Web-based tools for the interpretation of chain-like protein spot patterns on two-dimensional gels

Current Proteomics

Volumn 9, Issue 1, 2012, Pages 18-25

  Maurer, Martin H ^a,b  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b Hospital for Child and Adolescent Psychiatry   (Germany)

Author keywords

Isoelectric point; Post translational modification; Protein species shift; Proteomics; Two dimensional gel electrophoresis

Indexed keywords

ALTERNATIVE RNA SPLICING; AMINO ACID COMPOSITION; BIOINFORMATICS; COMPUTER PREDICTION; EXPERIMENTAL STUDY; HUMAN; INTERNET; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DEGRADATION; PROTEIN GLYCOSYLATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; REVIEW; SPECIES COMPARISON; SUMOYLATION; THEORETICAL MODEL; TWO DIMENSIONAL GEL ELECTROPHORESIS; UBIQUITINATION; VIRTUAL REALITY; WEB BROWSER;

EID: 84858321241     PISSN: 15701646     EISSN: None     Source Type: Journal    
DOI: 10.2174/157016412799746236     Document Type: Review

References (98)

1. Smithies, O. and Poulik, M.D. Two-dimensional electrophoresis of serum proteins. Nature, 1956, 177(4518), 1033.
2. Raymond, S. Acrylamide Gel Electrophoresis. Ann. N. Y. Acad. Sci., 1964, 121, 350-365.
3. Stegemann, H.; Francksen, H. and Macko, V. Potato proteins: genetic and physiological changes, evaluated by one-and twodimensional PAA-gel-techniques. Zeitschrift fur Naturforschung, 1973, 28(11), 722-732.
4. Klose, J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutation in mammals. Humangenetik, 1975, 26, 231-243.
5. O'Farrell, P.H. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem., 1975, 250, 4007-4021.
6. Scheele, G.A. Two-dimensional gel analysis of soluble proteins. Charaterization of guinea pig exocrine pancreatic proteins. J. Biol. Chem., 1975, 250(14), 5375-5385.
7. Klose, J. and Kobalz, U. Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis, 1995, 16(6), 1034-1059.
8. Mann, M.; Hendrickson, R.C. and Pandey, A. Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem., 2001, 70, 437-473.
9. Ramagli, L.S. Quantifying protein in 2-D PAGE solubilization buffers. Methods Mol. Biol., 1999, 112, 99-103.
10. Julka, S. and Regnier, F. Quantification in proteomics through stable isotope coding: a review. J. Proteome Res., 2004, 3(3), 350-363.
11. Witze, E.S.; Old, W.M.; Resing, K.A. and Ahn, N.G. Mapping protein post-translational modifications with mass spectrometry. Nat. Methods, 2007, 4(10), 798-806.
12. Rabilloud, T. Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics, 2002, 2(1), 3-10.
13. Herbert, B.R.; Harry, J.L.; Packer, N.H.; Gooley, A.A.; Pedersen, S.K. and Williams, K.L. What place for polyacrylamide in proteomics? Trends Biotechnol., 2001, 19(10 Suppl), S3-S9.
14. Ong, S.E. and Pandey, A. An evaluation of the use of twodimensional gel electrophoresis in proteomics. Biomol. Eng., 2001, 18(5), 195-205.
15. Shaw, M.M. and Riederer, B.M. Sample preparation for twodimensional gel electrophoresis. Proteomics, 2003, 3(8), 1408-1417.
16. Görg, A.; Obermaier, C.; Boguth, G.; Harder, A.; Scheibe, B.; Wildgruber, R. and Weiss, W. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis, 2000, 21(6), 1037-1053.
17. Patton, W.F. A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis, 2000, 21(6), 1123-1144.
18. Wirth, P.J. and Romano, A. Staining methods in gel electrophoresis, including the use of multiple detection methods. J. Chromatogr. A., 1995, 698(1-2), 123-143.
