Bioinformatics for Qualitative and Quantitative Proteomics

Methods in Molecular Biology

Volumn 719, Issue , 2011, Pages 331-349

  Bielow, Chris ^a   Gröpl, Clemens ^b   Kohlbacher, Oliver ^c   Reinert, Knut ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b UNIVERSITY OF GREIFSWALD   (Germany)

^c UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

Algorithm; ESI; HPLC; MALDI; Mass Spectrometry; MS; MS MS; Software; Tandem MS

Indexed keywords

ALGORITHM; ANALYTIC METHOD; AUTOMATION; BIOINFORMATICIAN; BIOINFORMATICS; HUMAN; PIPELINE; PROTEOMICS; SOFTWARE; TANDEM MASS SPECTROMETRY; ARTICLE; METHODOLOGY;

PEPTIDE; PROTEIN;

ALGORITHMS; PEPTIDES; PROTEINS; PROTEOMICS;

EID: 79958289858     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-027-0_15     Document Type: Chapter

References (34)

1. Perkins, D. N., Pappin, D. J. C., Creasy, D. M., Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567.
2. Craig, R., Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466–1467.
3. Kohlbacher, O., Reinert, K., Gröpl, C., et al. (2007) TOPP – the OpenMS proteomics pipeline. Bioinformatics 23, e191–e197.
4. Ruckstuhl, A. (2001) Baseline subtraction using robust local regression estimation. J Quant Spectrosc Radiat Transfer 68, 179–193.
5. Williams, B., Cornett, S., Dawant, B., Crecelius, A., Bodenheimer, B., Caprioli, R. An algorithm for baseline correction of MALDI mass spectra. New York, New York, USA: ACM Press, 2005.
6. Savitzky, A., Golay, M. J. E. (1964) Smoothing and differentiation of data by simplified least squares procedures. Anal Chem 36, 1627–1639.
7. Li, X.-J., Yi, E. C., Kemp, C. J., Zhang, H., Aebersold, R. (2005) A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol Cell Proteomics 4, 1328–1340.
8. Lange, E., Gröpl, C., Reinert, K., Kohlbacher, O., Hildebrandt, A. High accuracy peak-picking of proteomics data using wavelet techniques. In: Proceedings of the 11th Pacific Symposium on Biocomputing (PSB06). 2006 243–254.
9. Schulz-Trieglaff, O., Machtejevas, E., Reinert, K., Schlüter, H., Thiemann, J., Unger, K. (2009) Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments. BioData Min 2, 4.
10. Cox, J., Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26, 1367–1372.
11. Zhang, Z., Marshall, A. (1998) A universal algorithm for fast and automated charge state deconvolution of electrospray mass-to-charge ratio spectra. J Am Soc Mass Spectrom 9, 225–233.
12. Horn, D. (2000) Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J Am Soc Mass Spectrom 11, 320–332.
13. Schulz-Trieglaff, O., Hussong, R., Gröpl, C., Hildebrandt, A., Reinert, K. A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry data. In: Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology. 2007 473–487.
14. Bellew, M., Coram, M., Fitzgibbon, M., et al. (2006) A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 22, 1902–1909.
15. Katajamaa, M., Miettinen, J., Oresic, M. (2006) MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. BMC Bioinformatics 6, 634–636.
16. Tautenhahn, R., Böttcher, C., Neumann, S. Annotation of LC/ESI-MS mass signals. In: BIRD, Hochreiter, S., Wagner, R., eds., vol. 4414 of Lecture Notes in Computer Science. Springer, 2007 371–380.
17. Lange, E., Gröpl, C., Schulz-Trieglaff, O., Leinenbach, A., Huber, C., Reinert, K. (2007) A geometric approach for the alignment of liquid chromatography-mass spectrometry data. Bioinformatics 23, i273–i281.
18. Smith, C. A., Want, E. J., O’Maille, G., Abagyan, R., Siuzdak, G. (2006) XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 78, 779–787.
19. Prince, J. T., Marcotte, E. M. (2006) Chromatographic alignment of ESI-LC-MS proteomics datasets by ordered bijective interpolated warping. Anal Chem 78, 6140–6152.
20. Lange, E., Tautenhahn, R., Neumann, S., Gröpl, C. (2008) Critical assessment of alignment procedures for LC-MS proteomics and metabolomic measurements. BMC Bioinformatics 9, 375.
21. Prakash, A., Mallick, P., Whiteaker, J., et al. (2005) Signal maps for mass spectrometry-based comparative proteomics. Mol Cell Proteomics 5, 423–432.
22. Listgarten, J., Neal, R. M., Roweis, S. T., Wong, P., Emili, A. (2007) Difference detection in LC-MS data for protein biomarker discovery. Bioinformatics 23, e198–e204.
23. Vandenbogaert, M., Li-Thiao-Té, S., Kaltenbach, H.-M., Zhang, R., Aittokallio, T., Schwikowski, B. (2008) Alignment of LC-MS images, with applications to biomarker discovery and protein identification. Proteomics 8, 650–672.
24. Gupta, N., Pevzner, P. A. (2009) False discovery rates of protein identifications: a strike against the two-peptide rule. J Proteome Res 8, 4173–4181.
25. Nesvizhskii, A. I., Keller, A., Kolker, E., Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75, 4646–4658.
26. Li, Y. F., Arnold, R. J., Li, Y., Radivojac, P., Sheng, Q., Tang, H. (2009) A bayesian approach to protein inference problem in shotgun proteomics. J Comput Biol 16, 1183–1193.
27. Dost, B., Bandeira, N., Li, X., Shen, Z., Briggs, S., Bafna, V. Shared Peptides in Mass Spectrometry Based Protein Quantification. In: Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology, Batzoglou, S., ed., vol. 5541 of Lecture Notes in Computer Science. Springer, 2009 356–371.
28. Carrillo, B., Yanofsky, C., Laboissiere, S., Nadon, R., Kearney, R. E. (2009) Methods for combining peptide intensities to estimate relative protein abundance. Bioinformatics.
29. Brusniak, M.-Y., Bodenmiller, B., Campbell, D., et al. (2008) Corra: computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics 9, 542.
30. Jaffe, J. D., Mani, D. R., Leptos, K. C., Church, G. M., Gillette, M. A., Carr, S. A. (2006) PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics 5, 1927–1941.
31. Palagi, P. M., Walther, D., Quadroni, M., et al. (2005) MSight: an image analysis software for liquid chromatography-mass spectrometry. Proteomics 5, 2381–2384.
32. Schulze, W. X., Mann, M. (2004) A novel proteomic screen for peptide-protein interactions. J Biol Chem 279, 10756–10764.
33. Kessner, D., Chambers, M., Burke, R., Agus, D., Mallick, P. (2008) ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24, 2534–2536.
34. Mueller, L. N., Rinner, O., Schmidt, A., et al. (2007) SuperHirn – a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 7, 3470–3480.