Quantification of isotopically overlapping deamidated and 18O-labeled peptides using isotopic Envelope mixture modeling

Journal of Proteome Research

Volumn 8, Issue 3, 2009, Pages 1263-1270

  Dasari, Surendra ^a   Wilmarth, Phillip A ^b   Reddy, Ashok P ^c   Robertson, Lucinda J G ^b   Nagalla, Srinivasa R ^a,c   David, Larry L ^b  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^b OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^c Proteogenix Inc   (United States)

Author keywords

Bioinformatics; Cataracts, 18o labeling; Crystallin; Deamidation; Human lens; Insolubility; Isotopic envelope modeling; Mass spectrometry; Post translational modification; Proteomics; Q TOF; Quantification; Reverse phase chromatography; Software

Indexed keywords

AGED; AMINO ACID SEQUENCE; ARTICLE; CATARACT; CONTROLLED STUDY; DEAMINATION; HUMAN; HUMAN TISSUE; ISOMERIZATION; ISOTOPE LABELING; ISOTOPIC ENVELOPE MIXTURE MODELING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEOMICS;

ADULT; AGED; AGED, 80 AND OVER; AMIDES; CATARACT; CHILD, PRESCHOOL; CHROMATOGRAPHY, LIQUID; HUMANS; INFANT, NEWBORN; ISOTOPE LABELING; LENS, CRYSTALLINE; MODELS, CHEMICAL; OXYGEN ISOTOPES; PEPTIDES; TANDEM MASS SPECTROMETRY;

EID: 65249098316     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr801054w     Document Type: Article

References (23)

1. Mueller, L. N.; Brusniak, M. Y.; Mani, D. R.; Aebersold, R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res. 2008, 7 (1), 51-61.
2. Dasari, S.; Wilmarth, P. A.; Rustvold, D. L.; Riviere, M. A.; Nagalla, S. R.; David, L. L. Reliable detection of deamidated peptides from lens crystallin proteins using changes in reversed-phase elution times and parent ion masses. J. Proteome Res. 2007, 6 (9), 3819-3826.
3. Wilmarth, P. A.; Tanner, S.; Dasari, S.; Nagalla, S. R.; Riviere, M. A.; Bafna, V.; Pevzner, P. A.; David, L. L. Age-related changes in human crystallins determined from comparative analysis of post-trans-lational modifications in young and aged lens: Does deamidation contribute to crystallin insolubility. J. Proteome Res. 2006, 5 (10), 2554-2566.
4. McKerrow, J. H. Non-enzymatic, post-translational, amino acid modifications in ageing. A brief review. Mech. Ageing Dev. 1979, 10 (6), 371-377.
5. Watanabe, A.; Hong, W. K.; Dohmae, N.; Takio, K.; Morishima-Kawashima, M.; Ihara, Y. Molecular aging of tau: Disulfide-independent aggregation and non-enzymatic degradation in vitro and in vivo. J. Neurochem. 2004, 90 (6), 1302-1311.
6. Watanabe, A.; Takio, K.; Ihara, Y. Deamidation and isoaspartate formation in smeared tau in paired helical filaments. Unusual properties of the microtubule-binding domain of tau. J. Biol. Chem. 1999, 274 (11), 7368-7378.
7. Wakankar, A. A.; Borchardt, R. T. Formulation considerations for proteins susceptible to asparagine deamidation and aspartate isomerization. J. Pharm. Sci. 2006, 95 (11), 2321-2336.
8. Lapko, V. N.; Purkiss, A. G.; Smith, D. L.; Smith, J. B. Deamidation in human γS-crystallin from cataractous lenses is influenced by surface exposure. Biochemistry 2002, 41 (27), 8638-8648.
9. Takemoto, L.; Boyle, D. Increased deamidation of asparagine during human senile cataractogenesis. Mol. Vis. 2000, 6, 164-168.
10. 18O-labeled isotopic clusters. Mol. Cell. Proteomics 2007, 6 (2), 305-318.
11. 18O labeling with a correction for labeling efficiency. Mol. Cell. Proteomics 2007, 6 (7), 1274-1286.
12. Eng, J. K.; McCormack, A. L.; Yates, J. R., III. An approach to correlate tandem mass sectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
13. Tabb, D. L.; McDonald, W. H.; Yates, J. R., III. DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 2002, 1 (1), 21-26.
14. Senko, M. W.; Beu, S. C.; McLafferty, F. W. Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom. 1995, 6, 229-233.
15. Aarnio, P. A.; Nikkinen, M. T.; Routti, J. T. SAMPO 90 high resolution interactive γ-spectrum analysis including automation with macros. J. Radioanal. Nucl. Chem. 1992, 160 (1), 289-295.
16. Bevington, P. R. Data Reduction and Error Analysis for the Physical Sciences; McGraw-Hill, Inc.: New York, 1969.
17. Searle, B. C.; Dasari, S.; Turner, M.; Reddy, A. P.; Choi, D.; Wilmarth, P. A.; McCormack, A. L.; David, L. L.; Nagalla, S. R. High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/ MS de novo sequencing results. Anal. Chem. 2004, 76 (8), 2220-2230.
18. Takemoto, L. Deamidation of Asn-143 of γS-crystallin from protein aggregates of the human lens. Curr. Eye Res. 2001, 22 (2), 148-153.
19. Purkiss, A. G.; Bateman, O. A.; Goodfellow, J. M.; Lubsen, N. H.; Slingsby, C. The X-ray crystal structure of human γS-crystallin C-terminal domain. J. Biol. Chem. 2002, 277 (6), 4199-4205.
20. 18O labeling for comparative proteomics: Model studies with two serotypes of adenovirus. Anal. Chem. 2001, 73 (13), 2836-2842.
21. 16O quantitative proteomics experiments by incorporation of immobilized trypsin into the initial digestion step. Anal. Chem. 2007, 79 (5), 2158-2162.
22. May, D.; Fitzgibbon, M.; Liu, Y.; Holzman, T.; Eng, J.; Kemp, C. J.; Whiteaker, J.; Paulovich, A.; McIntosh, M. A platform for accurate mass and time analyses of mass spectrometry data. J. Proteome Res. 2007, 6 (7), 2685-2694.
23. Faca, V.; Coram, M.; Phanstiel, D.; Glukhova, V.; Zhang, Q.; Fitzgibbon, M.; McIntosh, M.; Hanash, S. Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS. J. Proteome Res. 2006, 5 (8), 2009-2018.