Integration of high accuracy N-terminus identification in peptide sequencing and comparative protein analysis via isothiocyanate-based isotope labeling reagent with ESI Ion-trap TOF MS

Journal of the American Society for Mass Spectrometry

Volumn 22, Issue 7, 2011, Pages 1204-1213

  Leng, Jiapeng ^a   Wang, Haoyang ^a   Zhang, Li ^a   Zhang, Jing ^a   Wang, Hang ^a   Cai, Tingting ^a   Yao, Jinting ^b   Guo, Yinlong ^a  

^a SHANGHAI INSTITUTE OF ORGANIC CHEMISTRY   (China)

^b Shimadzu Global COE for Application and Technical Development   (China)

Author keywords

4,6 dimethoxy pyrimidine 2 isothiocyanate; b 1 ions; Comparative protein analysis; Isotope labeling; N terminus identification

Indexed keywords

4,6-DIMETHOXY PYRIMIDINE-2-ISOTHIOCYANATE; BOVINE SERUM ALBUMINS; COMPARATIVE ANALYSIS; COMPARATIVE PROTEIN ANALYSIS; DIRECT MS; FRAGMENT IONS; ION TRAPS; ISOTOPE LABELING; LABELING REAGENT; LABELING STRATEGY; N-TERMINUS IDENTIFICATION; PEPTIDE SEQUENCING; PHENYL ISOTHIOCYANATE; PROTEIN ANALYSIS; RELATIVE ABUNDANCE; REPRODUCIBILITIES; SENSITIVITY ENHANCEMENTS; TOF MASS SPECTROMETRY;

AMINO ACIDS; AROMATIC COMPOUNDS; BODY FLUIDS; IONS; ISOTOPES; MASS SPECTROMETRY;

PEPTIDES;

4,6 DIMETHOXY PYRIMIDINE 2 ISOTHIOCYANATE; BOVINE SERUM ALBUMIN; ISOLEUCINE; ISOTHIOCYANIC ACID DERIVATIVE; LEUCINE; PHENYL ISOTHIOCYANATE; UNCLASSIFIED DRUG;

ACCURACY; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; COMPARATIVE STUDY; CONTROLLED STUDY; ION TRAP MASS SPECTROMETRY; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; PROTEIN ANALYSIS; SENSITIVITY ANALYSIS; SYNTHESIS; TIME OF FLIGHT MASS SPECTROMETRY; VALIDATION PROCESS;

AMINO ACID SEQUENCE; ANIMALS; CATTLE; ISOTHIOCYANATES; ISOTOPE LABELING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PEPTIDE MAPPING; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SERUM ALBUMIN, BOVINE; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

BOVINAE;

EID: 79959955798     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-011-0129-5     Document Type: Article

References (44)

