Analysis of mass spectrometry data in proteomics

Methods in Molecular Biology

Volumn 453, Issue , 2008, Pages 105-122

  Matthiesen, Rune ^a   Jensen, Ole N ^b  

^a CIC BIOGUNE   (Spain)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

Database searching; De novo sequencing; Peptide fragmentation fingerprinting; Peptide mass fingerprinting; Quantitation

Indexed keywords

EID: 84934440601     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-429-6_4     Document Type: Article

References (54)

1. Kozak, M. (2006) Rethinking some mechanisms invoked to explain translational regulation in eukaryotes. Gene Available online 22 June.
2. Seet, B. T., Dikic, I., Zhou, M. M., et al. (2006) Reading protein modifications with interaction domains. Nat Rev Mol Cell Biol 7, 473-483.
3. Jensen, O. N. (2006) Interpreting the protein language using proteomics. Nat Rev Mol Cell Biol 7, 391-403.
4. Aebersold, R., Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207.
5. Patterson, S. D., Aebersold, R. (1995) Mass spectrometric approaches for the 120 Matthiesen and Jensen identification of gel-separated proteins. Electrophoresis 16, 1791-1814.
6. Domon, B, Aebersold, R. (2006) Challenges and opportunities in proteomic data analysis. Mol Cell Proteomics. Available online 8 August.
7. Patterson S. D. (2003) Data analysis: the Achilles heel of proteomics. Nat Biotechnol 21, 221-222.
8. Steen, H., Mann, M. (2004) The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol 5, 699-711.
9. Fridriksson, E. K., Beavil, A., Holowka, D., et al. (2000) Heterogeneous glycosylation of immunoglobulin E constructs characterized by top-down high-resolution 2-D mass spectrometry. Biochemistry 39, 3369-3376.
10. Jensen, O. N., Larsen, M. R., Roepstorff, P. (1998) Mass spectrometric identification and microcharacterization of proteins from electrophoretic gels: strategies and applications. Proteins 2, 74-89.
11. Roepstorff, P., Fohlman, J. (1984) Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom 11, 601.
12. Wysocki, V. H., Tsaprailis, G., Smith, L. L., et al. (2000) Mobile and localized protons: a framework for understanding peptide dissociation. J Mass Spectrom 35, 1399-1406.
13. Laskin, J., Futrell, J. H. (2003) Collisional activation of peptide ions in FT-ICR. Mass Spectrom Rev 22, 158-181.
14. Pedrioli, P. G., Eng, J. K., Hubley, R., et al. (2004) A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 22, 1459-1466.
15. Orchard, S., Kersey, P., Hermjakob, H., et al. (2003) The HUPO Proteomics Standards Initiative meeting: towards common standards for exchanging proteomics data. Comp Funct Genom 4, 16-19.
16. Cottingham, K. (2006) CPAS: a proteomics data management system for the masses. J Proteome Res 5, 14.
17. Matthiesen, R., Trelle, M. B., Hojrup, P., et al. (2005) VEMS 3.0: Algorithms and computational tools for tandem mass spectrometry based identification of posttranslational modifications in proteins. J Proteome Res 4, 2338-2347.
18. Fenyo, D., Qin, J., Chait, B.T. (1998) Protein identification using mass spectrometric information. Electrophoresis 19, 998-1005.
19. Matthiesen, R., Bunkenborg, J., Stensballe, A., et al. (2004) Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0. Proteomics 4, 2583-2593.
20. Fermin, D., Allen, B. B., Blackwell, T. W., et al. (2006) Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol 7, R35.
21. Fenyö, D., Beavis, R. C. (2003) A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem 75, 768-774.
22. Creasy, D. M., Cottrell, J. S. (2002) Error tolerant searching of tandem mass spectrometry data not yet interpreted. Proteomics 2, 1426-1434.
23. Craig, R., Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra, Bioinformatics 20, 1466-1467.
24. Woodsmall, R. M., Benson, D. A., (1993) Information resources at the National Center for Biotechnology Information. Bull Med Libr Assoc 81, 282-284.
25. LinksKersey, P. J., Duarte, J., Williams, A., Karavidopoulou, Y., Birney, E., Apweiler, R. (2004) The International Protein Index: an integrated database for proteomics experiment. Proteomics 4, 1985-1988.
