Skip to main content
SpringerLink
Log in

Applications of Chemical Tagging Approaches in Combination with 2DE and Mass Spectrometry

  • Protocol
  • First Online:
Two-Dimensional Electrophoresis Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 519))

Summary

Chemical modification reactions play an important role in various protocols for mass-spectrometry-based proteome analysis; this applies to both gel-based and gel-free proteomics workflows. In combination with two-dimensional gel electrophoresis (2DE), the addition of “tags” by means of chemical reactions serves several purposes. Potential benefits include increased sensitivity or sequence coverage for peptide mass fingerprinting and improved peptide fragmentation for de novo sequencing studies. Tagging strategies can also be used to obtain complementary quantitative information in addition to densitometry, and they may be employed for the study of post-translational modifications. In combination with the unique advantages of 2DE as a separation technique, such approaches provide a powerful toolbox for proteomic research. In this review, relevant examples from recent literature will be given to illustrate the capabilities of chemical tagging approaches, and methodological requirements will be discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Henzel, W. J., Billeci, T. M., Stults, J. T., Wong, S. C., Grimley, C., and Watanabe, C. (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. U.S.A. 90, 5011–5015

    Article  PubMed  CAS  Google Scholar 

  2. Yates, III, J. R., Speicher, S., Griffin, P. R., and Hunkapiller, T. (1993) Peptide mass maps: a highly informative approach to protein identification. Anal. Biochem. 214, 397–408

    Article  PubMed  CAS  Google Scholar 

  3. James, P., Quadroni, M., Carafoli, E., and Gonnet, G. (1994) Protein identification in DNA databases by peptide mass ­fingerprinting. Protein Sci. 3, 1347–1350

    Article  PubMed  CAS  Google Scholar 

  4. Pappin, D. J. C., Hojrup, P., and Bleasby, A. J. (1993) Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 3, 327–332

    Article  PubMed  CAS  Google Scholar 

  5. Mann, M., Hojrup, P., and Roepstorff, P. (1993) Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol. Mass Spectrom. 22, 338–345

    Article  PubMed  CAS  Google Scholar 

  6. Nesvizhskii, A. I., and Aebersold, R. (2005) Interpretation of shotgun proteomic data – the protein inference problem. Mol. Cell. Proteomics 4, 1419–1440

    Article  PubMed  CAS  Google Scholar 

  7. Canelle, L., Pionneau, C., Marie, A., Bousquet, J., Bigeard, J., Lutomski, D., et al (2004) Automating proteome analysis: improvements in throughput, quality and accuracy of protein identification by peptide mass fingerprinting. Rapid Commun. Mass Spectrom. 18, 2785–2794

    Article  PubMed  CAS  Google Scholar 

  8. Jahn, O., Hesse, D., Reinelt, M., and Kratzin, H. D. (2006) Technical innovations for the automated identification of gel-separated proteins by MALDI-TOF mass spectrometry. Anal. Bioanal. Chem. 386, 92–103

    Article  PubMed  CAS  Google Scholar 

  9. Sun, W., Gao, S. J., Wang, L. J., Chen, Y., Wu, S. Z., Wang, X. R., et al (2006) Microwave-assisted protein preparation and enzymatic digestion in proteomics. Mol. Cell. Proteomics 5, 769–776

    PubMed  CAS  Google Scholar 

  10. Lopez-Ferrer, D., Capelo, J. L., and Vazquez, J. (2006) Ultra fast trypsin digestion of proteins by high intensity focused ultrasound. J. Proteome Res. 4, 1569–1574

    Article  Google Scholar 

  11. Bienvenut, W. V., Deon, C., Pasquarello, C., Campbell, J. M., Sanchez, J. C., Vesta, M. L., et al (2002) Matrix-assisted laser desorption/ionization-tandem mass spectrometry with high resolution and sensitivity for identification and characterization of proteins. Proteomics 2, 868–876

    Article  PubMed  CAS  Google Scholar 

  12. Xu, C., and Ma, B. (2006) Software for computational peptide identification from MS-MS data. Drug Disc. Today 11, 595–600