19. Patton, W.F. Detection technologies in proteome analysis. J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci., 2002, 771(1-2), 3-31.
20. Maurer, M.H. Simple method for three-dimensional representation of 2-DE spots using a spreadsheet program. J. Proteome Res., 2004, 3(3), 665-666.
21. Chakravarti, D.N.; Chakravarti, B. and Moutsatsos, I. Informatic tools for proteome profiling. Biotechniques, 2002, Suppl, 4-10, 2-5.
22. Maurer, M.H. Software analysis of two-dimensional electrophoretic gels in proteomic experiments. Curr. Bioinformatics, 2006, 1(2), 255-262.
23. Maurer, M.H.; Feldmann, R.E. Jr.; Brömme, J.O. and Kalenka, A. Comparison of statistical approaches for the analysis of proteome expression data of differentiating neural stem cells. J. Proteome Res., 2005, 4(1), 96-100.
24. Maurer, M.H. Comparison of large proteomic datasets. Curr. Proteomics, 2005, 2(3), 179-189.
25. Jungblut, P.; Thiede, B.; Zimny-Arndt, U.; Muller, E.C.; Scheler, C.; Wittmann-Liebold, B. and Otto, A. Resolution power of twodimensional electrophoresis and identification of proteins from gels. Electrophoresis, 1996, 17(5), 839-847.
26. IUPAC-IUB Commission on Biochemical Nomenclature. The nomenclature of multiple forms of enzymes recommendations. J. Biol. Chem., 1971, 216(20), 6127-6328.
27. Gunning, P.; Weinberger, R.; Jeffrey, P. and Hardeman, E. Isoform sorting and the creation of intracellular compartments. Annu. Rev. Cell. Dev. Biol., 1998, 14, 339-372.
28. Steen, H. and Mann, M. The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol., 2004, 5(9), 699-711.
29. Appel, R.D. and Bairoch, A. Post-translational modifications: a challenge for proteomics and bioinformatics. Proteomics, 2004, 4(6), 1525-1526.
30. Lopez, M.F. Proteome analysis. I. Gene products are where the biological action is. J. Chromatogr. B. Biomed. Sci. Appl., 1999, 722(1-2), 191-202.
31. Ohmori, O.; Hirano, H. and Mita, T. Shifted cytosolic NADP+-dependent isocitrate dehydrogenase on 2-D gel in the brain of genetically epileptic E1 mice. Neurochem. Res., 1999, 24(3), 365-369.
32. Merril, C.R. and Goldman, D. Quantitative two-dimensional protein electrophoresis for studies of inborn errors of metabolism. Clin. Chem., 1982, 28(4 Pt 2), 1015-1020.
33. Okkels, L.M.; Muller, E.C.; Schmid, M.; Rosenkrands, I.; Kaufmann, S.H.; Andersen, P. and Jungblut, P.R. CFP10 discriminates between nonacetylated and acetylated ESAT-6 of Mycobacterium tuberculosis by differential interaction. Proteomics, 2004, 4(10), 2954-2960.
34. Gasteiger, E.; Hoogland, C.; Gattiker, A.; Duvaud, S.; Wilkins, M.R.; Appel, R.D. and A., B. Protein Identification and Analysis Tools on the ExPASy Server. In: The Proteomics Protocols Handbook; (ed. Walker, J.M.); Humana Press: Totowa, NJ, 2005, pp. 571-607.
35. Tabb D.L. An algorithm for isoelectric point estimation. URL: http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm. pdf (Accessed July 01, 2011).
36. Kiraga, J.; Mackiewicz, P.; Mackiewicz, D.; Kowalczuk, M.; Biecek, P.; Polak, N.; Smolarczyk, K.; Dudek, M.R. and Cebrat, S. The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms. BMC genomics, 2007, 8, 163.
37. Larsen, M.R.; Trelle, M.B.; Thingholm, T.E. and Jensen, O.N. Analysis of posttranslational modifications of proteins by tandem mass spectrometry. BioTechniques, 2006, 40(6), 790-798.