1. 1 Ions in Peptide Phenylthiocarbamoyl Derivatives: Analogies with Condensed-phase Chemistry. J. Mass Spectrom. 32, 225-231(1997) (Pubitemid 27087389)
2. Summerfield, S. G., Steen, H., O'Malley, M., Gaskell, S. J.: Phenyl Thiocarbamoyl and Related Derivatives of Peptides: Edman Chemistry in the Gas Phase. Int. J. Mass Spectrom. 188, 95-103(1999)
3. 1 Ion as a Mass Tag for Peptide Sequencing Using Dimethyl Labeling. J. Proteome Res. 4, 101-108(2005)
4. 1 Ions and Application for Peptide Sequencing and Protein Identification. J. Am. Soc. Mass Spectrom. 20, 1214-1223(2009)
5. Wilkins, M. R., Gasteiger, E., Tonella, L., Ou, K., Tyler, M., Sanchez, J. C., Gooley, A. A., Walsh, B. J., Bairoch, A., Appel, R. D., Williams, K. L., Hochstrasser, D. F.: Protein Identification with N-and C-terminal Sequence Tags in Proteome Projects. J. Mol. Biol. 278, 599-608(1998) (Pubitemid 28224857)
6. Ji, C., Guo, N., Li, L.: Differential Dimethyl Labeling of N-Termini of Peptides After Guanidination for Proteome Analysis. J. Proteome Res. 4, 2099-2108(2005) (Pubitemid 41814276)
7. Fu, Q., Li, L.: De Novo Sequencing of Neuropeptides Using Reductive Isotopic Methylation and Investigation of ESI QTOF MS/MS Fragmentation Pattern of Neuropeptides with N-Terminal Dimethylation. Anal. Chem. 77, 7783-7795(2005) (Pubitemid 41746247)
8. Chacon, A., Masterson, D. S., Yin, H. Y., Liebler, D. C., Porter, N. A.: N-Terminal Amino Acid Side-Chain Cleavage of Chemically Modified Peptides in the Gas Phase: A Mass Spectrometry Technique for N-Terminus Identification. Bioorg. Med. Chem. 14, 6213-6222(2006) (Pubitemid 44224084)
9. Shen, P. T., Hsu, J. L., Chen, S. H.: Dimethyl Isotope-coded Affinity Selection for the Analysis of Free and Blocked N-Termini of Proteins Using LC-MS/MS. Anal. Chem. 79, 9520-9530(2007)
10. Yamaguchi, M., Obama, T., Kuyama, H., Nakayama, D., Ando, E., Okamura, T. A., Ueyama, N., Nakazawa, T., Norloka, S., Nishimura, O., Tsunasawa, S.: Specific Isolation of N-Terminal Fragments from Proteins and Their High-fidelity De Novo Sequencing. Rapid Commun. Mass Spectrom. 21, 3329-3336(2007) (Pubitemid 47598786)
11. 1 Fragmentation for Dimethylated Proteins and Its Applications for N-terminal Identification and Comparative Protein Quantitation. J. Proteome Res. 6, 2376-2383(2007)
12. Nakazawa, T., Yamaguchi, M., Okamura, T., Ando, E., Nishimura, O., Tsunasawa, S.: Terminal Proteomics: N-and C-Terminal Analyses for High-fidelity Identification of Proteins Using MS. Proteomics 8, 673-685(2008) (Pubitemid 351362929)
13. van der Rest, G., He, F., Emmett, M. R., Marshall, A. G., Gaskell, S. J.: Gas-Phase Cleavage of PTC-derivatized Electrosprayed Tryptic Peptides in an FT-ICR Trapped-ion Cell: Mass-based Protein Identification without Liquid Chromatographic Separation. J. Am. Soc. Mass Spectrom. 12, 288-295(2001) (Pubitemid 34546624)
14. Brancia, F. L., Butt, A., Beynon, R. J., Hubbard, S. J., Gaskell, S. J., Oliver, S. G.: A Combination of Chemical Derivatization and Improved Bioinformatic Tools Optimizes Protein Identification for Proteomics. Electrophoresis 22, 552-559(2001) (Pubitemid 32166580)
15. Onisko, B., Dynin, I., Requena, J. R., Silva, C. J., Erickson, M., Carter, J. M.: Mass Spectrometric Detection of Attomole Amounts of the Prion Protein by Nano LC/MS/MS. J. Am. Soc. Mass Spectrom. 18, 1070-1079(2007) (Pubitemid 46755582)