    Article  CAS  Google Scholar 

  13. Palagi, P. M., Hernandez, P., Walther, D., and Appel, R. D. (2006) Proteome informatics I: bioinformatics tools for processing experimental data. Proteomics 6, 5435–5444

    Article  PubMed  CAS  Google Scholar 

  14. Leitner, A., and Lindner, W. (2004) Current chemical tagging strategies for proteome analysis by mass spectrometry. J. Chromatogr. B 813, 1–26

    Article  CAS  Google Scholar 

  15. Mirzaei, H., and Regnier, F. (2005) Structure specific chromatographic selection in targeted proteomics. J. Chromatogr. B 817, 23–34

    Article  CAS  Google Scholar 

  16. Ong, S.-E., and Mann, M. (2005) Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1, 252–262

    Article  PubMed  CAS  Google Scholar 

  17. Regnier, F. E., and Julka, S. (2006) Primary amine coding as a path to comparative proteomics. Proteomics 6, 3968–3979

    Article  PubMed  CAS  Google Scholar 

  18. Leitner, A., and Lindner, W. (2006) Chemistry meets proteomics: the use of chemical tagging reactions for mass spectrometry-based proteomics. Proteomics 6, 5418–5434

    Article  PubMed  CAS  Google Scholar 

  19. Krause, E., Wenschuh, H., and Jungblut, P. R. (1999) The dominance of arginine-­containing peptides in MALDI-derived tryptic mass fingerprints of proteins. Anal. Chem. 71, 4160–4165

    Article  PubMed  CAS  Google Scholar 

  20. Baumgart, S., Lindner, Y., Kühne, R., ­Oberemm, A., Wenschuh, H., and Krause, E. (2004) The contributions of specific amino acid side chains to signal intensities of peptides in matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 18, 863–868

    Article  PubMed  CAS  Google Scholar 

  21. Schlosser, G., Pocsfalvi, G., Huszár, E., Malorni, A., and Hudesz, F. (2005) MALDI-TOF mass spectrometry of a combinatorial peptide library: effect of matrix composition on signal suppression. J. Mass Spectrom. 40, 1590–1594

    Article  PubMed  CAS  Google Scholar 

  22. Miller, I., Crawford, J., and Gianazza, E. (2006) Protein stains for proteomic applications: which, when, why? Proteomics 6, 5385–5408

    Article  PubMed  CAS  Google Scholar 

  23. Jacobs, J. M., Adkins, J. N., Qian, W.-J., Liu, T., Shen, Y. F., et al (2005) Utilizing human blood plasma for proteomic biomarker discovery. J. Proteome Res. 4, 1073–1085

    Article  PubMed  CAS  Google Scholar 

  24. Gong, Y., Li, X., Yang, B., Ying, W. T., Li, D., Zhang, Y. J., et al (2006) Different immunoaffinity fractionation strategies to characterize the human plasma proteome. J. Proteome Res. 5, 1379–1387

    Article  PubMed  CAS  Google Scholar 

  25. Brancia, F. L., Oliver, S. G., and Gaskell, S. J. (2000) Improved matrix-assisted laser desorption/ionization mass spectrometric analysis of tryptic hydrolysates of proteins following guanidination of lysine-containing peptides. Rapid Commun. Mass Spectrom. 14, 2070–2073

    Article  PubMed  CAS  Google Scholar 

  26. Beardsley, R. L., and Reilly, J. P. (2002) Optimization of guanidination procedures for MALDI mass mapping. Anal. Chem. 74, 1884–1890

    Article  PubMed  CAS  Google Scholar 

  27. Beardsley, R. L., Sharon, L. A., and Reilly, J. P. (2005) Peptide de novo sequencing facilitated by a dual-labeling strategy. Anal. Chem. 77, 6300–6309

    Article  PubMed  CAS  Google Scholar 

  28. Brancia, F. L., Butt, A., Beynon, R. J., Hubbard, S. J., Gaskell, S. J., and Oliver, S. G. (2001) A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics. Electrophoresis 22, 552–559

