, Fenyo D, Alewood PF, Chait BT. 2009. Rapid sensitive analysis of cysteine rich peptide venom components. Proc Natl Acad Sci USA 106:6910–6915.
150. UniProt C. 2014. Activities at the Universal Protein Resource (UniProt). Nucl Acids Res 42:D191–D198.
151. Uszkoreit J, Plohnke N, Rexroth S, Marcus K, Eisenacher M. 2014. The bacterial proteogenomic pipeline. BMC Genomics 15:S19.
152. Van Damme P, Gawron D, Van Criekinge W, Menschaert G. 2014. N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men. Mol Cell Proteomics 13:1245–1261.
153. Vanderperre B, Lucier JF, Roucou X. 2012. HAltORF: A database of predicted out-of-frame alternative open reading frames in human. Database (Oxford) 2012:bas025.
154. Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L. 2011. SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics 11:996–999.
155. Vaudel M, Burkhart JM, Zahedi RP, Oveland E, Berven FS, Sickmann A, Martens L, Barsnes H. 2015. PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nat Biotechnol 33:22–24.
156. Volders PJ, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P. 2015. An update on LNCipedia: A database for annotated human lncRNA sequences. Nucl Acids Res 43:D174–D180.
157. Volkening JD, Bailey DJ, Rose CM, Grimsrud PA, Howes-Podoll M, Venkateshwaran M, Westphall MS, Ane JM, Coon JJ, Sussman MR. 2012. A proteogenomic survey of the Medicago truncatula genome. Mol Cell Proteomics 11:933–944.
158. Wan J, Qian SB. 2014. TISdb: A database for alternative translation initiation in mammalian cells. Nucl Acids Res 42:D845–D850.
159. Wang X, Zhang B. 2013. CustomProDB: An R package to generate customized protein databases from RNA-Seq data for proteomics search. Bioinformatics 29:3235–3237.
160. Wang X, Liu Q, Zhang B. 2014. Leveraging the complementary nature of RNA-Seq and shotgun proteomics data. Proteomics 14:2676–2687.
161. Wen B, Xu S, Sheynkman GM, Feng Q, Lin L, Wang Q, Xu X, Wang J, Liu S. 2014. SapFinder: An R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments. Bioinformatics 30:3136–3138.
162. Wethmar K, Barbosa-Silva A, Andrade-Navarro MA, Leutz A. 2014. UORFdb-a comprehensive literature database on eukaryotic uORF biology. Nucl Acids Res 42:D60–D67.
163. Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S, Soiland-Reyes S, Dunlop I, Nenadic A, Fisher P, Bhagat J, Belhajjame K, Bacall F, Hardisty A, Nieva de la Hidalga A, Balcazar Vargas MP, Sufi S, Goble C. 2013. The Taverna workflow suite: Designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucl Acids Res 41:W557–W561.
164. Woo S, Cha SW, Na S, Guest C, Liu T, Smith RD, Rodland KD, Payne S, Bafna V. 2014. Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data. Proteomics 14:2719–2730.
165. Xie C, Yuan J, Li H, Li M, Zhao G, Bu D, Zhu W, Wu W, Chen R, Zhao Y. 2014. NONCODEv4: Exploring the world of long non-coding RNA genes. Nucl Acids Res 42:D98–103.
166. Yadav M, Jhunjhunwala S, Phung QT, Lupardus P, Tanguay J, Bumbaca S, Franci C, Cheung TK, Fritsche J, Weinschenk T, Modrusan Z, Mellman I, Lill JR, Delamarre L. 2014. Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing. Nature 515:572–576.
167. Yang S, Zhang X, Diao H, Guo F, Wang D, Liu Z, Li H, Zheng J, Pan J, Nice EC, Li D, He F. 2015. CAPER 3.0: A scalable cloud-based system for data-intensive analysis of Chromosome-centric Human Proteome Project datasets. J Proteome Res 14:3720–3728.
168. Zhang Q, Xiao X. 2015. Genome sequence-independent identification of RNA editing sites. Nat Methods 12:347–350.
169. Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC, Nci C. 2014. Proteogenomic characterization of human colon and rectal cancer. Nature 513:382–387.
170. Zhang C, Xu P, Zhu Y. 2014. [Progress in proteogenomics of prokaryotes]. Sheng wu gong cheng xue bao = Chin J Biotechnol 30:1026–1035.