16. Sanchez, A., Perez-Riverol, Y., González, L. J., Noda, J., Betancourt, L., Ramos, Y., Gil, J., Vera, R., Padrón, G., Besada, V.: Evaluation of Phenylthiocarbamoyl-Derivatized Peptides by Electrospray Ionization Mass Spectrometry: Selective Isolation and Analysis of Modified Multiply Charged Peptides for Liquid Chromatography-Tandem Mass Spectrometry Experiments. Anal. Chem 82, 8492-8501(2000)
17. Oe, T., Maekawa, M., Satoh, R., Lee, S. H., Goto, T.: Combining [13C6]-Phenylisothiocyanate and the Edman Degradation Reaction: A Possible Breakthrough for Absolute Quantitative Proteomics Together with Protein Identification. Rapid Commun. Mass Spectrom. 24, 173-179(2000)
18. Diego, P. A. C., Bajrami, B., Jiang, H., Shi, Y., Gascon, J. A., Yao, X. D.: Site-Preferential Dissociation of Peptides with Active Chemical Modification for Improving Fragment Ion Detection. Anal. Chem. 82, 23-27(2000)
19. Lee, Y. H., Kim, M. S., Choie, W. S., Min, H. K., Lee, S. W.: Highly Informative Proteome Analysis by Combining Improved N-Terminal Sulfonation for De Novo Peptide Sequencing and Online Capillary Reverse-Phase Liquid Chromatography/Tandem Mass Spectrometry. Proteomics 4, 1684-1694(2004) (Pubitemid 38738325)
20. Johnson, R. S., Martin, S. A., Biemann, K., Stults, J. T., Watson, J. T.: Novel Fragmentation Process of Peptides by Collision-Induced Decomposition in a Tandem Mass Spectrometer: Differentiation of Leucine and Isoleucine. Anal. Chem. 59, 2621-2625(1997)
21. Nakamura, T., Nagaki, H., Ohki, Y., Kinoshita, T.: Differentiation of Leucine and Isoleucine Residues in Peptides by Consecutive Reaction Mass Spectrometry. Anal. Chem. 62, 311-313(1990) (Pubitemid 20103330)
22. - Ions of Phenylthiohydantoin Leu and Ile. Rapid Commun. Mass Spectrom. 9, 1241-1243(1995)
23. Hulst, A. G., Kientz, C. E.: Differentiation Between the Isomeric Amino Acids Leucine and Isoleucine Using Low-Energy Collision-Induced Dissociation Tandem Mass Spectroscopy. J. Mass Spectrom. 31, 1188-1190(1996) (Pubitemid 26360256)
24. (n), n=2, 3) of Copper (II)-Diimine Complexes. J. Mass Spectrom. 3, 566-571(2000) (Pubitemid 30215995)
25. Armirotti, A., Millo, E., Damonte, G.: How to Discriminate Between Leucine and Isoleucine by Low Energy ESI-TRAP MSn. J. Am. Soc. Mass Spectrom. 18, 57-63(2007) (Pubitemid 46038165)
26. Soltwisch, J., Dreisewerd, K.: Discrimination of Isobaric Leucine and Isoleucine Residues and Analysis of Post-Translational Modifications in Peptides by MALDI In-Source Decay Mass Spectrometry Combined with Collisional Cooling. Anal. Chem. 82, 5628-5635(2000)
27. Zhang, J., Guo, Y. L.: A Novel Modification Reagent for Proteins: Monitoring by Matrix-assisted Laser Desorption/Ionization Time-offlight Mass Spectrometry. Rapid Commun. Mass Spectrom. 19, 2461-2464(2005) (Pubitemid 41284996)
28. Zhang, J., Zhang, L., Zhou, Y., Guo, Y. L.: A Novel Pyrimidine-Based Stable-Isotope Labeling Reagent and Its Application to Quantitative Analysis Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry. J. Mass Spectrom. 42, 1514-1521(2007) (Pubitemid 350113469)
29. Fang, F., Zhang, J., Zhang, L., Guo, Y. L.: A Stable Isotopic Predigestion Labeling Method for Protein Quantitative Analysis Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry. Chin. J. Chem. 27, 2397-2404(2009)
30. Fang, F., Liu, P., Wang, H. Y., Zhang, L., Zhang, J., Gao, Y. P., Zeng, L. M., Guo, Y. L.: Studies of Keratins in Tongue Coating Samples of Hepatitis B Patients by Mass Spectrometry. Rapid Commun. Mass Spectrom. 23, 1703-1709(2009)