    Article  PubMed  CAS  Google Scholar 

  29. Cockrill, S. L., Foster, K. L., Wildsmith, J., Goodrich, A. R., Dapron, A. R., Hassell, T. C., et al (2005) Efficient micro-recovery and guanidination of peptides directly from MALDI target spots. Biotechniques 38, 301–304

    Article  PubMed  CAS  Google Scholar 

  30. Sergeant, K., Samyn, B., Debyser, G., and Van Beeumen, J. (2005) De novo sequence analysis of N-terminal sulfonated peptides after in-gel guanidination. Proteomics 5, 2369–2380

    Article  PubMed  CAS  Google Scholar 

  31. Warwood, S., Mohammed, S., Cristea, I. M., Evans, C., Whetton, A. D., and Gaskell, S. J. (2006) Guanidination chemistry for qualitative and quantitative proteomics. Rapid Commun. Mass Spectrom. 20, 3245–3256

    Article  PubMed  CAS  Google Scholar 

  32. Ji, C., Guo, N., and Li, L. (2005) Differential dimethyl labeling of N-termini of peptides after guanidination for proteome analysis. J. Proteome Res. 4, 2099–2108

    Article  PubMed  CAS  Google Scholar 

  33. Beardsley, R. L., and Reilly, J. P. (2003) Quantitation using enhanced signal tags: a technique for comparative proteomics. J. Proteome Res. 2, 15–21

    Article  PubMed  CAS  Google Scholar 

  34. Peters, E. C., Horn, D. M., Tully, D. C., and Brock, A. (2001) A novel multifunctional labeling reagent for enhanced protein characterization with mass spectrometry. Rapid Commun. Mass Spectrom. 15, 2387–2392

    Article  PubMed  CAS  Google Scholar 

  35. Cindric, M., Cepo, T., Skrlin, A., Vuletic, M., and Bindila, L. (2006) Accelerated on-column lysine derivatization and cysteine methylation by imidazole reaction in a deuterated environment for enhanced product ion analysis. Rapid Commun. Mass Spectrom. 20, 694–702

    Article  PubMed  CAS  Google Scholar 

  36. Fierro-Monti, I., Mohammed, S., Matthiesen, R., Santoro, R., Burns, J. S., Williams, D. J., et al (2006) Quantitative proteomics identifies Gemin5, a scaffolding protein involved in ribonucleoprotein assembly, as a novel partner for eukaryotic initiation factor 4E. J. Proteome Res. 5, 1367–1378

    Article  PubMed  CAS  Google Scholar 

  37. Cindric, M., Bindila, L., Cepo, T., and Peter-Katalinic, J. (2006) Mass spectrometry-based glycoproteomic approach involving lysine derivatization for structural characterization of recombinant human erythropoietin. J. Proteome Res. 5, 3066–3076

    Article  PubMed  CAS  Google Scholar 

  38. Joss, J. L., Molloy, M. P., Hinds, L. A., and Deane, A. M. (2006) Evaluation of chemical derivatisation methods for protein identification using MALDI MS/MS. Int. J. Pept. Res. Ther. 12, 225–235

    Article  CAS  Google Scholar 

  39. Pashkova, A., Moskovets, E., and Karger, B. L. (2004) Coumarin tags for improved analysis of peptides by MALDI-TOF MS and MS/MS. 1. Enhancement in MALDI MS signal intensities. Anal. Chem. 76, 4550–4557

    Article  PubMed  CAS  Google Scholar 

  40. Pashkova, A., Chen, H.-S., Rejtar, T., Zang, X., Giese, R., Andreev, V., et al (2005) Coumarin tags for analysis of peptides by MALDI-TOF MS and MS/MS. 2. Alexa Fluor 350 tag for increased peptide and protein identification by LC-MALDI-TOF/TOF MS. Anal. Chem. 77, 2085–2096

    Article  PubMed  CAS  Google Scholar 

  41. Ullmer, R., Plematl, A., and Rizzi, A. (2006) Derivatization by 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate for enhancing the ionization yield of small peptides and glycopeptides in matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry. Rapid Commun. Mass Spectrom. 20, 1469–1479

