Large-scale quantification of single amino-acid variations by a variation-associated database search strategy

Journal of Proteome Research

Volumn 13, Issue 1, 2014, Pages 241-248

  Song, Chunxia ^a,b   Wang, Fangjun ^a   Cheng, Kai ^a   Wei, Xiaoluan ^a   Bian, Yangyang ^a   Wang, Keyun ^a   Tan, Yexiong ^c   Wang, Hongyang ^c   Ye, Mingliang ^a   Zou, Hanfa ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b RESEARCH INSTITUTE OF PETROLEUM PROCESSING   (China)

^c SECOND MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

liver cancer; proteomics; quantification; single amino acid variations

Indexed keywords

AMINO ACID; PEPTIDE; STABLE ISOTOPE;

AMINO ACID SEQUENCE; ARTICLE; CANCER GROWTH; CHROMOSOME 1; CHROMOSOME 20; CHROMOSOME 8; CHRONIC HEPATITIS; COLLISIONALLY ACTIVATED DISSOCIATION; COMPARATIVE STUDY; CONTROLLED STUDY; ENERGY; HUMAN; HUMAN TISSUE; ISOTOPE LABELING; LIVER CELL CARCINOMA; LIVER CIRRHOSIS; LIVER VENOOCCLUSIVE DISEASE; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN EXPRESSION; PROTEOMICS; PULMONARY HYPERTENSION; REVERSED PHASE LIQUID CHROMATOGRAPHY; TANDEM MASS SPECTROMETRY;

AMINO ACIDS; CARCINOMA, HEPATOCELLULAR; DATABASES, PROTEIN; HUMANS; LIVER NEOPLASMS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 84891810621     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400544j     Document Type: Article

References (42)