38. Perkins, D.N.; Pappin, D.J.; Creasy, D.M. and Cottrell, J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 1999, 20(18), 3551-3567.
39. Eng, J.K.; McCormack, A.L. and Yates, J.R.3rd; An approach to correlate tandem mass spectra data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom., 1994, 5(11), 976-989.
40. Tanner, S.; Shu, H.; Frank, A.; Wang, L.C.; Zandi, E.; Mumby, M.; Pevzner, P.A. and Bafna, V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem., 2005, 77(14), 4626-4639.
41. Shilov, I.V.; Seymour, S.L.; Patel, A.A.; Loboda, A.; Tang, W.H.; Keating, S.P.; Hunter, C.L.; Nuwaysir, L.M. and Schaeffer, D.A. The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol. Cell Proteomics, 2007, 6(9), 1638-1655.
42. Tsur, D.; Tanner, S.; Zandi, E.; Bafna, V. and Pevzner, P.A. Identification of post-translational modifications by blind search of mass spectra. Nat. Biotechnol., 2005, 23(12), 1562-1567.
43. Chung, C.; Liu, J.; Emili, A. and Frey, B.J. Computational refinement of post-translational modifications predicted from tandem mass spectrometry. Bioinformatics, 2011, 27(6), 797-806.
44. Tsur, D.; Tanner, S.; Zandi, E.; Bafna, V. and Pevzner, P.A. Identification of post-translational modifications via blind search of mass-spectra. Proc. IEEE Comput. Syst. Bioinform. Conf., 2005, 157-166.
45. Lubec, G. and Afjehi-Sadat, L. Limitations and pitfalls in protein identification by mass spectrometry. Chem. Rev., 2007, 107(8), 3568-3584.
46. Galperin, M.Y. The Molecular Biology Database Collection: 2005 update. Nucleic Acids Res., 2005, 33(Database issue), D5-D24.
47. Manning, G.; Whyte, D.B.; Martinez, R.; Hunter, T. and Sudarsanam, S. The protein kinase complement of the human genome. Science, 2002, 298(5600), 1912-1934.
48. Ishida, A.; Kameshita, I.; Sueyoshi, N.; Taniguchi, T. and Shigeri, Y. Recent advances in technologies for analyzing protein kinases. J. Pharmacol. Sci., 2007, 103(1), 5-11.
49. Spickett, C.M.; Pitt, A.R.; Morrice, N. and Kolch, W. Proteomic analysis of phosphorylation, oxidation and nitrosylation in signal transduction. Biochimica. Et. Biophysica. Acta., 2006, 1764(12), 1823-1841.
50. Halligan, B.D.; Ruotti, V.; Jin, W.; Laffoon, S.; Twigger, S.N. and Dratz, E.A. ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on twodimensional gels. Nucleic Acids Res., 2004, 32(Web Server issue), W638-W644.
51. Schlags, W.; Lachmann, B.; Walther, M.; Kratzel, M. and Noe, C.R. Two-dimensional electrophoresis of recombinant human erythropoietin: A future method for the European Pharmacopoeia? Proteomics, 2002, 2(6), 679-682.
52. Higuchi, M.; Oh-eda, M.; Kuboniwa, H.; Tomonoh, K.; Shimonaka, Y. and Ochi, N. Role of sugar chains in the expression of the biological activity of human erythropoietin. J. Biol. Chem., 1992, 267(11), 7703-7709.
53. Sasaki, H.; Bothner, B.; Dell, A. and Fukuda, M. Carbohydrate structure of erythropoietin expressed in Chinese hamster ovary cells by a human erythropoietin cDNA. J. Biol. Chem., 1987, 262(25), 12059-12076.
