Shifting Unoccupied Spectral Space in Mass Spectrum of Peptide Fragment Ions

Journal of the American Society for Mass Spectrometry

Volumn 20, Issue 11, 2009, Pages 2124-2134

  Bajrami, Bekim ^a   Shi, Yu ^a   Lapierre, Pascal ^a   Yao, Xudong ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID RESIDUES; INTERFERING IONS; LABORATORY EXPERIMENTS; MASS DEFECT; MASS SPECTRA; MASS-TO-CHARGE RATIO; N-BUTANOL; PEPTIDE FRAGMENTS; PHOSPHOTYROSINE; SCALING FACTORS; SIDE-CHAIN; SPECTRAL SPACES; THEORETICAL CALCULATIONS;

AMINES; AMINO ACIDS; CARBOXYLATION; DEFECTS; ESTERIFICATION; ESTERS; MASS SPECTROMETERS; MASS SPECTROMETRY; ORGANIC ACIDS; PEPTIDES;

IONS;

AMINO ACID; ASPARTIC ACID; BUTANOL; CARBOXYLIC ACID DERIVATIVE; CYCLOPHOSPHORAMIDATE; GLUTAMIC ACID; PEPTIDE FRAGMENT; PHOSPHORAMIDIC ACID DERIVATIVE; PHOSPHOTYROSINE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CALCULATION; CELL LYSATE; CHEMICAL MODIFICATION; CONTROLLED STUDY; ESTERIFICATION; HUMAN; HUMAN CELL; MASS SPECTROMETER; MASS SPECTROMETRY; MOLECULAR WEIGHT; PROTEIN ANALYSIS;

1-BUTANOL; AMINO ACID SEQUENCE; ANIMALS; ASPARAGINE; CATTLE; CHICKENS; CHROMATOGRAPHY, LIQUID; ESTERIFICATION; GLUTAMIC ACID; IONS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEIN STRUCTURE, SECONDARY; SENSITIVITY AND SPECIFICITY; TANDEM MASS SPECTROMETRY;

EID: 70349767010     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2009.07.005     Document Type: Article

References (36)

