Systematic studies on TiO2-based phosphopeptide enrichment procedures upon in-solution and in-gel digestions of proteins. Are there readily applicable protocols suitable for matrix-assisted laser desorption/ionization mass spectrometrybased phosphopeptide stability estimations?

European Journal of Mass Spectrometry

Volumn 17, Issue 5, 2011, Pages 507-523

  Eickner, Thomas ^a   Mikkat, Stefan ^a   Lorenz, Peter ^a   Sklorz, Martin ^a,b   Zimmermann, Ralf ^a,b   Thiesen, Hans Jürgen ^a   Glockera, Michael O ^a  

^a UNIVERSITY OF ROSTOCK   (Germany)

^b INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

Affinity mass spectrometry; Chemical dephosphorylation; Citric acid; Dephosphorylation; MALDI MS; Mass spectrometry; NuTips; Phosphopeptide analysis; Phosphopeptide enrichment; Phosphorylation; TiO2; Titanium dioxide

Indexed keywords

2,4,6 TRIHYDROXYACETOPHENONE; 2,4,6-TRIHYDROXYACETOPHENONE; 2,5-DIHYDROXYBENZOIC ACID; ACETOPHENONE DERIVATIVE; CASEIN; CITRIC ACID; GENTISIC ACID; PHOSPHOPEPTIDE; REPRESSOR PROTEIN; STATHMIN; STMN1 PROTEIN, RAT; TITANIUM; TITANIUM DIOXIDE; TRIM28 PROTEIN, HUMAN;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; CRYSTALLIZATION; GEL; ISOLATION AND PURIFICATION; MASS SPECTROMETRY; METHODOLOGY; MOLECULAR GENETICS; PHOSPHORYLATION; POLYACRYLAMIDE GEL ELECTROPHORESIS; SOLUTION AND SOLUBILITY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ACETOPHENONES; AMINO ACID SEQUENCE; CASEINS; CITRIC ACID; CRYSTALLIZATION; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GELS; GENTISATES; MOLECULAR SEQUENCE DATA; PHOSPHOPEPTIDES; PHOSPHORYLATION; REPRESSOR PROTEINS; SOLUTIONS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; STATHMIN; TITANIUM;

EID: 84255209634     PISSN: 14690667     EISSN: None     Source Type: Journal    
DOI: 10.1255/ejms.1134     Document Type: Article

References (44)