31. Okajima, N., Aoki, I., Kuragano, T., Okada, Y.: Synthesis and Herbicidal Activity of 2-(1, 3-Dimethyl-4-Substituted-5-Pyrazolyl) Sulfonylimino-5, 7-Disubstututed-2 H-1, 2, 4-Thiadiazolo2, 3-α-Pyrimidine Derivatives. Pestic. Sci. 32, 91-104(1991)
32. Jefferson, E. A., Seth, P. P., Robinson, D. E., Winter, D. K., Miyaji, A., Osgood, S. A., Swayze, E. E., Risen, L. M.: Biaryl Guanidine Inhibitors of In Vitro HCV-IRES Activity. Bioorg. Med. Chem. Lett. 14, 5139-5143(2004) (Pubitemid 39233382)
33. Wang, H. Y., Zhang, X., Guo, Y. L., Lu, L.: Mass Spectrometric Studies of the Gas Phase Retro-Michael Type Fragmentation Reactions of 2-Hydroxybenzyl-N-Pyrimidinylamine Derivatives. J. Am. Soc. Mass Spectrom. 16, 1561-1573(2005) (Pubitemid 41169865)
34. Wang, H. Y., Zhang, X., Guo, Y. L., Tang, Q. H., Lu, L.: Using Tandem Mass Spectrometry to Predict Chemical Transformations of 2-Pyrimidinyloxy-N- Arylbenzyl Amine Derivatives in Solution. J. Am. Soc. Mass Spectrom. 17, 253-263(2006) (Pubitemid 43185251)
35. Wang, D. X., Fang, S. A., Wohlhueter, R. M.: N-Terminal Derivatization of Peptides with Isothiocyanate Analogues Promoting Edman-Type Cleavage and Enhancing Sensitivity in Electrospray Ionization Tandem Mass Spectrometry Analysis. Anal. Chem. 81, 1893-1900(2009)
36. Lee, Y. H., Han, H., Chang, S. B., Lee, S. W.: Isotope-coded N-terminal Sulfonation of Peptides Allows Quantitative Proteomic Analysis with Increased De Novo Peptide Sequencing Capability. Rapid Commun. Mass Spectrom. 18, 3019-3027(2004) (Pubitemid 39664902)
37. Noga, M. J., Asperger, A., Silberring, J.: N-Terminal H-3/D-3-Acetylation for Improved High-Throughput Peptide Sequencing by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry with a Time-of-flight/Time-of-Flight Analyzer. Rapid Commun. Mass Spectrom. 20, 1823-1827(2006) (Pubitemid 43893330)
38. Hennrich, M. L., Mohammed, S., Altelaar, A. F. M., Heck, A. J. R.: Dimethyl Isotope Labeling Assisted De Novo Peptide Sequencing. J. Am. Soc. Mass Spectrom. 21, 1957-1965(2000)
39. Heller, M., Mattou, H., Menzel, C., Yao, X. D.: Trypsin Catalyzed O-16-to-O-18 Exchange for Comparative Proteomics: Tandem Mass Spectrometry Comparison Using MALDI-TOF, ESI-QTOF, and ESI-Ion Trap Mass Spectrometers. J. Am. Soc. Mass Spectrom. 14, 704-718(2003) (Pubitemid 36870953)
40. Schmidt, F., Donahoe, S., Hagens, K., Mattow, J., Schaible, U. E., Kaufmann, S. H. E., Aebersold, R., Jungblut, P. R.: Complementary Analysis of the Mycobacterium Tuberculosis Proteome by Two-dimensional Electrophoresis and Isotope-Coded Affinity Tag Technology. Mol. Cell. Proteom. 3, 24-42(2004) (Pubitemid 38697102)
41. Schmidt, A., Kellermann, J., Lottspeich, F.: A Novel Strategy for Quantitative Proteomics Using Isotope-Coded Protein Labels. Proteomics 5, 4-15(2005) (Pubitemid 40189632)
42. Wu, W. W., Wang, G. H., Baek, S. J., Shen, R. F.: 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(2006) (Pubitemid 43364106)
43. Chong, P. K., Gan, C. S., Pham, T. K., Wright, P. C.: Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) Reproducibility: Implication of Multiple Injections. J. Proteome Res. 5, 1232-1240(2006) (Pubitemid 43727802)
44. Bateman, R. J., Munsell, L. Y., Chen, X. H., Holtzman, D. M., Yarasheski, K. E.: Stable Isotope Labeling Tandem Mass Spectrometry (SILT) to Quantify Protein Production and Clearance Rates. J. Am. Soc. Mass Spectrom. 18, 997-1006(2007) (Pubitemid 46755574)