1. Thusberg, J.; Vihinen, M. Pathogenic or Not? And If So, Then How? Studying the effects of missense mutations using bioinformatics methods Hum. Mutat. 2009, 30 (5) 703-714
2. Su, Z. D.; Sun, L.; Yu, D. X.; Li, R. X.; Li, H. X.; Yu, Z. J.; Sheng, Q. H.; Lin, X.; Zeng, R.; Wu, J. R. Quantitative detection of single amino acid polymorphisms by targeted proteomics J. Mol. Cell Biol. 2011, 3 (5) 309-315
3. Grasbon-Frodl, E.; Lorenz, H.; Mann, U.; Nitsch, R. M.; Windl, O.; Kretzschmar, H. A. Loss of glycosylation associated with the T183A mutation in human prion disease Acta Neuropathol. 2004, 108 (6) 476-484
4. Scott, L. J.; Mohlke, K. L.; Bonnycastle, L. L.; Willer, C. J.; Li, Y.; Duren, W. L.; Erdos, M. R.; Stringham, H. M.; Chines, P. S.; Jackson, A. U.; Prokunina-Olsson, L.; Ding, C. J.; Swift, A. J.; Narisu, N.; Hu, T.; Pruim, R.; Xiao, R.; Li, X. Y.; Conneely, K. N.; Riebow, N. L.; Sprau, A. G.; Tong, M.; White, P. P.; Hetrick, K. N.; Barnhart, M. W.; Bark, C. W.; Goldstein, J. L.; Watkins, L.; Xiang, F.; Saramies, J.; Buchanan, T. A.; Watanabe, R. M.; Valle, T. T.; Kinnunen, L.; Abecasis, G. R.; Pugh, E. W.; Doheny, K. F.; Bergman, R. N.; Tuomilehto, J.; Collins, F. S.; Boehnke, M. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants Science 2007, 316 (5829) 1341-1345
5. Zhang, H. X.; Zhai, Y.; Hu, Z. B.; Wu, C.; Qian, J.; Jia, W. H.; Ma, F. C.; Huang, W. F.; Yu, L. X.; Yue, W.; Wang, Z. F.; Li, P. Y.; Zhang, Y.; Liang, R. X.; Wei, Z. L.; Cui, Y.; Xie, W. M.; Cai, M.; Yu, X. S.; Yuan, Y. F.; Xia, X.; Zhang, X. M.; Yang, H.; Qiu, W.; Yang, J. M.; Gong, F.; Chen, M. S.; Shen, H. B.; Lin, D. X.; Zeng, Y. X.; He, F. C.; Zhou, G. Q. Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular carcinoma in chronic hepatitis B virus carriers Nat. Genet. 2010, 42 (9) 755-U39
6. Wu, J. R.; Zeng, R. Molecular basis for population variation: From SNPs to SAPs FEBS Lett. 2012, 586 (18) 2841-2845
7. Schandorff, S.; Olsen, J. V.; Bunkenborg, J.; Blagoev, B.; Zhang, Y.; Andersen, J. S.; Mann, M. A mass spectrometry-friendly database for cSNP identification Nat. Methods 2007, 4 (6) 465-466
8. Bunger, M. K.; Cargile, B. J.; Sevinsky, J. R.; Deyanova, E.; Yates, N. A.; Hendrickson, R. C.; Stephenson, J. L. Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data J. Proteome Res. 2007, 6 (6) 2331-2340
9. Li, J.; Su, Z. L.; 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
10. Jaenisch, R.; Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals Nat. Genet. 2003, 33, 245-254
11. Tuch, B. B.; Laborde, R. R.; Xu, X.; Gu, J.; Chung, C. B.; Monighetti, C. K.; Stanley, S. J.; Olsen, K. D.; Kasperbauer, J. L.; Moore, E. J.; Broomer, A. J.; Tan, R. Y.; Brzoska, P. M.; Muller, M. W.; Siddiqui, A. S.; Asmann, Y. W.; Sun, Y. M.; Kuersten, S.; Barker, M. A.; De La Vega, F. M.; Smith, D. I. Tumor Transcriptome Sequencing Reveals Allelic Expression Imbalances Associated with Copy Number Alterations. PLoS One 2010, 5 (2).
12. Wang, Q.; Chaerkady, R.; Wu, J. A.; Hwang, H. J.; Papadopoulos, N.; Kopelovich, L.; Maitra, A.; Matthaei, H.; Eshleman, J. R.; Hruban, R. H.; Kinzler, K. W.; Pandey, A.; Vogelstein, B. Mutant proteins as cancer-specific biomarkers Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (6) 2444-2449
13. Taniguchi, Y.; Choi, P. J.; Li, G. W.; Chen, H. Y.; Babu, M.; Hearn, J.; Emili, A.; Xie, X. S. Quantifying E-coli proteome and transcriptome with single-molecule sensitivity in single cells Science 2010, 329 (5991) 533-538
14. Gry, M.; Rimini, R.; Strömberg, S.; Asplund, A.; Pontén, F.; Uhlén, M.; Nilsson, P. Correlations between RNA and protein expression profiles in 23 human cell lines BMC Genomics 2009, 10 (1) 365
