Automated precursor ion exclusion during LC-MS/MS data acquisition for optimal ion identification

Journal of the American Society for Mass Spectrometry

Volumn 23, Issue 8, 2012, Pages 1400-1407

  Zhang, Zhongqi ^a  

^a AMGEN INC   (United States)

Author keywords

Data dependent acquisition; Intersample; Ion trap; Metabolomics; Mixtures; Orbitrap; Precursor ion exclusion; Proteomics; Tandem mass spectrometry

Indexed keywords

DATA-DEPENDENT ACQUISITION; INTERSAMPLE; ION EXCLUSION; ION TRAPS; METABOLOMICS; ORBITRAP; PROTEOMICS; TANDEM MASS SPECTROMETRY;

AUTOMATION; DATA ACQUISITION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MIXTURES; MOLECULAR BIOLOGY;

IONS;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANALYTIC METHOD; ARTICLE; AUTOANALYSIS; COLLISIONALLY ACTIVATED DISSOCIATION; ELECTROSPRAY; ION TRAP MASS SPECTROMETRY; LIQUID CHROMATOGRAPHY; NOISE MEASUREMENT; PRECURSOR ION EXCLUSION; PROTEIN ANALYSIS; PROTEIN PROCESSING; PROTEOMICS; SIGNAL NOISE RATIO; TANDEM MASS SPECTROMETRY;

ANTIBODIES; CHROMATOGRAPHY, LIQUID; DATABASES, PROTEIN; IONS; METABOLOMICS; PEPTIDE FRAGMENTS; PROTEOMICS; TANDEM MASS SPECTROMETRY; TRYPSIN;

EID: 84865773974     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-012-0401-3     Document Type: Article

References (18)

1. Yates, J.R., Ruse, C.I., Nakorchevsky, A.: Proteomics by mass spectrometry: Approaches, advances, and applications. Annu. Rev. Biomed. Eng. 11, 49-79 (2009)
2. Bedair, M., Sumner, L.W.: Current and emerging mass-spectrometry technologies for metabolomics. Trac-Trends Anal. Chem. 27, 238-250 (2008)
3. Srebalus Barnes, C.A., Lim, A.: Applications of mass spectrometry for the structural characterization of recombinant protein pharmaceuticals. Mass Spectrom. Rev. 26, 370-388 (2007) (Pubitemid 46750375)
4. Zhang, Z., Pan, H., Chen, X.: Mass spectrometry for structural characterization of therapeutic antibodies. Mass Spectrom. Rev. 28, 147-176 (2009)
5. Zhang, Z., Smith, D.L.: Determination of amide hydrogen exchange by mass spectrometry: A new tool for protein structure elucidation. Prot. Sci. 2, 522-531 (1993) (Pubitemid 23119303)
6. Engen, J.R.: Analysis of protein conformation and dynamics by hydrogen/deuterium exchange MS. Anal. Chem. 81, 7870-7875 (2009)
7. Xu, G., Chance, M.R.: Hydroxyl radical-mediated modification of proteins as probes for structural proteomics. Chem. Rev. 107, 3514- 3543 (2007) (Pubitemid 47333548)
8. Novak, P., Giannakopulos, A.E.: Chemical cross-linking and mass spectrometry as structure determination tools. Eur. J. Mass Spectrom. 13, 105-113 (2007)
9. Wang, N., Li, L.: Exploring the precursor ion exclusion feature of liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry for improving protein identification in shotgun proteome analysis. Anal. Chem. 80, 4696-4710 (2008) (Pubitemid 351842350)
10. Hoopmann, M.R., Merrihew, G.E., von Haller, P.D., MacCoss, M.J.: Post-analysis data acquisition for the iterative ms/ms sampling of proteomics mixtures. J. Proteome Res. 8, 1870-1875 (2009)
11. Zhang, Z.: Large-scale identification and quantification of covalent modifications in therapeutic proteins. Anal. Chem. 81, 8354-8364 (2009)
12. Ren, D., Pipes, G.D., Liu, D., Shih, L.-Y., Nichols, A.C., Treuheit, M.J., Brems, D.N., Bondarenko, P.V.: An improved trypsin digestion method minimizes digestion-induced modifications on proteins. Anal. Biochem. 392, 12-21 (2009)
13. Zhang, Z: Retention time alignment of LC/MS data by a divideand- conquer algorithm. J. Am. Soc. Mass Spectrom. 23, 764-772 (2012)
14. Zhang, Z.: Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 76, 3908-3922 (2004) (Pubitemid 38943659)
15. Zhang, Z.: Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. Anal. Chem. 77, 6364-6373 (2005) (Pubitemid 41436975)
16. Zhang, Z., Shah, B.: Prediction of collision-induced dissociation spectra of common n-glycopeptides for glycoform identification. Anal. Chem. 82, 10194-10202 (2010)
17. Zhang, Z.: Prediction of collision-induced-dissociation spectra of peptides with post-translational or process-induced modifications. Anal. Chem. 83, 8642-8651 (2011)
18. Zhang, Z.: De novo peptide sequencing based on a divide-and-conquer algorithm and peptide tandem spectrum simulation. Anal. Chem. 76, 6374-6383 (2004) (Pubitemid 39458471)