    Article  PubMed  CAS  Google Scholar 

  42. Park, S.-J., Song, J.-S., and Kim, H.-J. (2005) Dansylation of tryptic peptides for increased sequence coverage in protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric peptide mass fingerprinting. Rapid Commun. Mass Spectrom. 19, 3089–3096

    Article  PubMed  CAS  Google Scholar 

  43. Amoresano, A., Monti, G., Cirulli, C., and Marino, G. (2006) Selective detection and identification of phosphopeptides by dansyl MS/MS/MS fragmentation. Rapid Commun. Mass Spectrom. 20, 1400–1404

    Article  PubMed  CAS  Google Scholar 

  44. Cramer, R., and Corless, S. (2001) The nature of collision-induced dissociation processes of doubly protonated peptides: comparative study for the future use of matrix-assisted laser desorption/ionization on a hybrid quadrupole time-of-flight mass spectrometer in proteomics. Rapid Commun. Mass Spectrom. 15, 2058–2066

    Article  PubMed  CAS  Google Scholar 

  45. Keough, T., Youngquist, R. S., and Lacey, M. P. (1999) A method for high-sensitivity peptide sequencing using post-source decay matrix-assisted laser desorption ionisation mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 96, 7131–7136

    Article  PubMed  CAS  Google Scholar 

  46. Keough, T., Lacey, M. P., and Youngquist, R. S. (2002) Solid-phase derivatization of tryptic peptides for rapid protein identification by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 16, 1003–1015

    Article  PubMed  CAS  Google Scholar 

  47. Samyn, B., Sergeant, K., Memmi, S., Debyser, G., Devreese, B., and van Beeumen, J., (2006) MALDI-TOF/TOF de novo sequence analysis of 2-D PAGE-separated proteins from Halorhodospira halophila, a bacterium with unsequenced genome. Electrophoresis 27, 2702–2711

    Article  PubMed  CAS  Google Scholar 

  48. Samyn, B., Sergeant, K., Carpentier, S., Debyser, G., Panis, B., Swennen, R., et al (2007) Functional proteome analysis of the banana plant (Musa spp.) using de novo sequence analysis of derivatized peptides. J. Proteome Res. 6, 70–80

    Article  PubMed  CAS  Google Scholar 

  49. Gevaert, K., Demol, H., Martens, L., ­Hoorelbeke, B., Pupye, M., Goethals, M, et al (2001) Protein identification based on matrix assisted laser desorption/ionization-post source decay-mass spectrometry. Electrophoresis 22, 1645–1651

    Article  PubMed  CAS  Google Scholar 

  50. Chen, P., Nie, S., Mi, W., Wang, X.-C., and Liang, S.-P. (2004) De novo sequencing of tryptic peptides sulfonated by 4-sulfophenyl isothiocyanate for unambiguous protein identification using post-source decay ­matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 18, 191–198

    Article  PubMed  CAS  Google Scholar 

  51. Hjernø, K., Alm, R., Canbäck, B., Matthiesen, R., Trajkovski, K., Bjork, L., et al (2006) Down-regulation of the strawberry Bet v 1-homologous allergen in concert with the flavonoid biosynthesis pathway in colorless strawberry mutant. Proteomics 6, 1574–1587

    Article  PubMed  Google Scholar 

  52. Wang, D., Kalb, S. R., and Cotter, R. J. (2004) Improved procedures for N-terminal sulfonation of peptides for matrix-assisted laser desorption/ionization post-source decay peptide sequencing. Rapid Commun. Mass Spectrom. 18, 96–102

    Article  PubMed  CAS  Google Scholar 

  53. Wang, D., and Cotter, R. J. (2005) Approach for determining protein ubiquitination sites by MALDI-TOF mass spectrometry. Anal. Chem. 77, 1458–1466

    Article  PubMed  CAS  Google Scholar 

  54. Guillaume, E., Panchaud, A., Affolter, M., Desvergnes, V., and Kussmann, M. (2006) Differentially isotope-coded N-terminal protein sulphonation: combining protein identification and quantification. Proteomics 6, 2338–2349