1. T.E. Thingholm, O.N. Jensen and M.R. Larsen, "Analytical strategies for phosphoproteomics", Proteomics 9(6), 1451 (2009). doi. 10.1002/pmic.200800454
2. M.R. Larsen, T.E. Thingholm, O.N. Jensen, P. Roepstorff and T.J.D. Jorgensen, "Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns", Mol. Cell. Proteomics 4(7), 873 (2005). doi: 10.1074/mcp.T500007-MCP200 (Pubitemid 41309146)
3. S.S. Jensen and M.R. Larsen, "Evaluation of the impact of some experimental procedures on different phophopeptide enrichment techniques", Rapid Commun. Mass Spectrom. 21, 3635 (2007). doi: 10.1002/rcm.3254 (Pubitemid 350124632)
4. S. Mikkat, C. Koy, M. Ulbrich, B. Ringel and M.O. Glocker, "Mass spectrometric protein structure characterization reveals cause of migration differences of haptoglobin α-chains in two dimensional gel electrophoresis", Proteomics 4, 3921 (2004). doi: 10.1002/pmic.200400825 (Pubitemid 39657467)
5. M.B. Gates, K.B. Tomer and L.J. Deterding, "Comparison of metal and metal oxide media for phosphopeptide enrichment prior to mass spectrometric analyses", J. Am. Soc. Mass. Spectrom. 21(10), 1649 (2010). doi: 10.1016/j.jasms.2010.06.005
6. T.E. Thingholm, T.J. Jorgensen, O.N. Jensen and M.R. Larsen, "Highly selective enrichment of phosphorylated peptides using titanium dioxide", Nat. Protoc. 1(4), 1929 (2006). doi: 10.1038/nprot.2006.185 (Pubitemid 46773313)
7. S. Mikkat, P. Lorenz, C. Scharf, X. Yu, M.O. Glocker and S.M. Ibrahim, "MS characterization of qualitative protein polymorphisms in the spinal cords of inbred mouse strains", Proteomics 10(5), 1050 (2010). doi: 10.1002/pmic.200800932
8. X. Yang, H. Wu, T. Kobayashi, R.J. Solaro and R.B. van Breemen, "Enhanced ionization of phosphorylated peptides during MALDI TOF mass spectrometry", Anal. Chem. 76(5), 1532 (2004). doi: 10.1021/ac035203v (Pubitemid 38280506)
9. S.I. Snovida, J.M. Rak-Banville and H. Perreault, "On the use of DHB/aniline and DHB/N,N-dimethylaniline matrices for improved detection of carbohydrates: Automated identification of oligosaccharides and quantitative analysis of sialylated glycans by MALDI-TOF mass spectrometry", J. Am. Soc. Mass Spectrom. 19(8), 1138 (2008). doi: 10.1016/j.jasms.2008.04.033
10. D. Kang, Y.S. Gho, M. Suh and C. Kang, "Highly sensitive and fast protein detection with Coomassie brilliant blue in sodium dodecyl sulfate-polyacrylamide gel electrophoresis", Bull. Korean Chem. Soc. 23(11), 1511 (2002).
11. J.C. Heitner, C. Koy, M. Kreutzer, M. Gerber, T. Reimer and M.O. Glocker, "Differentiation of HELLP patients from healthy pregnant women by proteome analysis-On the way towards a clinical marker set", J. Chromatogr. B 840(1), 10 (2006). doi: 10.1016/j.jchromb.2006.06.002 (Pubitemid 44108804)
12. A. Sinz, M. Bantscheff, S. Mikkat, B. Ringel, S. Drynda, J. Kekow, H.-J. Thiesen and M.O. Glocker, "Mass spectrometric proteome analyses of synovial fluids and plasmas from patients suffering from rheumatoid arthritis and comparison to reactive arthritis or osteoarthritis", Electrophoresis 23, 3445 (2002). doi: 10.1002/1522-2683(200210)23:193.0.CO;2-J
13. M. Kienbaum, C. Koy, H.V. Montgomery, S. Drynda, P. Lorenz, H. Illges, K. Tanaka, J. Kekow, R. Guthke, H.J. Thiesen and M.O. Glocker, "MS characterization of apheresis samples from rheumatoid arthritis patients for the improvement of immunoadsorption therapy-a pilot study", Proteomics Clin. Appl. 3(7), 797 (2009). doi: 10.1002/prca.200800232