1. Mann, M. Useful tables of possible and probable peptide masses. Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics; Atlanta, GA, May, 1995.
2. Gay S., Binz P.A., Hochstrasser D.F., and Appel R.D. Modeling peptide mass fingerprinting data using the atomic composition of peptides. Electrophoresis 20 (1999) 3527-3534
3. Lehmann W.D., Bohne A., and von Der Lieth C.-W. The information encrypted in accurate peptide masses-improved protein identification and assistance in glycopeptide identification and characterization. J. Mass Spectrom 35 (2000) 1335-1341
4. Frahm J.L., Howard B.E., Heber S., and Muddiman D.C. Accessible proteomics space and its implications for peak capacity for zero-, one-, and two-dimensional separations coupled with FT-ICR and TOF mass spectrometry. J. Mass Spectrom 41 (2006) 281-288
5. Dodds E.D., An H.J., Hagerman P.J., and Lebrilla C.B. Enhanced peptide mass fingerprinting through high mass accuracy: Exclusion of non-peptide signals based on residual mass. J. Proteome Res 5 (2006) 1195-1203
6. Zubarev R., and Mann M. On the proper use of mass accuracy in proteomics. Mol. Cell. Proteom 6 (2007) 377-381
7. Schmidt F., Schmid M., Jungblut P.R., Mattow J., Facius A., and Pleissner K.P. Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis. J. Am. Soc. Mass Spectrom 14 (2003) 943-956
8. Senko M.W., Beu S.C., and McLafferty F.W. Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom 6 (1995) 229-233
9. Yao X., Diego P., Ramos A.A., and Shi Y. Averagine-scaling analysis and fragment ion mass defect labeling in peptide mass spectrometry. Anal. Chem 80 (2008) 7383-7391
10. Hernandez H., Niehauser S., Boltz S.A., Gawandi V., Phillips R.S., and Amster I.J. Mass defect labeling of cysteine for improving peptide assignment in shotgun proteomic analyses. Anal. Chem 78 (2006) 3417-3423
11. Hall M.P., Ashrafi S., Obegi I., Petesch R., Peterson J.N., and Schneider L.V. "Mass defect" tags for biomolecular mass spectrometry. J. Mass Spectrom 38 (2003) 809-816
12. Hall M.P., and Schneider L.V. Isotope-differentiated binding energy shift tags (IDBEST) for improved targeted biomarker discovery and validation. Expert Rev. Proteom 1 (2004) 421-431
13. Matthiesen R., Bauw G., and Welinder K.G. Use of performic acid oxidation to expand the mass distribution of tryptic peptides. Anal. Chem 76 (2004) 6848-6852
14. Barsnes H., Eidhammer I., Cruciani V., and Mikalsen S.O. Protease-dependent fractional mass and peptide properties. Eur. J. Mass Spectrom 14 (2008) 311-317
15. Harris W.A., Janecki D.J., and Reilly J.P. Use of matrix clusters and trypsin autolysis fragments as mass calibrants in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom 16 (2002) 1714-1722
16. Pourshahian S., and Limbach P.A. Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry. J. Mass Spectrom 43 (2008) 1081-1088
17. Dodds E.D., Clowers B.H., Hagerman P.J., and Lebrilla C.B. Systematic characterization of high mass accuracy influence on false discovery and probability scoring in peptide mass fingerprinting. Anal. Biochem 372 (2008) 156-166
18. Steen H., Küster B., Fernandez M., Pandey A., and Mann M. Detection of tyrosine phosphorylated peptides by precursor ion scanning quadrupole TOF mass spectrometry in positive ion mode. Anal. Chem 73 (2001) 1440-1448
19. Steen H., Küster B., and Mann M. Quadrupole time-of-flight versus triple-quadrupole mass spectrometry for the determination of phosphopeptides by precursor ion scanning. J. Mass Spectrom 36 (2001) 782-790
20. Salek M., Alonso A., Pipkorn R., and Lehmann W.D. Analysis of protein tyrosine phosphorylation by nanoelectrospray ionization high-resolution tandem mass spectrometry and tyrosine-targeted product ion scanning. Anal. Chem 75 (2003) 2724-2729
21. Shi Y., and Yao X. Oxygen isotopic substitution of peptidyl phosphates for modification-specific mass spectrometry. Anal. Chem 79 (2007) 8454-8462
22. Shi Y., Bajrami B., Morton M., and Yao X. Cyclophosphoramidate ion as mass defect marker for efficient detection of protein serine phosphorylation. Anal. Chem 80 (2008) 7614-7623
23. Macek B., Mann M., and Olsen J.V. Global and site-specific quantitative phosphoproteomics: Principles and applications. Annu. Rev. Pharmacol. Toxicol 49 (2009) 199-221
24. Kendrick E. Mass scale based on CH2 = 14.0000 for high-resolution mass spectrometry of organic compounds. Anal. Chem 35 (1963) 2146-2154
25. Hughey C.A., Hendrickson C.L., Rodgers R.P., Marshall A.G., and Qian K. Kendrick mass defect spectrum: A compact visual analysis for ultrahigh-resolution broadband mass spectra. Anal. Chem 73 (2001) 4676-4681
26. Purvine S., Eppel J.-T., Yi E.C., and Goodlett D.R. Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 3 (2003) 847-850
27. E: A virtue of parallel MS acquisition. Mol. Cell. Proteom 5 (2006) 144-156
28. Ramos A.A., Yang H., Rosen L.E., and Yao X. Tandem parallel fragmentation of peptides for mass spectrometry. Anal. Chem 78 (2006) 6391-6397
29. Goodlett D.R., Keller A., Watts J.D., Newitt R., Yi E.C., Purvine S., Eng J.K., von Haller P., Aebersold R., and Kolker E. Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation. Rapid Commun. Mass Spectrom 15 (2001) 1214-1221
30. Carr S.A., Annan R.S., and Huddleston M.J. Mapping posttranslational modifications of proteins by MS-based selective detection: Application to phosphoproteomics. Methods Enzymol 405 (2005) 82-115
31. Mora J.F., Van Berkel G.J., Enke C.G., Cole R.B., Martinez-Sanchez M., and Fenn J.B. Electrochemical processes in electrospray ionization mass spectrometry. J. Mass Spectrom 35 (2000) 939-952
32. Frahm J.L., Bori I.D., Comins D.L., Hawkridge A.M., and Muddiman D.C. Achieving augmented limits of detection for peptides with hydrophobic alkyl tags. Anal. Chem 79 (2007) 3989-3995
33. Williams Jr. D.K., Meadows C.W., Bori I.D., Hawkridge A.M., Comins D.L., and Muddiman D.C. Synthesis, characterization, and application of iodoacetamide derivatives utilized for the ALiPHAT strategy. J. Am. Chem. Soc 130 (2008) 2122-2123
34. Mirzaei H., and Regnier F. Enhancing electrospray ionization efficiency of peptides by derivatization. Anal. Chem 78 (2006) 4175-4183
35. Bruce C., Shifman M.A., Miller P., and Gulcicek E.E. Probabilistic enrichment of phosphopeptides by their mass defect. Anal. Chem 78 (2006) 4374-4382
36. Shi Y., Bajrami B., and Yao X. Passive and active fragment Ion mass defect labeling: Distinct proteomics potential of iodine-based reagents. Anal. Chem (2009) E-pub June 29, 2009