54. Martin, P.T. and Freeze, H.H. Glycobiology of neuromuscular disorders. Glycobiology, 2003, 13(8), 67R-75R.
55. Sagi, D.; Kienz, P.; Denecke, J.; Marquardt, T. and Peter-Katalinic, J. Glycoproteomics of N-glycosylation by in-gel deglycosylation and matrix-assisted laser desorption/ionisation-time of flight mass spectrometry mapping: application to congenital disorders of glycosylation. Proteomics, 2005, 5(10), 2689-2701.
56. Gupta, R.; Birch, H.; Rapacki, K.; Brunak, S. and Hansen, J.E. OGLYCBASE version 4.0: a revised database of O-glycosylated proteins. Nucleic Acids Res., 1999, 27(1), 370-372.
57. Xu, P. and Peng, J. Dissecting the ubiquitin pathway by mass spectrometry. Biochimica. Et. Biophysica. Acta, 2006, 1764(12), 1940-1947.
58. Weissman, A.M.; Shabek, N. and Ciechanover, A. The predator becomes the prey: regulating the ubiquitin system by ubiquitylation and degradation. Nat. Rev. Mol. Cell. Biol., 2011, 12(9), 605-620.
59. Chernorudskiy, A.L.; Garcia, A.; Eremin, E.V.; Shorina, A.S.; Kondratieva, E.V. and Gainullin, M.R. UbiProt: a database of ubiquitylated proteins. BMC Bioinformatics, 2007, 8, 126.
60. Radivojac, P.; Vacic, V.; Haynes, C.; Cocklin, R.R.; Mohan, A.; Heyen, J.W.; Goebl, M.G. and Iakoucheva, L.M. Identification, analysis, and prediction of protein ubiquitination sites. Proteins, 2010, 78(2), 365-380.
61. Kessler, B.M. and Edelmann, M.J. PTMs in conversation: activity and function of deubiquitinating enzymes regulated via posttranslational modifications. Cell Biochem. Biophys., 2011, 60(1-2), 21-38.
62. Sarge, K.D. and Park-Sarge, O.K. SUMO and its role in human diseases. Int. Rev. Cell. Mol. Biol., 2011, 288, 167-183.
63. Gareau, J.R. and Lima, C.D. The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nat. Rev. Mol. Cell Biol., 2010, 11(12), 861-871.
64. Ren, J.; Gao, X.; Jin, C.; Zhu, M.; Wang, X.; Shaw, A.; Wen, L.; Yao, X. and Xue, Y. Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0. Proteomics, 2009, 9(12), 3409-3412.
65. Maurer, M.H.; Haux, D.; Sakowitz, O.W.; Unterberg, A.W. and Kuschinsky, W. Identification of early markers for symptomatic vasospasm in human cerebral microdialysate after subarachnoid hemorrhage: Preliminary results of a proteome-wide screening. J. Cereb. Blood Flow Metab., 2007, 27(10), 1675-1683.
66. Maurer, M.H. Proteomics of brain extracellular fluid (ECF) and cerebrospinal fluid (CSF). Mass. Spectrom. Rev., 2010, 29(1), 17-28.
67. Maurer, M.H.; Haux, D.; Unterberg, A.W. and Sakowitz, O.W. Proteomics of human cerebral microdialysate: From detection of biomarkers to clinical application. Proteomics Clin. Appl., 2008, 2(3), 437-443.
68. Maurer, M.H.; Feldmann, R.E.; Fütterer, C.D.; Butlin, J. and Kuschinsky, W. Comprehensive proteome expression profiling of undifferentiated vs. differentiated neural stem cells from adult rat hippocampus. Neurochem. Res., 2004, 29(6), 1129-1144.
69. Maurer, M.H.; Feldmann, R.E. Jr.; Fütterer, C.D. and Kuschinsky, W. The proteome of neural stem cells from adult rat hippocampus. Proteome Sci., 2003, 1(1), 4.
70. Garavelli, J.S. The RESID Database of Protein Modifications: 2003 developments. Nucleic Acids Res., 2003, 31(1), 499-501.