14. M.R. Larsen, P. Hojrup and P. Roepstorff, "Characterization of gel-separated glycoproteins using two-step proteolytic digestion combined with sequential microcolumns and mass spectrometry", Mol. Cell Proteomics 4(2), 107 (2005). doi: 10.1074/mcp.M400068-MCP200 (Pubitemid 40361174)
15. N. Sugiyama, T. Masuda, K. Shinoda, A. Nakamura, M. Tomita and Y. Ishihama, "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications", Mol. Cell Proteomics 6(6), 1103 (2007). doi: 10.1074/mcp.T600060-MCP200 (Pubitemid 47019410)
16. 2 nanoparticles in aqueous suspensions at acidic and circumneutral pH: surface coverage, surface speciation, and its impact on nanoparticle-nanoparticle interactions", J. Am. Chem. Soc. 132(42), 14986 (2010). doi: 10.1021/ja106091q
17. T.W. Jaskolla, W.D. Lehmann and M. Karas, "4-Chloro-alpha- cyanocinnamic acid is an advanced, rationally designed MALDI matrix", Proc. Natl. Acad. Sci. USA 105(34), 12200 (2008). doi: 10.1073/pnas.0803056105
18. P. Juhasz, C.E. Costello and K. Biemann, "Matrix-assisted laser desorption ionization mass-spectrometry with 2-(4-hydroxyphenylazo)benzoic acid matrix", J. Am. Soc. Mass Spectrom. 4(5), 399 (1993). doi: 10.1016/1044-0305(93)85005-I
19. S. Kjellstrom and O.N. Jensen, "Phosphoric acid as a matrix additive for MALDI MS analysis of phosphopeptides and phosphoproteins", Anal. Chem. 76(17), 5109 (2004). doi: 10.1021/ac0400257 (Pubitemid 39180341)
20. S. Liu, C. Zhang, J.L. Campbell, H. Zhang, K.K. Yeung, V.K. Han and G.A. Lajoie, "Formation of phosphopeptide- metal ion complexes in liquid chromatography/electrospray mass spectrometry and their influence on phosphopeptide detection", Rapid Commun. Mass Spectrom. 19(19), 2747 (2005). doi: 10.1002/rcm.2105 (Pubitemid 41383356)
21. R.D. Smith, R. Zhao, S.J. Ding, Y.F. Shen, D.G. Camp, E.A. Livesay and H. Udseth, "Automated metal-free multiple-column nanoLC for improved phosphopeptide analysis sensitivity and throughput", J. Chromatogr. B: Anal. Technol. Biomed. Life Sci. 877(8-9), 663 (2009). doi: 10.1016/j.jchromb. 2008.12.068
22. Y. Yu, J. Ahn, M. Gilar and J.C. Gebler, "Nano-scale ion pairing ultra-performance liquid chromatography coupled with QToF mass spectrometry for the separation analysis of phosphopeptides", J. Biomol. Technol. 18(1), 22 (2007).
23. A.C. Groner, S. Meylan, A. Ciuffi, N. Zangger, G. Ambrosini, N. Denervaud, P. Bucher and D. Trono, "KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading", PLoS Genet. 6(3), e1000869 (2010). doi: 10.1371/journal.pgen. 1000869
24. S. Iyengar and P.J. Farnham, "KAP1: An enigmatic master regulator of the genome", J. Biol. Chem. (2011). doi: 10.1074/jbc.R111.252569
25. J. Jakobsson, M.I. Cordero, R. Bisaz, A.C. Groner, V. Busskamp, J.C. Bensadoun, F. Cammas, R. Losson, I.M. Mansuy, C. Sandi and D. Trono, "KAP1-mediated epigenetic repression in the forebrain modulates behavioral vulnerability to stress", Neuron 60(5), 818 (2008). doi: 10.1016/j.neuron.2008.09.036
26. J.F. Margolin, J.R. Friedman, W.K. Meyer, H. Vissing, H.J. Thiesen and F.J. Rauscher, 3rd, "Kruppel-associated boxes are potent transcriptional repression domains", Proc. Natl. Acad. Sci. USA 91(10), 4509 (1994).
27. H.J. Thiesen, "Multiple genes encoding zinc finger domains are expressed in human T cells", New Biol. 2(4), 363 (1990).
28. R. Urrutia, "KRAB-containing zinc-finger repressor proteins", Genome Biol. 4(10), 231 (2003). doi: 10.1186/gb-2003-4-10-231 (Pubitemid 37361951)
