Analytical model of peptide mass cluster centres with applications

Proteome Science

Volumn 4, Issue , 2006, Pages

  Wolski, Witold E ^a,b   Farrow, Malcolm ^a   Emde, Anne Katrin ^b   Lehrach, Hans ^d   Lalowski, Maciej ^c   Reinert, Knut ^b  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^d MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PEPTIDE; PROTEINASE;

ACCURACY; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CLUSTER ANALYSIS; COMPUTER MODEL; CONTROLLED STUDY; GENE FREQUENCY; HUMAN; INFORMATION PROCESSING; MASS SPECTROMETRY; MOLECULAR WEIGHT; NONHUMAN; PEPTIDE ANALYSIS; PROBABILITY; PROTEIN DATABASE; PROTEIN DEGRADATION; SEQUENCE ANALYSIS;

EID: 33750221222     PISSN: 14775956     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-4-18     Document Type: Article

References (37)

1. Fenyo D: Identifying the proteome: software tools. Current Opinion in Biotechnology 2000, 11:391-395.
2. Griffin TJ, Aebersold R: Advances in proteome analysis by mass spectrometry. J Biol Chem 2001, 276:45497-500.
3. Patterson SD: Data analysis - the Achilles heel of proteomics. Nat Biotechnol 2003, 21(3):221-2.
4. Aebersold R, Mann M: Mass spectrometry-based proteomics. Nature 2003, 422(6928):198-207.
5. Mann M, Hojrup P, Roepstorff P: Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol Mass Spectrom 1993, 22(6):338-345.
6. Johnson R, Martin S, Biemann K, Stults J, Watson J: Novel Fragmentation Process of Peptides by Collision-Induced Decomposition in a Tandem Mass Spectrometer: Differentiation of Leucine and Isoleucine. Analytical Chemistry 1987, 59(21): 2621-2625.
7. Smith RD, Loo JA, Edmonds CG, Barinaga CJ, Udseth HR: New developments in biochemical mass spectrometry: electrospray ionization. Anal Chem 1990, 62(9):882-99.
8. Apweiler R, Bairoch A, Wu CH: Protein sequence databases. Curr Opin Chem Biol 2004, 8:76-80.
9. Gentzel M, Kocher T, Ponnusamy S, Wilm M: Preprocessing of tandem mass spectrometric data to support automatic protein identification. Proteomics 2003, 3(8):1597-610.
10. Wool A, Smilansky Z: Precalibration of matrix-assisted laser desorption/ ionization-time of flight spectra for peptide mass fingerprinting. Proteomics 2002, 2(10):1365-1373.
11. Gobom J, Mueller M, Egelhofer V, Theiss D, Lehrach H, Nordhoff E: A calibration method that simplifies and improves accurate determination of peptide molecular masses by MALDI-TOF MS. Anal Chem 2002, 74(15):3915-3923. [(eng)]
12. Wolski WE, Lalowski M, Jungblut P, Reinert K: Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. BMC Bioinformatics 2005, 6:203 [http://www.biomedcentral.com/1471-2105/6/203].
13. Levander F, Rognvaldsson T, Samuelsson J, James P: Automated methods for improved protein identification by peptide mass fingerprinting. Proteomics 2004, 4(9):2594-601.
14. Chamrad DC, Koerting G, Gobo J, Thiele H, Klose J, Meyer HE, Blueggel M: Interpretation of mass spectrometry data for high-throughput proteomics. Anal Bioanal Chem 2003, 376(7): 1014-22.
15. Gay S, Binz PA, Hochstrasser DF, Appel RD: Modeling peptide mass fingerprinting data using the atomic composition of peptides. Electrophoresis 1999, 20(18):3527-3534. [(eng)]
16. Wikipedia is a Web-based, free-content encyclopedia 2004 [http://www.wikipedia.org].
17. Giles J: Internet encyclopaedias go head to head. Nature 2005, 438(7070):900-1.
18. Pappin DJC, Hojrup P, Bleasby AJ: Rapid identification of proteins by peptide-mass fingerprinting. Curr Biol 1993, 3:327-332.
19. Gras R, Muller M, Gasteiger E, Gay S, Binz PA, Bienvenut W, Hoogland C, Sanchez JC, Bairoch A, Hochstrasser DF, Appel RD: Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection. Electrophoresis 1999, 20(18): 3535-3550. [(eng)]
20. Gobom J, Schürenberg M, Mueller M, Theiss D, Lehrach H, Nordhoff E: Alpha-cyano-4-hydroxycinnamic acid affinity sample preparation. A protocol for MALDI-MS peptide analysis in proteomics. Analytical Chemistry 2001, 73(3):434-438.
21. Zhen Y, Xu N, Richardson B, Becklin R, Savage JR, Blake K, Peltier JM: Development of an LC-MALDI method for the analysis of protein complexes. J Am Soc Mass Spectrom 2004, 15(6):803-22.
22. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20(18): 3551-3567.
23. Schmidt F, Schmid M, Jungblut PR, Mattow J, Facius A, Pleissner KP: Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis. J Am Soc Mass Spectrom 2003, 14(9): 943-56.
24. Tabb DL, MacCoss MJ, Wu CC, Anderson SD, Yates JRr: Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal Chem 2003, 75(10): 2470-7.
25. Wolski WE, Lalowski M, Martus P, Herwig R, Giavalisco P, Gobom J, Sickmann A, Lehrach H, Reinert K: Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. BMC Bioinformatics 2005, 6:285.
26. Cagney G, Amiri S, Premawaradena T, Lindo M, Emili A: In silico proteome analysis to facilitate proteomics experiments using mass spectrometry. Proteome Science 2003, 1:5 [http://www.Proteomesci.com/content/1/1/5].
27. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LSL: The Universal Protein Resource (UniProt). Nucleic Acids Res 2005:D154-9.
28. Becker RA, Chambers JM, Wilks AR: The New S Language London: Chapman & Hall; 1988.
29. Samuelsson J, Dalevi D, Levander F, Rognvaldsson T: Modular, Scriptable, and Automated Analysis Tools for High-Throughput Peptide Mass Fingerprinting. Bioinformatics 2004.
30. Venables WN, Ripley BD: Modern Applied Statistics with S Fourth 2002 [http://www.stats.ox.ac.uki/pub/MASS4/]. Springer [ISBN 0-38795457-0]
31. Bruker Daltonics - enabling life science tools based on mass spectrometry 2004 [http://www.bdal.com].
32. Giavalisco P, Nordhoff E, Kreitler T, Kloeppel KD, Lehrach H, Klose J, Gobom J: Proteome Analysis of Arabidopsis Thaliana by 2-D Electrophoresis and Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry. [To appear in Proteomics]
33. Klose J, Kobalz U: Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis 1995, 16(6):1034-59.
34. Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence project: update and current status. Nucleic Acids Res 2003, 31: 34-7.
35. Emde AK: Protein Sequence Digester. 2004 [http://www.inf.fuberlin.de/ ~emde/].
36. Mascot 2005 http://www.matrixscience.com].
37. Glockner FO, Kube M, Bauer M, Teeling H, Lombardot T, Ludwig W, Gade D, Beck A, Borzym K, Heitmann K, Rabus R, Schlesner H, Amann R, Reinhardt R: Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. Proc Natl Acad Sci USA 2003, 100(14):8298-303.