71. Garavelli, J.S. The RESID Database of Protein Modifications as a resource and annotation tool. Proteomics, 2004, 4(6), 1527-1533.
72. Apweiler, R.; Bairoch, A. and Wu, C.H. Protein sequence databases. Curr. Opin. Chem. Biol., 2004, 8(1), 76-80.
73. Farriol-Mathis, N.; Garavelli, J.S.; Boeckmann, B.; Duvaud, S.; Gasteiger, E.; Gateau, A.; Veuthey, A.L. and Bairoch, A. Annotation of post-translational modifications in the Swiss-Prot knowledge base. Proteomics, 2004, 4(6), 1537-1550.
74. Hulo, N.; Bairoch, A.; Bulliard, V.; Cerutti, L.; De Castro, E.; Langendijk-Genevaux, P.S.; Pagni, M. and Sigrist, C.J. The PROSITE database. Nucleic Acids Res., 2006, 34(Database issue), D227-D230.
75. Apweiler, R.; Bairoch, A.; Wu, C.H.; Barker, W.C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M.; Martin, M.J.; Natale, D.A.; O'Donovan, C.; Redaschi, N. and Yeh, L.S. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res., 2004, 32(Database issue), D115-D119.
76. Peri, S.; Navarro, J.D.; Amanchy, R.; Kristiansen, T.Z.; Jonnalagadda, C.K.; Surendranath, V.; Niranjan, V.; Muthusamy, B.; Gandhi, T.K.; Gronborg, M.; Ibarrola, N.; Deshpande, N.; Shanker, K.; Shivashankar, H.N.; Rashmi, B.P.; Ramya, M.A.; Zhao, Z.; Chandrika, K.N.; Padma, N.; Harsha, H.C.; Yatish, A.J.; Kavitha, M.P.; Menezes, M.; Choudhury, D.R.; Suresh, S.; Ghosh, N.; Saravana, R.; Chandran, S.; Krishna, S.; Joy, M.; Anand, S.K.; Madavan, V.; Joseph, A.; Wong, G.W.; Schiemann, W.P.; Constantinescu, S.N.; Huang, L.; Khosravi-Far, R.; Steen, H.; Tewari, M.; Ghaffari, S.; Blobe, G.C.; Dang, C.V.; Garcia, J.G.; Pevsner, J.; Jensen, O.N.; Roepstorff, P.; Deshpande, K.S.; Chinnaiyan, A.M.; Hamosh, A.; Chakravarti, A. and Pandey, A. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res., 2003, 13(10), 2363-2371.
77. Hornbeck, P.V.; Chabra, I.; Kornhauser, J.M.; Skrzypek, E. and Zhang, B. PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics, 2004, 4(6), 1551-1561.
78. Kumar, Y.; Khachane, A.; Belwal, M.; Das, S.; Somsundaram, K. and Tatu, U. ProteoMod: A new tool to quantitate protein posttranslational modifications. Proteomics, 2004, 4(6), 1672-1683.
79. Wurgler-Murphy, S.M.; King, D.M. and Kennelly, P.J. The Phosphorylation Site Database: A guide to the serine-, threonine-, and/or tyrosine-phosphorylated proteins in prokaryotic organisms. Proteomics, 2004, 4(6), 1562-1570.
80. Blom, N.; Sicheritz-Ponten, T.; Gupta, R.; Gammeltoft, S. and Brunak, S. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics, 2004, 4(6), 1633-1649.
81. Macek, B.; Gnad, F.; Soufi, B.; Kumar, C.; Olsen, J.V.; Mijakovic, I. and Mann, M. Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol. Cell Proteomics, 2008, 7(2), 299-307.
82. Olsen, J.V.; Blagoev, B.; Gnad, F.; Macek, B.; Kumar, C.; Mortensen, P. and Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell, 2006, 127(3), 635-648.
83. Diella, F.; Cameron, S.; Gemund, C.; Linding, R.; Via, A.; Kuster, B.; Sicheritz-Ponten, T.; Blom, N. and Gibson, T.J. Phospho. ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics, 2004, 5, 79.
