Tools for computational processing of LC-MS datasets: A user's perspective

Computer Methods and Programs in Biomedicine

Volumn 86, Issue 3, 2007, Pages 281-290

  Codrea, Marius C ^a   Jiménez, Connie R ^b   Heringa, Jaap ^a   Marchiori, Elena ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

^b Amsterdam Gastroenterology Metabolism   (Netherlands)

Author keywords

Label free proteomics; Liquid chromatography Mass spectrometry (LC MS) profiling; Software tools usability

Indexed keywords

ALGORITHMS; COMPUTER SOFTWARE; DATA REDUCTION; INFORMATION MANAGEMENT; INTEGRATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PEPTIDES; PROTEINS;

DATASETS MANAGEMENT; INTEGRATIVE DATA ANALYSIS; ION ABUNDANCES; LABEL-FREE PROTEOMICS; LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY (LC-MS) PROFILING; SOFTWARE TOOLS USABILITY; VISUAL TECHNIQUES;

COMPUTER AIDED SOFTWARE ENGINEERING;

ALGORITHM; ARTICLE; AUTOMATION; COMPUTER PROGRAM; DATA ANALYSIS; INFORMATION PROCESSING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METHODOLOGY; QUANTITATIVE ANALYSIS;

CHROMATOGRAPHY, LIQUID; DATABASES; MASS SPECTROMETRY; NETHERLANDS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 34247466401     PISSN: 01692607     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cmpb.2007.03.001     Document Type: Article

References (24)

1. Ruedi A., and Matthias M. Mass spectrometry-based proteomics. Nature 422 6928 (2003) 198-207
2. Listgarten J., and Emili A. Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteom. 4 (2005) 419-434
3. M. Katajamaa, J. Miettinen, M. Orešič, Mzmine: toolbox for processing and visualization of mass spectrometry based molecular profile data, Bioinformatics, 2006. doi:10.1093/bioinformatics/btk039.
4. Palagi P.M., Walther D., Quadroni M., Catherinet S., Burgess J., Zimmermann-Ivol C.G., Sanchez J.C., Binz P.A., Hochstrasser D.F., and Appel R.D. Msight: an image analysis software for liquid chromatography-mass spectrometry. Proteomics 5 (2005) 2381-2384
5. M. Bellew, M. Coram, M. Fitzgibbon, M. Igra, T. Randolph, P. Wang, D. May,J. Eng, R. Fang, C. Lin, J. Chen, D. Goodlett, J. Whiteaker, A. Paulovich, M. McIntosh A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS, Bioinformatics, Advance Access published June 9, 2006.
6. Vorst O., de Vos C.H.R., Lommen A., Staps R.V., Visser R.G.F., Bino R.J., and Hall R.D. A non-directed approach to the differential analysis of multiple LC-MS-derived metabolic profiles. Metabolomics 1 (2005) 169-180
7. Lange E., Gröpl C., Reinert K., Kohlbacher O., and Hildebrandt A. High accuracy peak-picking of proteomics data using wavelet techniques. Proceedings of the 11th Pacific Symposium on Biocomputing. PSB'06, Maui, Hawaii, January 3-7 (2006) 243-254
8. Leptos K.C., Sarracino D.A., Jaffe J.D., Krastins B., and Church G.M. Open-source software for large-scale protein quantitation. Proteomics 6 (2006) 1770-1782
9. Smith C.A., Want E.J., O'Maille G., Abagyan R., and Siuzdak G. Xcms: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 78 (2006) 779-787
10. Palagi P.M., Hernandez P., Walther D., and Appel R.D. Proteome informatics. I. Bioinformatics tools for processing experimental data. Proteomics 6 (2006) 5435-5444
11. Jaffe J.D., Mani D.R., Leptos K.C., Church G.M., Gillette M.A., and Carr SA S.A. Pepper, a platform for experimental proteomic pattern recognition. Mol. Cell. Proteom. 5 (2006) 1927-1941
12. Smith S.W. The Scientist and Engineer's Guide to Digital Signal Processing (1997), California Technical Publishing, USA
13. Hilario M., Kalousis A., Muller M., and Pellegrini C. Processing and classification of protein mass spectra. Mass Spectrom. Rev. 25 (2005) 409-449
14. Theodoridis S., and Koutroumbas K. Pattern Recognition. 2nd ed. (2003), Academic Press
15. M.C. Codrea, C.R. Jimenez, S. Piersma, J. Heringa, E. Marchiori Robust, Peak Detection and Alignment of nanoLC-FT Mass Spectrometry Data, in: Proceedings of The Fifth European Conference on Evolutionary Computation, Machine Learning and Datamining in Bioinformatics, EvoBIO'07, Valencia, April 11-13, 2007, pp. 35-46.
16. Lyons-Weiler J. Standards of excellence and open questions in cancer biomarker research: an informatics perspective. Cancer Inform. 1 (2005) 1-7
17. Rauch A., Bellew M., Eng J., Fitzgibbon M., Holzman T., Hussey P., Igra M., Maclean B., Lin C., Detter A., Fang R., Faca V., Gafken P., Zhang H., Whitaker J., States D., Hanash S., Paulovich A., and Mclntosh M. Computational proteomics analysis system (cpas): an extensible open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J. Proteome Res. 5 (2006) 112-121
18. Amster I.J. Fourier transform mass spectrometry. J. Mass Spectrom. 31 (1996) 1325-1337
19. Prakash A., Mallick P., Whiteaker J., Zhang H., Paulovich A., Flory M., Lee H., Aebersold R., and Schwikowski B. Signal maps for mass spectrometry based comparative proteomics. Mol. Cell. Proteom. 5 (2006) 423-432
20. Pedrioli P.G.A., Eng J.K., Hubley R., Vogelzang M., Deutsch E.W., Raught B., Pratt B., Nilsson E., Angeletti R.H., Cheung R.A.K., Costello C.E., Herm-jakob H., Huang S., Julian Jr. R.K., Kapp E., McComb M.E., Oliver S.G., Omenn G., Paton N.W., Simpson R., Smith R., Taylor C.F., Zhu W., and Aebersold R. A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 22 (2004) 1459-1466
21. Keurentjes J.J.B., Jingyuan F., de Vos C.H.R., Lommen A., Hall R.D., Bino R.J., van der Plas L.H.W., Jansen R.C., Vreugdenhil D., and Koornneef M. The genetics of plant metabolism. Nat. Genet. 38 (2006) 842-849
22. Li X.-J., Pedrioli P.G.A., Eng J., Martin D., Yi E.C., Lee H., and Aebersold R. A tool to visualize and evaluate data obtained by liquid chromatography/electrospray ionization/mass spectrometry. Anal. Chem. 76 (2004) 3856-3860
23. Linsen L., Löcherbach J., Berth M., Bernhardt J., and Becher D. Differential protein expression analysis via liquid-chromatography/mass-spectrometry data visualization. Proceedings of the IEEE Visualization Conference. VIS'05, Minneapolis, October 23-28 (2005) 447-454
24. P. Wang, M. Coram, H. Tang, M. Fitzgibbon, H. Zhang, E. Yi, R. Aebersold, M. Mcintosh. A Statistical Method for Chromatographic Alignment of LC-MS Data, Biostatistics, Advance Access Published online on July 31, 2006.