    Article  PubMed  CAS  Google Scholar 

  55. Alley Jr., W., Mechref, Y., Klouckova, I., and Novotny, M. V. (2007) Improved collision-induced dissociation analysis of peptides by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry through 3-sulfobenzoic acid succinimidyl ester labeling. J. Proteome Res. 6, 124–132

    Article  Google Scholar 

  56. Righetti, P. G., Castagna, A., Antonucci, F., Piubelli, C., Cecconi, D., Campostrini, N., et al (2004) Critical survey of quantitative proteomics in two-dimensional electrophoretic approaches. J. Chromatogr. A 1051, 3–17

    Article  PubMed  CAS  Google Scholar 

  57. Yan, W., and Chen, S. S. (2005) Mass spectrometry-based quantitative proteomic profiling. Brief. Funct. Genomic. Proteomic. 4, 27–38

    Article  PubMed  CAS  Google Scholar 

  58. Beynon, R. J., and Pratt, J. M. (2005) Metabolic labeling of proteins for proteomics. Mol. Cell. Proteomics 4, 857–872

    Article  PubMed  CAS  Google Scholar 

  59. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994–999

    Article  PubMed  CAS  Google Scholar 

  60. Smolka, M., and Zhou, H. (2002) Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry. Mol. Cell. Proteomics 1, 19–29

    Article  PubMed  CAS  Google Scholar 

  61. Hansen, K. C., Schmitt-Ulms, G., Chalkley, R. J., Hirsch, J., et al (2003) Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography. Mol. Cell. Proteomics 2, 299–314

    PubMed  CAS  Google Scholar 

  62. Ross, P. L., Huang, Y. L. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., et al (2004) Multiplexed protein quantitation on Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. ­Proteomics 3, 1154–1169

    Article  PubMed  CAS  Google Scholar 

  63. Froment, C., Uttenweiler-Joseph, S., Bousquet-Dubouch, M.-P., Matondo, M., Borges, J. P, Esmenjaud, C., et al (2005) A quantitative proteomic approach using two-dimensional gel electrophoresis and isotope-coded affinity tag labeling for studying human 20S proteasome heterogeneity. Proteomics 5, 2351–2363

    Article  PubMed  CAS  Google Scholar 

  64. Schmidt, F., Dahlmann, B., Janek, K., Kloß, A., Wacker, M., Ackermann, R., et al (2006) Comprehensive quantitative proteome analysis of 20S proteasome subtypes from rat liver by isotope coded affinity tag and 2-D gel-based approaches. Proteomics 6, 4622–4632

    Article  PubMed  CAS  Google Scholar 

  65. Sachon, E., Mohammed, S., Bache, N., and Jensen, O. N. (2006) Phosphopeptide quantitation using amine-reactive isobaric tagging reagents and tandem mass spectrometry: applications to proteins isolated by gel electrophoresis. Rapid Commun. Mass Spectrom. 20, 1127–1134

    Article  PubMed  CAS  Google Scholar 

  66. Borner, G. H. H., Harbour, M., Hester, S., Lilley, K. S., and Robinson, M. S. (2006) Comparative proteomics of clathrin-coated vesicles. J. Cell Biol. 175, 571–578

    Article  PubMed  CAS  Google Scholar 

  67. Schmidt, F., Donahoe, S., Hagens, K., ­Mattow, J., Schaible, V. E., Kaufmann, S. H. E., et al (2004) Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology. Mol. Cell. Proteomics 3, 24–42

    PubMed  CAS  Google Scholar 

  68. Choe, L. H., Aggarwal, K., Franck, Z., and Lee, K. H. (2005) A comparison of the consistency of proteome quantitation using two-dimensional electrophoresis and shotgun isobaric tagging in Escherichia coli cells. Electrophoresis 26, 2437–2449

    Article  PubMed  CAS  Google Scholar 

  69. Reinders, Y., Schulz, I., Gräf, R., and Sickmann, A. (2006) Identification of novel centrosomal proteins in Dictyostelium discoideum by comparative proteomic approaches. J. Proteome Res. 5, 589–598

