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Proteomics of nonmodel plant species

Bibliographic reference Champagne, Antoine ; Boutry, Marc. Proteomics of nonmodel plant species. In: Proteomics, Vol. 13, no. 3-4, p. 663-673 (February 2013)
Permanent URL http://hdl.handle.net/2078/120957
  1. The Arabidopsis Genome Initiative, 10.1038/35048692
  2. Cook Douglas R, Medicago truncatula — a model in the making!, 10.1016/s1369-5266(99)80053-3
  3. Heijden Robert, Jacobs Denise, Snoeijer Wim, Hallard Didier, Verpoorte Robert, The Catharanthus Alkaloids:Pharmacognosy and Biotechnology, 10.2174/0929867043455846
  4. Tissier Alain, Glandular trichomes: what comes after expressed sequence tags? : Glandular trichomes: what comes after ESTs?, 10.1111/j.1365-313x.2012.04913.x
  5. Bak Søren, Beisson Fred, Bishop Gerard, Hamberger Björn, Höfer René, Paquette Suzanne, Werck-Reichhart Danièle, Cytochromes P450, 10.1199/tab.0144
  6. Goff S. A., A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica), 10.1126/science.1068275
  7. Yu J., A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica), 10.1126/science.1068037
  8. Yu Jun, Wang Jun, Lin Wei, Li Songgang, Li Heng, Zhou Jun, Ni Peixiang, Dong Wei, Hu Songnian, Zeng Changqing, Zhang Jianguo, Zhang Yong, Li Ruiqiang, Xu Zuyuan, Li Shengting, Li Xianran, Zheng Hongkun, Cong Lijuan, Lin Liang, Yin Jianning, Geng Jianing, Li Guangyuan, Shi Jianping, Liu Juan, Lv Hong, Li Jun, Wang Jing, Deng Yajun, Ran Longhua, Shi Xiaoli, Wang Xiyin, Wu Qingfa, Li Changfeng, Ren Xiaoyu, Wang Jingqiang, Wang Xiaoling, Li Dawei, Liu Dongyuan, Zhang Xiaowei, Ji Zhendong, Zhao Wenming, Sun Yongqiao, Zhang Zhenpeng, Bao Jingyue, Han Yujun, Dong Lingli, Ji Jia, Chen Peng, Wu Shuming, Liu Jinsong, Xiao Ying, Bu Dongbo, Tan Jianlong, Yang Li, Ye Chen, Zhang Jingfen, Xu Jingyi, Zhou Yan, Yu Yingpu, Zhang Bing, Zhuang Shulin, Wei Haibin, Liu Bin, Lei Meng, Yu Hong, Li Yuanzhe, Xu Hao, Wei Shulin, He Ximiao, Fang Lijun, Zhang Zengjin, Zhang Yunze, Huang Xiangang, Su Zhixi, Tong Wei, Li Jinhong, Tong Zongzhong, Li Shuangli, Ye Jia, Wang Lishun, Fang Lin, Lei Tingting, Chen Chen, Chen Huan, Xu Zhao, Li Haihong, Huang Haiyan, Zhang Feng, Xu Huayong, Li Na, Zhao Caifeng, Li Shuting, Dong Lijun, Huang Yanqing, Li Long, Xi Yan, Qi Qiuhui, Li Wenjie, Zhang Bo, Hu Wei, Zhang Yanling, Tian Xiangjun, Jiao Yongzhi, Liang Xiaohu, Jin Jiao, Gao Lei, Zheng Weimou, Hao Bailin, Liu Siqi, Wang Wen, Yuan Longping, Cao Mengliang, McDermott Jason, Samudrala Ram, Wang Jian, Wong Gane Ka-Shu, Yang Huanming, The Genomes of Oryza sativa: A History of Duplications, 10.1371/journal.pbio.0030038
  9. Sequencing Project International Rice Genome , The map-based sequence of the rice genome, 10.1038/nature03895
  10. Strickler S. R., Bombarely A., Mueller L. A., Designing a transcriptome next-generation sequencing project for a nonmodel plant species1, 10.3732/ajb.1100292
  11. Ward J. A., Ponnala L., Weber C. A., Strategies for transcriptome analysis in nonmodel plants, 10.3732/ajb.1100334
  12. Lopez-Casado Gloria, Covey Paul A., Bedinger Patricia A., Mueller Lukas A., Thannhauser Theodore W., Zhang Sheng, Fei Zhangjun, Giovannoni James J., Rose Jocelyn K. C., Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case, 10.1002/pmic.201100164
  13. Renuse Santosh, Chaerkady Raghothama, Pandey Akhilesh, Proteogenomics, 10.1002/pmic.201000615