15. Song, C. X.; Wang, F. J.; Ye, M. L.; Cheng, K.; Chen, R.; Zhu, J.; Tan, Y. X.; Wang, H. Y.; Figeys, D.; Zou, H. F. Improvement of the quantification accuracy and throughput for phosphoproteome analysis by a pseudo triplex stable isotope dimethyl labeling approach Anal. Chem. 2011, 83 (20) 7755-7762
16. Song, C. X.; Ye, M. L.; Han, G. H.; Jiang, X. N.; Wang, F. J.; Yu, Z. Y.; Chen, R.; Zou, H. F. Reversed-phase-reversed-phase liquid chromatography approach with high orthogonality for multidimensional separation of phosphopeptides Anal. Chem. 2010, 82 (1) 53-56
17. Wang, F. J.; Chen, R.; Zhu, J.; Sun, D. G.; Song, C. X.; Wu, Y. F.; Ye, M. L.; Wang, L. M.; Zou, H. F. A fully automated system with online sample loading, isotope dimethyl labeling and multidimensional separation for high-throughput quantitative proteome analysis Anal. Chem. 2010, 82 (7) 3007-3015
18. Wu, C. H.; Apweiler, R.; Bairoch, A.; Natale, D. A.; Barker, W. C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R. The Universal Protein Resource (UniProt): an expanding universe of protein information Nucleic Acids Res. 2006, 34 (suppl 1) D187-D191
19. Cox, J.; Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Nat. Biotechnol. 2008, 26 (12) 1367-1372
20. Cox, J.; Neuhauser, N.; Michalski, A.; Scheltema, R. A.; Olsen, J. V.; Mann, M. Andromeda: A peptide search engine integrated into the MaxQuant environment J. Proteome Res. 2011, 10 (4) 1794-1805
21. Li, J.; Duncan, D. T.; Zhang, B. CanProVar: A human cancer proteome variation database Hum. Mutat. 2010, 31 (3) 219-228
22. Frese, C. K.; Altelaar, A. F. M.; Hennrich, M. L.; Nolting, D.; Zeller, M.; Griep-Raming, J.; Heck, A. J. R.; Mohammed, S. Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap velos J. Proteome Res. 2011, 10 (5) 2377-2388
23. Nagaraj, N.; D'Souza, R. C. J.; Cox, J.; Olsen, J. V.; Mann, M. Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation J. Proteome Res. 2010, 9 (12) 6786-6794
24. Olsen, J. V.; Schwartz, J. C.; Griep-Raming, J.; Nielsen, M. L.; Damoc, E.; Denisov, E.; Lange, O.; Remes, P.; Taylor, D.; Splendore, M.; Wouters, E. R.; Senko, M.; Makarov, A.; Mann, M.; Horning, S. A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed Mol. Cell. Proteomics 2009, 8 (12) 2759-2769
25. Abraham, P.; Adams, R.; Giannone, R. J.; Kalluri, U.; Ranjan, P.; Erickson, B.; Shah, M.; Tuskan, G. A.; Hettich, R. L. Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of populus using shotgun proteomics J. Proteome Res. 2012, 11 (1) 449-460
26. He, F. C. Human liver proteome project: plan, progress, and perspectives Mol. Cell. Proteomics 2005, 4 (12) 1841-1848
27. Elchuri, S.; Oberley, T. D.; Qi, W. B.; Eisenstein, R. S.; Roberts, L. J.; Van Remmen, H.; Jepstein, C. J.; Huang, T. T. CuZnSOD deficiency leads to persistent and widespread oxidative damage and hepatocarcinogenesis later in life Oncogene 2005, 24 (3) 367-380
28. Jiang, C.; Pecha, J.; Hoshino, I.; Ankrapp, D.; Xiao, H. TIP30 mutant derived from hepatocellular carcinoma specimens promotes growth of HepG2 cells through up-regulation of n-cadherin Cancer Res. 2007, 67 (8) 3574-3582
29. Guichard, C.; Amaddeo, G.; Imbeaud, S.; Ladeiro, Y.; Pelletier, L.; Ben Maad, I.; Calderaro, J.; Bioulac-Sage, P.; Letexier, M.; Degos, F.; Clement, B.; Balabaud, C.; Chevet, E.; Laurent, A.; Couchy, G.; Letouze, E.; Calvo, F.; Zucman-Rossi, J. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma Nat. Genet. 2012, 44 (6) 694-U120
30. Tao, Y.; Ruan, J.; Yeh, S. H.; Lu, X. M.; Wang, Y.; Zhai, W. W.; Cai, J.; Ling, S. P.; Gong, Q.; Chong, Z. C.; Qu, Z. Z.; Li, Q. Q.; Liu, J.; Yang, J.; Zheng, C. H.; Zeng, C. Q.; Wang, H. Y.; Zhang, J.; Wang, S. H.; Hao, L. T.; Dong, L. L.; Li, W. J.; Sun, M.; Zou, W.; Yu, C. X.; Li, C. H.; Liu, G. J.; Jiang, L.; Xu, J.; Huang, H. W.; Li, C. Y.; Mi, S. L.; Zhang, B.; Chen, B. X.; Zhao, W. M.; Hu, S. N.; Zhuang, S. M.; Shen, Y.; Shi, S. H.; Brown, C.; White, K. P.; Chen, D. S.; Chen, P. J.; Wu, C. I. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (29) 12042-12047
