Analyzing large-scale proteomics projects with latent semantic indexing

Journal of Proteome Research

Volumn 7, Issue 1, 2008, Pages 182-191

  Klie, Sebastian ^a   Martens, Lennart ^b   Vizcaíno, Juan Antonio ^b   Côté, Richard ^b   Jones, Phil ^b   Apweiler, Rolf ^b   Hinneburg, Alexander ^a   Hermjakob, Henning ^b  

^a MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Bioinformatics; Data mining; Latent semantic analysis; Proteomics

Indexed keywords

PEPTIDE; PROTEIN;

ALGORITHM; ARTICLE; BIOINFORMATICS; CALCULATION; COMPARATIVE STUDY; DATA BASE; HISTOGRAM; METHODOLOGY; NOISE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SAMPLING; SCORING SYSTEM; SEMANTICS; VALIDATION PROCESS;

ABSTRACTING AND INDEXING AS TOPIC; ALGORITHMS; GUIDELINES AS TOPIC; HUMANS; PROTEOMICS; SEMANTICS;

EID: 38649129380     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr070461k     Document Type: Article

References (30)

1. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422 (6928), 198-207.
2. Domon, B.; Aebersold, R. Mass spectrometry and protein analysis. Science 2006, 312 (5771), 212-217.
3. Prince, J. T.; Carlson, M. W.; Wang, R.; Lu, P.; Marcotte, E. M. The need for a public proteomics repository. Nat. Biotechnol. 2004, 22 (4), 471-472.
4. Hermjakob, H.; Apweiler, R. The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible. Expert Rev. Proteomics 2006, 3 (1), 1-3.
5. Craig, R.; Cortens, J. P.; Beavis, R. C. Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 2004, 3 (6), 1234-1242.
6. Martens, L.; Hermjakob, H.; Jones, P.; Adamski, M.; Taylor, C.; States, D.; Gevaert, K.; Vandekerckhove, J.; Apweiler, R. PRIDE: the proteomics identifications database. Proteomics 2005, 5 (13), 3537-3545.
7. Jones, P.; Cote, R. G.; Martens, L.; Quinn, A. F.; Taylor, C. F.; Derache, W.; Hermjakob, H.; Apweiler, R. PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 2006, 34 (Database issue), D659-663.
8. Desiere, F.; Deutsch, E. W.; Nesvizhskii, A. I.; Mallick, P.; King, N. L.; Eng, J. K.; Aderem, A.; Boyle, R.; Brunner, E.; Donohoe, S.; Fausto, N.; Hafen, E.; Hood, L.; Katze, M. G.; Kennedy, K. A.; Kregenow, F.; Lee, H.; Lin, B.; Martin, D.; Ranish, J. A.; Rawlings, D. J.; Samelson, L. E.; Shiio, Y.; Watts, J. D.; Wollscheid, B.; Wright, M. E.; Yan, W.; Yang, L.; Yi, E. C.; Zhang, H.; Aebersold, R. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. GenomeBiology 2005, 6 (1), R9.
9. Omenn, G. S.; States, D. J.; Adamski, M.; Blackwell, T. W.; Menon, R.; Hermjakob, H.; Apweiler, R.; Haab, B. B.; Simpson, R. J.; Eddes, J. S.; Kapp, E. A.; Moritz, R. L.; Chan, D. W.; Rai, A. J.; Admon, A.; Aebersold, R.; Eng, J.; Hancock, W. S.; Hefta, S. A.; Meyer, H.; Paik, Y. K.; Yoo, J. S.; Ping, P.; Pounds, J.; Adkins, J.; Qian, X.; Wang, R.; Wasinger, V.; Wu, C. Y.; Zhao, X.; Zeng, R.; Archakov, A.; Tsugita, A.; Beer, I.; Pandey, A.; Pisano, M.; Andrews, P.; Tammen, H.; Speicher, D. W.; Hanash, S. M. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005, 5 (13), 3226-3245.
10. Hamacher, M.; Apweiler, R.; Arnold, G.; Becker, A.; Bluggel, M.; Carrette, O.; Colvis, C.; Dunn, M. J.; Frohlich, T.; Fountoulakis, M.; van Hall, A.; Herberg, F.; Ji, J.; Kretzschmar, H.; Lewczuk, P.; Lubec, G.; Marcus, K.; Martens, L.; Palacios Bustamante, N.; Park, Y. M.; Pennington, S. R.; Robben, J.; Stuhler, K.; Reidegeld, K. A.; Riederer, P.; Rossier, J.; Sanchez, J. C.; Schrader, M.; Stephan, C.; Tagle, D.; Thiele, H.; Wang, J.; Wiltfang, J.; Yoo, J. S.; Zhang, C.; Klose, J.; Meyer, H. E. HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy. Proteomics 2006, 6 (18), 4890-4898.