    Article  PubMed  CAS  Google Scholar 

  70. Wu, W. W., Wang, G., Baek, S. J., and Shen, R.-F. (2006) Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. J. Proteome Res. 5, 651–658

    Article  PubMed  CAS  Google Scholar 

  71. Schmidt, A., Kellermann, J., and Lottspeich, F. (2005) A novel strategy for quantitative proteomics using isotope-coded labels. ­Proteomics 5, 4–15

    Article  PubMed  CAS  Google Scholar 

  72. Hochleitner, E. O., Kastner, B., Fröhlich, T., Schmidt, A., Luhrmann, R., Arnold, G., et al (2005) Protein stoichiometry of a multiprotein complex, the human spliceosomal U1 small nuclear ribonucleoprotein. J. Biol. Chem. 280, 2536–2542

    Article  PubMed  CAS  Google Scholar 

  73. Sarioglu, H., Brandner, S., Jacobsen, C., Meindl, T., Schmidt, A., Kellermann, J., et al (2006) Quantitative analysis of 2,3,7,8-­tetrachlorodibenzo-p-dioxin-induced proteome alterations in 5L rat hepatoma cells using isotope-coded protein labels. Proteomics 6, 2407–2421

    Article  PubMed  CAS  Google Scholar 

  74. Münchbach, M., Quadroni, M., Miotto, G., and James, P. (2000) Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety. Anal. Chem. 72, 4047–4057

    Article  PubMed  Google Scholar 

  75. Tabbert, A., Kappes, F., Knippers, R., Kellermann, J., Lottspeich, F., and Ferrando-May, E. (2006) Hypophosphorylation of the architectural chromatin protein DEK in death-receptor-induced apoptosis revealed by the isotope coded protein label proteomic platform. Proteomics 6, 5758–5772

    Article  PubMed  CAS  Google Scholar 

  76. Sechi, S. (2002) A method to identify and simultaneously determine the relative quantities of proteins isolated by gel electrophoresis. Rapid Commun. Mass Spectrom. 16, 1416–1424

    Article  PubMed  CAS  Google Scholar 

  77. Gehanne, S., Cecconi, D., Carboni, L., Righetti, P. G., Domenici, E., and Hamdan, M. (2002) Quantitative analysis of two-dimensional gel-separated proteins using isotopically marked alkylated agents and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 16, 1692–1698

    Article  PubMed  CAS  Google Scholar 

  78. Cahill, M. A., Wozny, W., Schwall, G., Schroer, K., Holzer, K., Poznanovic, S., et al (2003) Analysis of relative isotopologue abundances for quantitative profiling of complex protein mixtures labelled with the acrylamide/D3-acrylamide alkylation tag system. Rapid Commun. Mass Spectrom. 17, 1283–1290

    Article  PubMed  CAS  Google Scholar 

  79. Kurono, S., Kurono, T., Komori, N., Niwayama, S., and Matsumoto, H. (2006) Quantitative proteome analysis using D-labeled N-ethylmaleimide and 13C-labeled iodoacetanilide by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Bioorg. Med. Chem. 14, 8197–8209

    Article  PubMed  CAS  Google Scholar 

  80. Brancia, F. L., Montgomery, H., Tanaka, K., and Kumashiro, S. (2004) Guanidino labeling derivatization strategy for global characterization of peptide mixtures by liquid chromatography matrix-assisted laser desorption/ionization mass spectrometry. Anal. Chem. 76, 2748–2755

    Article  PubMed  CAS  Google Scholar 

  81. Sidhu, K. S., Sangvanich, P., Brancia, F. L., Sullivan, A. G., Gaskell, S. J., Wolkenhauer, O., et al (2001) Bioinformatic assessment of mass spectrometric chemical derivatisation techniques for proteome database searching. Proteomics 1, 1368–1377

    Article  PubMed  CAS  Google Scholar 

  82. Zou, J., Turner, A. N., and Phelps, R. G. (2003) Mass and composition matrix-assisted laser desorption ionization time of flight analysis enabling inference of the sequence of most peptides where the protein of origin is known. Anal. Chem. 75, 2653–2662