31. Huang, J.; Deng, Q.; Wang, Q.; Li, K. Y.; Dai, J. H.; Li, N.; Zhu, Z. D.; Zhou, B.; Liu, X. Y.; Liu, R. F.; Fei, Q. L.; Chen, H.; Cai, B.; Zhou, B. P.; Xiao, H. S.; Qin, L. X.; Han, Z. G. Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma Nat. Genet. 2012, 44 (10) 1117-1121
32. Paik, Y.-K.; Jeong, S.-K.; Omenn, G. S.; Uhlen, M.; Hanash, S.; Cho, S. Y.; Lee, H.-J.; Na, K.; Choi, E.-Y.; Yan, F. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome Nat. Biotechnol. 2012, 30 (3) 221-223
33. Hühmer, A. F. R.; Paulus, A.; Martin, L. B.; Millis, K.; Agreste, T.; Saba, J.; Lill, J. R.; Fischer, S. M.; Dracup, W.; Lavery, P. The Chromosome-Centric Human Proteome Project: A Call to Action J. Proteome Res. 2012, 12 (1) 28-32
34. Wu, S.; Li, N.; Ma, J.; Shen, H.; Jiang, D.; Chang, C.; Zhang, C.; Li, L.; Zhang, H.; Jiang, J.; Xu, Z.; Ping, L.; Chen, T.; Zhang, W.; Zhang, T.; Xing, X.; Yi, T.; Li, Y.; Fan, F.; Li, X.; Zhong, F.; Wang, Q.; Zhang, Y.; Wen, B.; Yan, G.; Lin, L.; Yao, J.; Lin, Z.; Wu, F.; Xie, L.; Yu, H.; Liu, M.; Lu, H.; Mu, H.; Li, D.; Zhu, W.; Zhen, B.; Qian, X.; Qin, J.; Liu, S.; Yang, P.; Zhu, Y.; Xu, P.; He, F. First Proteomic Exploration of Protein-Encoding Genes on Chromosome 1 in Human Liver, Stomach, and Colon J. Proteome Res. 2012, 12 (1) 67-80
35. Zhang, Y.; Yan, G.; Zhai, L.; Xu, S.; Shen, H.; Yao, J.; Wu, F.; Xie, L.; Tang, H.; Yu, H.; Liu, M.; Yang, P.; Xu, P.; Zhang, C.; Li, L.; Chang, C.; Li, N.; Wu, S.; Zhu, Y.; Wang, Q.; Wen, B.; Lin, L.; Wang, Y.; Zheng, G.; Zhou, L.; Lu, H.; Liu, S.; He, F.; Zhong, F. Proteome Atlas of Human Chromosome 8 and Its Multiple 8p Deficiencies in Tumorigenesis of the Stomach, Colon, and Liver J. Proteome Res. 2012, 12 (1) 81-88
36. Wang, Q.; Wen, B.; Yan, G.; Wei, J.; Xie, L.; Xu, S.; Jiang, D.; Wang, T.; Lin, L.; Zi, J.; Zhang, J.; Zhou, R.; Zhao, H.; Ren, Z.; Qu, N.; Lou, X.; Sun, H.; Du, C.; Chen, C.; Zhang, S.; Tan, F.; Xian, Y.; Gao, Z.; He, M.; Chen, L.; Zhao, X.; Xu, P.; Zhu, Y.; Yin, X.; Shen, H.; Zhang, Y.; Jiang, J.; Zhang, C.; Li, L.; Chang, C.; Ma, J.; Yan, G.; Yao, J.; Lu, H.; Ying, W.; Zhong, F.; He, Q.-Y.; Liu, S. Qualitative and Quantitative Expression Status of the Human Chromosome 20 Genes in Cancer Tissues and the Representative Cell Lines J. Proteome Res. 2012, 12 (1) 151-161
37. Kovanich, D.; Cappadona, S.; Raijmakers, R.; Mohammed, S.; Scholten, A.; Heck, A. J. R. Applications of stable isotope dimethyl labeling in quantitative proteomics Anal. Bioanal. Chem. 2012, 404 (4) 991-1009
38. Wang, F. J.; Song, C. X.; Cheng, K.; Jiang, X. N.; Ye, M. L.; Zou, H. F. Perspectives of Comprehensive Phosphoproteome Analysis Using Shotgun Strategy Anal. Chem. 2011, 83 (21) 8078-8085
39. Kallianpur, A. R.; Hall, L. D.; Yadav, M.; Byrne, D. W.; Speroff, T.; Dittus, R. S.; Haines, J. L.; Christman, B. W.; Summar, M. L. The hemochromatosis C282Y allele: a risk factor for hepatic veno-occlusive disease after hematopoietic stem cell transplantation Bone Marrow Transplant. 2005, 35 (12) 1155-1164
40. Pearson, D. L.; Dawling, S.; Walsh, W. F.; Haines, J. L.; Christman, B. W.; Bazyk, A.; Scott, N.; Summar, M. L. Neonatal pulmonary hypertension-Urea- cycle intermediates, nitric oxide production, and carbamoyl-phosphate synthetase function N. Engl. J. Med. 2001, 344 (24) 1832-1838
41. Zhao, J.; Zhang, X.; Shi, M.; Xu, H.; Jin, J.; Ni, H. D.; Yang, S. L.; Dai, J. X.; Wu, M. C.; Guo, Y. J. TIP30 inhibits growth of HCC cell lines and inhibits HCC xenografts in mice in combination with 5-FU Hepatology 2006, 44 (1) 205-215
42. Ito, M.; Jiang, C.; Krumm, K.; Zhang, X.; Pecha, J.; Zhao, X.; Guo, Y. J.; Roeder, R. G.; Xiao, H. TIP30 deficiency increases susceptibility to tumorigenesis Cancer Res. 2003, 63 (24) 8763-8767