A Method to Enhance a1 Ions and Application for Peptide Sequencing and Protein Identification

Journal of the American Society for Mass Spectrometry

Volumn 20, Issue 6, 2009, Pages 1214-1223

  Liu, Ning ^a   Chan, Wan ^a   Lee, Kim Chung ^a   Cai, Zongwei ^a  

^a HONG KONG BAPTIST UNIVERSITY   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SEARCHES; FRAGMENTATION PATTERNS; LC-MS/MS; MODEL PEPTIDES; N TERMINALS; PEPTIDE SEQUENCING; PROTEIN EXTRACTS; PROTEIN IDENTIFICATIONS; RAT HEARTS; TANDEM MASS SPECTRUM; TRYPTIC DIGESTS;

INFORMATION RETRIEVAL; IONS; MASS SPECTROMETERS; MASS SPECTROMETRY; PROTEINS; SEARCH ENGINES;

AMINES;

IODOACETAMIDE; MYOGLOBIN; PEPTIDE; PROTEIN;

ANIMAL TISSUE; ARTICLE; FRAGMENTATION REACTION; LIQUID CHROMATOGRAPHY; METHYLATION; NONHUMAN; PROTEIN ANALYSIS; RAT; SEQUENCE ANALYSIS; TANDEM MASS SPECTROMETRY; ANIMAL; CHEMISTRY; HEART MUSCLE; METHODOLOGY; REPRODUCIBILITY;

RATTUS;

ANIMALS; CHROMATOGRAPHY, LIQUID; IODOACETAMIDE; MYOCARDIUM; MYOGLOBIN; PEPTIDES; PROTEINS; RATS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, PROTEIN; TANDEM MASS SPECTROMETRY;

EID: 65549134211     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2009.02.021     Document Type: Article

References (33)