84. Jimenez, J.L.; Hegemann, B.; Hutchins, J.R.; Peters, J.M. and Durbin, R. A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database. Genome Biol., 2007, 8(5), R90.
85. Zanzoni, A.; Ausiello, G.; Via, A.; Gherardini, P.F. and Helmer-Citterich, M. Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucleic Acids Res., 2007, 35(Database issue), D229-D231.
86. Gribskov, M.; Fana, F.; Harper, J.; Hope, D.A.; Harmon, A.C.; Smith, D.W.; Tax, F.E. and Zhang, G. PlantsP: a functional genomics database for plant phosphorylation. Nucleic Acids Res., 2001, 29(1), 111-113.
87. Tchieu, J.H.; Fana, F.; Fink, J.L.; Harper, J.; Nair, T.M.; Niedner, R.H.; Smith, D.W.; Steube, K.; Tam, T.M.; Veretnik, S.; Wang, D. and Gribskov, M. The PlantsP and PlantsT Functional Genomics Databases. Nucleic Acids Res., 2003, 31(1), 342-344.
88. Obenauer, J.C.; Cantley, L.C. and Yaffe, M.B. Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res., 2003, 31(13), 3635-3641.
89. Amanchy, R.; Periaswamy, B.; Mathivanan, S.; Reddy, R.; Tattikota, S.G. and Pandey, A. A curated compendium of phosphorylation motifs. Nat. Biotechnol., 2007, 25(3), 285-286.
90. Doubet, S.; Bock, K.; Smith, D.; Darvill, A. and Albersheim, P. The complex carbohydrate structure database. Trends Biochem. Sci., 1989, 14(12), 475-477.
91. Cooper, C.A.; Joshi, H.J.; Harrison, M.J.; Wilkins, M.R. and Packer, N.H. GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003 update. Nucleic Acids Res., 2003, 31(1), 511-513.
92. Loss, A.; Bunsmann, P.; Bohne, A.; Loss, A.; Schwarzer, E.; Lang, E. and von der Lieth, C.W. SWEET-DB: an attempt to create annotated data collections for carbohydrates. Nucleic Acids Res., 2002, 30(1), 405-408.
93. Lee, T.Y.; Huang, H.D.; Hung, J.H.; Huang, H.Y.; Yang, Y.S. and Wang, T.H. dbPTM: an information repository of protein posttranslational modification. Nucleic Acids Res., 2006, 34(Database issue), D622-D627.
94. Vinayagam, A.; Pugalenthi, G.; Rajesh, R. and Sowdhamini, R. DSDBASE: a consortium of native and modelled disulphide bonds in proteins. Nucleic Acids Res., 2004, 32(Database issue), D200-D202.
95. Poisson, G.; Chauve, C.; Chen, X. and Bergeron, A. FragAnchor: A Large-scale predictor of glycosylphosphatidylinositol anchors in eukaryote protein sequences by qualitative scoring. Genomics, Proteomics Bioinformatics / Beijing Genomics Institute, 2007, 5(2), 121-130.
96. Creasy, D.M. and Cottrell, J.S. Unimod: Protein modifications for mass spectrometry. Proteomics, 2004, 4(6), 1534-1536.
97. Wilkins, M.R.; Gasteiger, E.; Gooley, A.A.; Herbert, B.R.; Molloy, M.P.; Binz, P.A.; Ou, K.; Sanchez, J.C.; Bairoch, A.; Williams, K.L. and Hochstrasser, D.F. High-throughput mass spectrometric discovery of protein post-translational modifications. J. Mol. Biol., 1999, 289(3), 645-657.
98. Hummel, J.; Niemann, M.; Wienkoop, S.; Schulze, W.; Steinhauser, D.; Selbig, J.; Walther, D. and Weckwerth, W. ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites. BMC Bioinformatics, 2007, 8, 216.