  14. Liska Adam J., Shevchenko Andrej, Expanding the organismal scope of proteomics: Cross-species protein identification by mass spectrometry and its implications, 10.1002/pmic.200390004
  15. Wright J. C., Beynon R. J., Hubbard S. J., Cross Species Proteomics, Methods in Molecular Biology (2010) ISBN:9781607614432 p.123-135, 10.1007/978-1-60761-444-9_9
  16. Witters Erwin, Laukens Kris, Deckers Peter, Dongen Walter Van, Esmans Eddy, Onckelen Harry Van, Fast liquid chromatography coupled to electrospray tandem mass spectrometry peptide sequencing for cross-species protein identification, 10.1002/rcm.1173
  17. Huang Mei, Chen Tong, Chan ZhuLong, An evaluation for cross-species proteomics research by publicly available expressed sequence tag database search using tandem mass spectral data, 10.1002/rcm.2631
  18. Bräutigam Andrea, Shrestha Roshan P., Whitten Doug, Wilkerson Curtis G., Carr Kevin M., Froehlich John E., Weber Andreas P.M., Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: Comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes, 10.1016/j.jbiotec.2008.02.007
  19. Gan Xiangchao, Stegle Oliver, Behr Jonas, Steffen Joshua G., Drewe Philipp, Hildebrand Katie L., Lyngsoe Rune, Schultheiss Sebastian J., Osborne Edward J., Sreedharan Vipin T., Kahles André, Bohnert Regina, Jean Géraldine, Derwent Paul, Kersey Paul, Belfield Eric J., Harberd Nicholas P., Kemen Eric, Toomajian Christopher, Kover Paula X., Clark Richard M., Rätsch Gunnar, Mott Richard, Multiple reference genomes and transcriptomes for Arabidopsis thaliana, 10.1038/nature10414
  20. Champagne Antoine, Rischer Heiko, Oksman-Caldentey Kirsi-Marja, Boutry Marc, In-depth proteome mining of culturedCatharanthus roseuscells identifies candidate proteins involved in the synthesis and transport of secondary metabolites, 10.1002/pmic.201200218
  21. Habermann Bianca, Oegema Jeffrey, Sunyaev Shamil, Shevchenko Andrej, The Power and the Limitations of Cross-Species Protein Identification by Mass Spectrometry-driven Sequence Similarity Searches, 10.1074/mcp.m300073-mcp200
  22. Junqueira Magno, Spirin Victor, Santana Balbuena Tiago, Waridel Patrice, Surendranath Vineeth, Kryukov Grigoriy, Adzhubei Ivan, Thomas Henrik, Sunyaev Shamil, Shevchenko Andrej, Separating the Wheat from the Chaff: Unbiased Filtering of Background Tandem Mass Spectra Improves Protein Identification, 10.1021/pr800140v
  23. Bern M., Goldberg D., McDonald W. H., Yates J. R., Automatic Quality Assessment of Peptide Tandem Mass Spectra, 10.1093/bioinformatics/bth947
  24. Savitski Mikhail M., Nielsen Michael L., Zubarev Roman A., New Data Base-independent, Sequence Tag-based Scoring of Peptide MS/MS Data Validates Mowse Scores, Recovers Below Threshold Data, Singles Out Modified Peptides, and Assesses the Quality of MS/MS Techniques, 10.1074/mcp.t500009-mcp200
  25. Shevchenko Andrej, Valcu Cristina-Maria, Junqueira Magno, Tools for exploring the proteomosphere, 10.1016/j.jprot.2009.01.012
  26. Allmer Jens, Algorithms for thede novosequencing of peptides from tandem mass spectra, 10.1586/epr.11.54
  27. Hughes Christopher, Ma Bin, Lajoie Gilles A., De Novo Sequencing Methods in Proteomics, Methods in Molecular Biology (2010) ISBN:9781607614432 p.105-121, 10.1007/978-1-60761-444-9_8
  28. Seidler Joerg, Zinn Nico, Boehm Martin E., Lehmann Wolf D., De novosequencing of peptides by MS/MS, 10.1002/pmic.200900459
  29. Granvogl Bernhard, Reisinger Veronika, Eichacker Lutz Andreas, Mapping the proteome of thylakoid membranes byde novo sequencing of intermembrane peptide domains, 10.1002/pmic.200500924