    Article  PubMed  CAS  Google Scholar 

  83. Leitner, A., Amon, S., Rizzi, A., and Lindner, W. (2007) Use of the arginine-specific butanedione/phenylboronic acid tag for analysis of peptides and protein digests using matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 21, 1321–1330

    Article  PubMed  CAS  Google Scholar 

  84. Righetti, P. G., Boschetti, E., Lomas, L., and Citterio, A. (2006) Protein equalizer (TM) technology: the quest for a “democratic proteome”. Proteomics 6, 3980–3992

    Article  PubMed  CAS  Google Scholar 

  85. Jaffrey, S. R., Erdjument-Bromage, H., Ferris, C. D., Tempst, P., and Snyder, S. H. (2001) Protein S-nitrosylation: a physiological signal for neuronal nitric oxide. Nat. Cell Biol. 3, 193–197

    Article  PubMed  CAS  Google Scholar 

  86. Dall’Agnol, M., Bernstein, C., Bernstein, H., Garewal, H., and Payne, C. M. (2006) Identification of S-nitrosylated proteins after chronic exposure of colon epithelial cells to deoxycholate. Proteomics 6, 1654–1662

    Article  PubMed  Google Scholar 

  87. Greco, T. M., Hodara, R., Parastatidis, I., Heijnen, H. F. G., Dennehy, M. K., ­Liebler, D. C., et al (2006) Identification of S-nitrosylation motifs by site-specific mapping of the S-nitrocysteine proteome in human vascular smooth muscle cells. Proc. Natl. Acad. Sci. U.S.A. 103, 7420–7425

    Article  PubMed  CAS  Google Scholar 

  88. Hao, G., Derakshan, B., Shi, L., Campagne, F., and Gross, S. S. (2006) SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures. Proc. Natl. Acad. Sci. U.S.A. 103, 1012–1017

    Article  PubMed  CAS  Google Scholar 

  89. Shin, B. K., Wang, H., Yim, A. M., Le Naour, F., Brichory, F., Jang, J. H., et al (2003) Global profiling of the cell surface proteome of cancer cells uncovers an abundance of proteins with chaperone function. J. Biol. Chem. 278, 7607–7616

    Article  PubMed  CAS  Google Scholar 

  90. Jang, J. H., and Hanash, S. (2003) Profiling of the cell surface proteome. Proteomics 3, 1947–1954

    Article  PubMed  CAS  Google Scholar 

  91. Yoo, Y. S., and Regnier, F. E. (2004) Proteomic analysis of carbonylated proteins in two-dimensional gel electrophoresis using avidin–fluorescein affinity staining. Electrophoresis 25, 1334–1341

    Article  PubMed  CAS  Google Scholar 

  92. Holland, J. W., Deeth, H. C., and Alewood, P. F. (2006) Resolution and characterisation of multiple isoforms of bovine kappa-casein by 2-DE following a reversible cysteine-tagging enrichment strategy. Proteomics 6, 3087–3095

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Analytical Chemistry and Food Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria

    Alexander Leitner & Wolfgang Lindner

Authors
  1. Alexander Leitner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wolfgang Lindner
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alexander Leitner .

Editor information

Editors and Affiliations

    Rights and permissions

    Reprints and permissions

    Copyright information

    © 2009 Humana Press, a part of Springer Science+Business Media, LLC

    About this protocol

    Cite this protocol

    Leitner, A., Lindner, W. (2009). Applications of Chemical Tagging Approaches in Combination with 2DE and Mass Spectrometry. In: Tyther, R., Sheehan, D. (eds) Two-Dimensional Electrophoresis Protocols. Methods in Molecular Biology, vol 519. Humana Press. https://doi.org/10.1007/978-1-59745-281-6_6

    Download citation

    • DOI: https://doi.org/10.1007/978-1-59745-281-6_6

    • Published:

    • Publisher Name: Humana Press

    • Print ISBN: 978-1-58829-937-6

    • Online ISBN: 978-1-59745-281-6

    • eBook Packages: Springer Protocols

    Publish with us

    Policies and ethics

    Search

    Navigation