11. Mallick, P.; Schirle, M.; Chen, S. S.; Flory, M. R.; Lee, H.; Martin, D.; Ranish, J.; Raught, B.; Schmitt, R.; Werner, T.; Kuster, B.; Aebersold, R. Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 2007, 25 (1), 125-131.
12. Nesvizhskii, A. I.; Aebersold, R. Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 2005, 4 (10), 1419-1440.
13. Kersey, P. J.; Duarte, J.; Williams, A.; Karavidopoulou, Y.; Birney, E.; Apweiler, R. The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004, 4 (7), 1985-1988.
14. Martens, L.; Muller, M.; Stephan, C.; Hamacher, M.; Reidegeld, K. A.; Meyer, H. E.; Bluggel, M.; Vandekerckhove, J.; Gevaert, K.; Apweiler, R. A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies. Proteomics 2006, 6 (18), 5076-5086.
15. Dumais, S. Improving the retrieval of information from external sources. Behav. Res. Methods, Instrum. Comput. 1991, 23 (2), 229-236.
16. Salton, G.; Wong, A.; Yang, C. S. Vector-space model for automatic indexing. Commun. ACM 1975, 18 (11), 613-620.
17. Salton, G.; McGill, M. J. Introduction to Modern Information Retrieval; McGraw-Hill: New York, 1983; p. xv, p. 448.
18. Anderson, N. L.; Anderson, N. G. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 2002, 1 (11), 845-867.
19. Katz, S. M. Estimation of probabilities from sparse data for the language model component of a speech recognizer. IEEE Trans. Acoust., Speech Signal Process. 1987, 35 (3), 400-401.
20. Gevaert, K.; Van Damme, P.; Ghesquière, B.; Impens, F.; Martens, L.; Helsens, K.; Vandekerckhove, J. A la carte proteomics with an emphasis on gel-free techniques. Proteomics 2007, 7(16), 2698-2718.
21. Landauer, T. K.; Foltz, P. W.; Laham, D. (An introduction to latent semantic analysis). Discourse Processes 1998, 25 (2), 259-284.
22. Deerwester, S.; Dumais, S. T.; Furnas, G. W.; Landauer, T. K.; Harshman, R. Indexing by Latent Semantic Analysis. J. Am. Soc. Inf. Sci. 1990, 41 (6), 391-407.
23. Furnas, G. W.; Deerwester, S.; Dumais, S. T.; Landauer, T. K.; Harshman, R. A.; Streeter, L. A.; Lochbaum, K. E. Information retrieval using a singular value decomposition model of latent semantic structure, SIGIR '88. In Proceedings of the 11th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval; ACM; New York, 1988; pp. 465-480.
24. Martens, L.; Vandekerckhove, J.; Gevaert, K. DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics 2005, 21 (17), 3584-3585.
25. Team, D. C. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing: Vienna, Austria, 2005.
26. Reidegeld, K. A.; Muller, M.; Stephan, C.; Bluggel, M.; Hamacher, M.; Martens, L.; Korting, G.; Chamrad, D. C.; Parkinson, D.; Apweiler, R.; Meyer, H. E.; Marcus, K. The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results. Proteomics 2006, 6 (18), 4997-5014.
27. Adkins, J. N.; Monroe, M. E.; Auberry, K. J.; Shen, Y.; Jacobs, J. M.; Camp, D. G., 2nd; Vitzthum, F.; Rodland, K. D.; Zangar, R. C.; Smith, R. D.; Pounds, J. G. A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy. Proteomics 2005, 5 (13), 3454-3466.
28. Zolotarjova, N.; Martosella, J.; Nicol, G.; Bailey, J.; Boyes, B. E.; Barrett, W. C. Differences among techniques for high-abundant protein depletion. Proteomics 2005, 5 (13), 3304-3313.
29. Smellie, A. Accelerated K-means clustering in metric spaces. J. Chem. Inf. Comput. Sci. 2004, 44 (6), 1929-1935.
30. Steinley, D. K-means clustering: A half-century synthesis. Br. J. Math. Stat. Psychol. 2006, 59, 1-34.