29. S. Gauci, A.O. Helbig, M. Slijper, J. Krijgsveld, A.J. Heck and S. Mohammed, "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach", Anal. Chem. 81(11), 4493 (2009). doi: 10.1021/ac9004309
30. J.V. Olsen, B. Blagoev, F. Gnad, B. Macek, C. Kumar, P. Mortensen and M. Mann, "Global, in vivo, and site-specific phosphorylation dynamics in signal ing networks", Cell 127(3), 635 (2006). doi: 10.1016/j.cell.2006.09. 026 (Pubitemid 44647421)
31. B. Wang, R. Malik, E.A. Nigg and R. Korner, "Evaluation of the low-specificity protease elastase for large-scale phosphoproteome analysis", Anal. Chem. 80(24), 9526 (2008). doi: 10.1021/ac801708p
32. B.W. Gibson and P. Cohen, "Liquid secondary ion mass spectrometry of phosphorylated and sulfated peptides and proteins", Methods Enzymol. 193, 480 (1990). doi: 10.1016/0076-6879(90)93434-M
33. E.S. Simon, M. Young, A. Chan, Z.Q. Bao and P.C. Andrews, "Improved enrichment strategies for phosphorylated peptides on titanium dioxide using methyl esterification and pH gradient elution", Anal. Biochem. 377(2), 234 (2008). doi: 10.1016/j.ab.2008.03.024
34. R.S. Annan and S.A. Carr, "Phosphopeptide analysis by matrix-assisted laser desorption time-of-flight mass spectrometry", Anal. Chem. 68(19), 3413 (1996). doi: 10.1021/ac960221g (Pubitemid 26359705)
35. T. Kirschstein, S. Mikkat, U. Mikkat, R. Bender, M. Kreutzer, R. Schulz, R. Köhling and M.O. Glocker, "The 27-kDa heat shock protein (HSP27) is a reliable hippocampal marker of full developement of pilocarpine- induced status epilepticus", Epilepsia Res. in press, (2011).
36. 2S complex with two tubulin molecules", Biochemistry 36(36), 10817 (1997). doi: 10.1021/bi971491b (Pubitemid 27396235)
37. A. Tholey, J. Reed and W.D. Lehmann, "Electrospray tandem mass spectrometric studies of phosphopeptides and phosphopeptide analogues", J. Mass Spectrom. 34(2), 117 (1999). doi: 10.1002/(SICI)1096-9888(199902)34:23.0. CO;2-V
38. F. Tan, Y. Zhang, J. Wang, J. Wei, Y. Cai and X. Qian, "An efficient method for dephosphorylation of phosphopeptides by cerium oxide", J. Mass Spectrom. 43(5), 628 (2008). doi: 10.1002/jms.1362 (Pubitemid 351785688)
39. S. Sun, H. Ma, G. Han, R. Wu, H. Zou and Y. Liu, "Efficient enrichment and identification of phosphopeptides by cerium oxide using on-plate matrix-assisted laser desorption/ ionization time-of-flight mass spectrometric analysis", Rapid Commun. Mass Spectrom. 25(13), 1862 (2011). doi: 10.1002/rcm.5055
40. F. Kjeldsen, M.M. Savitski, M.L. Nielsen, L. Shi and R.A. Zubarev, "On studying protein phosphorylation patterns using bottom-up LC-MS/MS: the case of human alpha-casein", Analyst 132(8), 768 (2007). doi: 10.1039/b701902e (Pubitemid 47101563)
41. D.W. West, "Structure and function of the phosphorylated residues of casein", J. Dairy Res. 53(2), 333 (1986).
42. K.L. Haas and K.J. Franz, "Application of metal coordination chemistry to explore and manipulate cell biology", Chem. Rev. 109(10), 4921 (2009). doi: 10.1021/cr900134a
43. D. Barford, "Molecular mechanisms of the protein serine/ threonine phosphatases", Trends Biochem. Sci. 21(11), 407 (1996). doi: 10.1016/S0968-0004(96)10060-8 (Pubitemid 26393726)
44. J. Su, C. Schlicker and K. Forchhammer, "A third metal is required for catalytic activity of the signal-transducing protein phosphatase M tPphA", J. Biol. Chem. 286(15), 13481 (2011). doi: 10.1074/jbc.M109.036467