1. Nesvizhskii A.I. Protein Identification by Tandem Mass Spectrometry and Sequence Database Searching. Methods Mol. Biol. 367 (2007) 87-119
2. Biemann K. Contributions of Mass Spectrometry to Peptide and Protein Structure. Biomed. Environ. Mass Spectrom. 16 (1988) 99-111
3. Roepstorff P., and Fohlman J. Proposal for a Common Nomenclature for Sequence Ions in Mass Spectra of Peptides. Biomed. Mass Spectrom. 11 (1984) 601
4. + Ions of Peptides. Side Chain Specific Sequence Ions. Int. J. Mass Spectrom. Ion Processes 86 (1988) 137-154
5. Ambihapathy K., Yalcin T., Leung H.-W., and Harrison A.G. Pathways to Immonium Ions in the Fragmentation of Protonated Peptides. J. Mass Spectrom. 32 (1997) 209-215
6. Ji C., and Li L. Quantitative Proteome Analysis Using Differential Stable Isotopic Labeling and Microbore LC-MALDI MS and MS/MS. J. Proteome Res. 4 (2005) 734-742
7. Alves G., Wu W.W., Wang G., Shen R.F., and Yu Y.K. Enhancing Peptide Identification Confidence by Combining Search Methods. J. Proteome Res. 7 (2008) 3102-3113
8. Sweet S.M., Mardakheh F.K., Ryan K.J., Langton A.J., Heath J.K., and Cooper H.J. Targeted Online Liquid Chromatography Electron Capture Dissociation Mass Spectrometry for the Localization of Sites of in Vivo Phosphorylation in Human Sprouty2. Anal. Chem. 80 (2008) 6650-6657
9. Shen Y., Tolić N., Hixson K.K., Purvine S.O., Pasa-Tolić L., Qian W.J., Adkins J.N., Moore R.J., and Smith R.D. Proteome-Wide Identification of Proteins and Their Modifications with Decreased Ambiguities and Improved False Discovery Rates Using Unique Sequence Tags. Anal. Chem. 80 (2008) 1871-1882
10. El Aribi H., Rodriquez C.F., Almeida D.R., Ling Y., Mak W.W., Hopkinson A.C., and Michael Siu K.W. Elucidation of Fragmentation Mechanisms of Protonated Peptide Ions and Their Products: A Case Study on Glycylglycylglycine Using Density Functional Theory and Threshold Collision-Induced Dissociation. J. Am. Chem. Soc. 125 (2003) 9229-9236
11. Yalcin T., Csizmadia I.G., Peterson M.R., and Harrison A.G. The Structure and Fragmentation of Bn (n ≥ 3) ions in peptide spectra. J. Am. Soc. Mass Spectrom. 7 (1996) 233-242
12. Keough T., Youngquist R.S., and Lacey M.P. A Method for High-Sensitivity Peptide Sequencing Using Post-Source Decay Matrix-Assisted Laser Desorption Ionization Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A. 96 (1999) 7131-7136
13. Noga M.J., Lewandowski J.J., Suder P., and Silberring J. An enhanced method for peptides sequencing by N-terminal derivatization and MS. Proteomics 5 (2005) 4367-4375
14. 1 Ions in Peptide Phenylthiocarbamoyl Derivatives: Analogies with Condensed-Phase Chemistry. J. Mass Spectrom. 32 (1997) 225-231
15. Marekov L.N., and Steinert P.M. Charge Derivatization by 4-SIulfophenyl isothiocyanate Enhances Peptide Sequencing by Post-Source Decay Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. J. Mass Spectrom. 38 (2003) 373-377
16. Yu Y., Cui J., Wang X., Liu Y., and Yang P. Studies on Peptide Acetylation for Stable-Isotope Labeling After 1-D PAGE Separation in Quantitative Proteomics. Proteomics 4 (2004) 3112-3120
17. Cárdenas M.S., van der Heeft E., and de Jong A.P.J.M. On-Line Derivatization of Peptides for Improved Sequence Analysis by Microcolumn Liquid Chromatography Coupled with Electrospray Ionization-Tandem Mass Spectrometry. Rapid Commun. Mass Spectrom. 11 (1997) 1271-1278
18. Huang Z.H., Wu J., Roth K.D., Yang Y., Gage D.A., and Watson J.T. A Picomole-Scale Method for Charge Derivatization of Peptides for Sequence Analysis by Mass Spectrometry. Anal. Chem. 69 (1997) 137-144
19. 1 Ion in MS/MS and Post-Source Decay: Potential Applications in Proteomics. Anal. Chem. 76 (2004) 3958-3970
20. 1 Fragmentation for Dimethylated Proteins and Its Applications for N-Terminal Identification and Comparative Protein Quantitation. J. Proteome Res. 6 (2007) 2376-2383
21. Yang Z., and Attygalle A.B. LC/MS Characterization of Undesired Products Formed During Iodoacetamide Derivatization of Sulfhydryl Groups of Peptides. J. Mass Spectrom. 42 (2007) 233-243
22. Boja E.S., and Fales H.M. Overalkylation of a Protein Digest with Iodoacetamide. Anal. Chem. 73 (2001) 3576-3582
23. Chong P.K., and Wright P.C. Identification and Characterization of the Sulfolobus solfataricus P2 Proteome. J. Proteome Res. 4 (2005) 1789-1798
24. Zhang J., Xu X., Gao M., Yang P., and Zhang X. Comparison of 2-D LC and 3-D LC with Post- and Pre-tryptic Digestion SEC Fractionation for Proteome Analysis of Normal Human Liver Tissue. Proteomics 7 (2007) 500-512
25. Hoffert J.D., Pisitkun T., Wang G., Shen R.F., and Knepper M.A. Quantitative Phosphoproteomics of Vasopressin-Sensitive Renal Cells: Regulation of Aquaporin-2 Phosphorylation at Two Sites. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 7159-7164
26. Benschop J.J., Mohammed S., O'Flaherty M., Heck A.J., Slijper M., and Menke F.L. Quantitative Phosphoproteomics of Early Elicitor Signaling in Arabidopsis. Mol. Cell. Proteom. 6 (2007) 1198-1214
27. Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., and Jensen O.N. Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway. Mol. Cell. Proteom. 4 (2005) 310-327
28. Nielsen M.L., Vermeulen M., Bonaldi T., Cox J., Moroder L., and Mann M. Iodoacetamide-Induced Artifact Mimics Ubiquitination in Mass Spectrometry. Nat. Methods 5 (2008) 459-460
29. Creasy D.M., and Cottrell J.S. Error Tolerant Searching of Uninterpreted Tandem Mass Spectrometry data. Proteomics 2 (2002) 1426-1434
30. Mann M., and Wilm M. Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags. Anal. Chem. 66 (1994) 4390-4399
31. Chu I.K., Cox D.M., Guo X., Kireeva I., Lau T.C., McDermott J.C., and Michael Siu K.W. Sequencing of Argentinated Peptides by Means of Matrix-Assisted Laser Desorption/Ionization Tandem Mass Spectrometry. Anal. Chem. 74 (2002) 2072-2082
32. Sunyaev S., Liska A.J., Golod A., Shevchenko A., and Shevchenko A. MultiTag: Multiple Error-Tolerant Sequence Tag Search for the Sequence-Similarity Identification of Proteins by Mass Spectrometry. Anal. Chem. 75 (2003) 1307-1315
33. Liska A.J., Sunyaev S., Shilov I.N., Schaeffer D.A., and Shevchenko A. Error-Tolerant EST Database Searches by Tandem Mass Spectrometry and MultiTag Software. Proteomics 5 (2005) 4118-4122