  30. Jorge Inmaculada, Navarro Rafael M., Lenz Christof, Ariza David, Porras Carlos, Jorrín Jesús, The Holm Oak leaf proteome: Analytical and biological variability in the protein expression level assessed by 2-DE and protein identification tandem mass spectrometryde novosequencing and sequence similarity searching, 10.1002/pmic.200400893
  31. Liska Adam J., Shevchenko Andrej, Combining mass spectrometry with database interrogation strategies in proteomics, 10.1016/s0165-9936(03)00507-7
  32. Liska A. J., Enhanced Photosynthesis and Redox Energy Production Contribute to Salinity Tolerance in Dunaliella as Revealed by Homology-Based Proteomics, 10.1104/pp.104.039438
  33. Samyn Bart, Sergeant Kjell, Carpentier Sebastien, Debyser Griet, Panis Bart, Swennen Rony, Van Beeumen Jozef, Functional Proteome Analysis of the Banana Plant (Musaspp.) UsingdeNovoSequence Analysis of Derivatized Peptides, 10.1021/pr0601943
  34. Shevchenko Andrej, Sunyaev Shamil, Loboda Alexander, Shevchenko Anna, Bork Peer, Ens Werner, Standing Kenneth G., Charting the Proteomes of Organisms with Unsequenced Genomes by MALDI-Quadrupole Time-of-Flight Mass Spectrometry and BLAST Homology Searching, 10.1021/ac0013709
  35. Mackey Aaron J., Haystead Timothy A. J., Pearson William R., Getting More from Less : Algorithms for Rapid Protein Identification with Multiple Short Peptide Sequences, 10.1074/mcp.m100004-mcp200
  36. Thomas Henrik, Shevchenko Andrej, Simplified validation of borderline hits of database searches, 10.1002/pmic.200800250
  37. Wielsch Natalie, Thomas Henrik, Surendranath Vineeth, Waridel Patrice, Frank Ari, Pevzner Pavel, Shevchenko Andrej, Rapid Validation of Protein Identifications with the Borderline Statistical Confidence via De Novo Sequencing and MS BLAST Searches, 10.1021/pr060200v
  38. Grossmann Jonas, Fischer Bernd, Baerenfaller Katja, Owiti Judith, Buhmann Joachim M., Gruissem Wilhelm, Baginsky Sacha, A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments, 10.1002/pmic.200700474
  39. Vertommen A., Møller A.L.B., Cordewener J.H.G., Swennen R., Panis B., Finnie C., America A.H.P., Carpentier S.C., A workflow for peptide-based proteomics in a poorly sequenced plant: A case study on the plasma membrane proteome of banana, 10.1016/j.jprot.2011.02.008
  40. Waridel Patrice, Frank Ari, Thomas Henrik, Surendranath Vineeth, Sunyaev Shamil, Pevzner Pavel, Shevchenko Andrej, Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automatedde novo sequencing, 10.1002/pmic.200700003
  41. Ståhl Patrik L., Lundeberg Joakim, Toward the Single-Hour High-Quality Genome, 10.1146/annurev-biochem-060410-094158
  42. Henson Joseph, Tischler German, Ning Zemin, Next-generation sequencing and large genome assemblies, 10.2217/pgs.12.72
  43. Hamilton John P., Robin Buell C., Advances in plant genome sequencing : Advances in plant genome sequencing, 10.1111/j.1365-313x.2012.04894.x
  44. Schneider Grégory F, Dekker Cees, DNA sequencing with nanopores, 10.1038/nbt.2181
  45. Schilmiller A. L., Miner D. P., Larson M., McDowell E., Gang D. R., Wilkerson C., Last R. L., Studies of a Biochemical Factory: Tomato Trichome Deep Expressed Sequence Tag Sequencing and Proteomics, 10.1104/pp.110.157214
  46. Castellana N. E., Payne S. H., Shen Z., Stanke M., Bafna V., Briggs S. P., Discovery and revision of Arabidopsis genes by proteogenomics, 10.1073/pnas.0811066106