26. LinksBairoach, A., Apweiler, R. (1998) The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res 26, 38-42.
27. Colinge, J., Masselot, A., Cusin, I., et al. (2004) High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics 4, 1977-1984.
28. López-Ferrer, D., Martinez-Bartolomé, S., Villar, M., et al. (2004) Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST. Anal Chem 76, 6853-6860.
29. Dancik, V., Addona, T., Clauser, K., et al. (1999) De novo peptide sequencing via tandem mass spectrometry. J Comput Biol 6, 327-342.
30. Frank, A., Pevzner, P. (2005) PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal Chem 77, 964-973.
31. Johnson, R. S., Taylor, J. A. (2002) Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry. Mol Biotechnol 22, 301-315.
32. Shevchenko, A., Sunyaev, S., Loboba, A., et al. (2001) Charting the proteomes of organisms with unsequenced genomes by Analysis of Data in Proteomics 121 122 Matthiesen and Jensen MALDI-Quadrupole time-of flight mass spectrometry and BLAST homologuey searching. Anal Chem 73, 1917-1926.
33. Andersen, J. S., Wilkinson, C. J., Mayor,
34. T., Mortensen, P., Nigg, E. A., Mann, M. (2003) Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426, 570-574.
35. MacCoss, M. J., Wu, C. C., Liu, H., et al.
36. (2003) A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal Chem 75, 6912-6921.
37. Venable, J. D., Dong, M. Q., Wohlschlegel, J., et al. (2004) Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods 1, 39-45.
38. Listgarten, J., Emili, A. (2005) Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 4, 419-434.
39. Beck, H. C., Nielsen, E. C., Matthiesen, R., et al. (2006) Quantitative proteomic analysis of post-translational modifications of human histones. Mol Cell Proteomics 5, 1314-1325.
40. Zar, J. H. (1999) Biostatistical Analysis. Prentice-Hall, Upper Saddle River, NJ.
41. Tusher, V. G., Tibshirani, R., Chu, G., et al. (2001) Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98, 5116-5121.
42. Gerber, S. A., Rush, J., Stemman, O., et al. (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A 100, 6940-6945.
43. Turecek, F. (2002) Mass spectrometry in coupling with affinity capture-release and isotope-coded affinity tags for quantitative protein analysis. J Mass Spectrom 37, 1-14.
44. Ong, S. E., Blagoev, B., Kratchmarova, I., et al. (2002) Stable istotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteom 1, 376-386.
45. Yang, W. C., Mirzaei, H., Liu, X., et al. (2006) Enhancement of amino Acid detection and quantification by electrospray ionization mass spectrometry. Anal Chem 78, 4702-4708.
46. Gruhler, A., Schulze, W. X., Matthiesen, R., et al. (2005) Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry. Mol Cell Proteom 4, 1697-709.
47. Ballif, B. A., Roux, P. P., Gerber, S. A., et al. (2005) Quantitative phosphorylation profiling of the ERK/p90 ribosomal S6 kinase-signaling cassette and its targets, the tuberous sclerosis tumor suppressors. Proc Natl Acad Sci U S A 102, 667-672.
48. Fierro-Monti, I., Mohammed, S., Matthiesen, R., et al. (2005) Quantitative proteomics identifies Gemin5, a scaffolding protein involved in ribonucleoprotein assembly, as a novel partner for eukaryotic initiation factor 4. J Proteome Res 5, 1367-1378.
49. Romijn, E. P., Christis, C., Wieffer, M., et al. (2006) Expression clustering reveals detailed co-expression patterns of functionally related proteins during B cell differentiation. Molecular & Cellular Proteomics 4, 1297-1310.
50. Blagoev, B., Kratchmarova, I., Ong, S. E., et al. (2003) A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol 21, 315-318.
51. http://www.yass.sdu.dk/yassdb/
52. Craig, R.., Cortens, J. P., Beavis, R. C. (2004) Open source system for analyzing, validating, and storing protein identification data. J Proteome Res 3, 1234-1242.
53. Jones, P., Cote, R. G., Martens, L., et al. (2006) PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res 34, D659-663.
54. Gärdén, P., Alm, R., Häkkinen, J. (2005) Proteios: an open source proteomics initiative. Bioinformatics 21, 2085-2087.