  47. Helmy Mohamed, Tomita Masaru, Ishihama Yasushi, OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics, 10.1186/1471-2229-11-63
  48. Baerenfaller K., Grossmann J., Grobei M. A., Hull R., Hirsch-Hoffmann M., Yalovsky S., Zimmermann P., Grossniklaus U., Gruissem W., Baginsky S., Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics, 10.1126/science.1157956
  49. Grobei M. A., Qeli E., Brunner E., Rehrauer H., Zhang R., Roschitzki B., Basler K., Ahrens C. H., Grossniklaus U., Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function, 10.1101/gr.089060.108
  50. Galperin Michael Y., Koonin Eugene V., From complete genome sequence to ‘complete’ understanding?, 10.1016/j.tibtech.2010.05.006
  51. Van Cutsem Emmanuel, Simonart Géraldine, Degand Hervé, Faber Anne-Marie, Morsomme Pierre, Boutry Marc, Gel-based and gel-free proteomic analysis of Nicotiana tabacum trichomes identifies proteins involved in secondary metabolism and in the (a)biotic stress response, 10.1002/pmic.201000356
  52. Haynes Paul A., Roberts Thomas H., Subcellular shotgun proteomics in plants: Looking beyond the usual suspects, 10.1002/pmic.200700216
  53. Lee Yie Hou, Tan Hwee Tong, Chung Maxey C. M., Subcellular fractionation methods and strategies for proteomics, 10.1002/pmic.201000289
  54. Agrawal Ganesh Kumar, Jwa Nam-Soo, Lebrun Marc-Henri, Job Dominique, Rakwal Randeep, Plant secretome: Unlocking secrets of the secreted proteins, 10.1002/pmic.200900514
  55. Hanton Sally L., Bortolotti Lauren E., Renna Luciana, Stefano Giovanni, Brandizzi Federica, Crossing the Divide - Transport Between the Endoplasmic Reticulum and Golgi Apparatus in Plants : Protein Traffic at the Plant ER-Golgi Interface, 10.1111/j.1600-0854.2005.00278.x
  56. Hicks Glenn R, Raikhel Natasha V, Advances in dissecting endomembrane trafficking with small molecules, 10.1016/j.pbi.2010.08.008
  57. Ly Linda, Wasinger Valerie C., Protein and peptide fractionation, enrichment and depletion: Tools for the complex proteome, 10.1002/pmic.201000394
  58. Yates John R., Ruse Cristian I., Nakorchevsky Aleksey, Proteomics by Mass Spectrometry: Approaches, Advances, and Applications, 10.1146/annurev-bioeng-061008-124934
  59. Chevalier François, Highlights on the capacities of "Gel-based" proteomics, 10.1186/1477-5956-8-23
  60. Malerod Helle, Lundanes Elsa, Greibrokk Tyge, Recent advances in on-line multidimensional liquid chromatography, 10.1039/b9ay00194h
  61. Carpentier Sebastien Christian, Panis Bart, Vertommen Annelies, Swennen Rony, Sergeant Kjell, Renaut Jenny, Laukens Kris, Witters Erwin, Samyn Bart, Devreese Bart, Proteome analysis of non-model plants: A challenging but powerful approach, 10.1002/mas.20170
  62. Remmerie Noor, De Vijlder Thomas, Laukens Kris, Dang Thanh Hai, Lemière Filip, Mertens Inge, Valkenborg Dirk, Blust Ronny, Witters Erwin, Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications, 10.1016/j.phytochem.2011.01.003
  63. Vestal Marvin L., The Future of Biological Mass Spectrometry, 10.1007/s13361-011-0108-x
  64. Yang, J. Biomol. Tech., 18, 226 (2007)
  65. Angel Thomas E., Aryal Uma K., Hengel Shawna M., Baker Erin S., Kelly Ryan T., Robinson Errol W., Smith Richard D., Mass spectrometry-based proteomics: existing capabilities and future directions, 10.1039/c2cs15331a
  66. Han Xuemei, Aslanian Aaron, Yates John R, Mass spectrometry for proteomics, 10.1016/j.cbpa.2008.07.024