Rapid optimization of MRM-MS instrument parameters by subtle alteration of precursor and product m/z targets

Journal of Proteome Research

Volumn 8, Issue 7, 2009, Pages 3746-3751

  Sherwood, Carly A ^a   Eastham, Ashley ^a   Lee, Lik Wee ^a   Risler, Jenni ^a   Mirzaei, Hamid ^a   Falkner, Jayson A ^b   Martin, Daniel B ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b Single Organism Software Inc   (United States)

Author keywords

Collision energy; Cone voltage; Multiple reaction monitoring (MRM); Optimization; Selective reaction monitoring (SRM); Targeted proteomics; Triple quadrupole

Indexed keywords

ARTICLE; ELECTRIC POTENTIAL; ENERGY; MASS SPECTROMETRY; MULTIPLE REACTION MONITORING; PRIORITY JOURNAL; PROTEIN ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; AREA UNDER CURVE; BIOLOGICAL MARKERS; COMPUTATIONAL BIOLOGY; FUNGAL PROTEINS; HAEMOPHILUS INFLUENZAE; IONS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEOME; PROTEOMICS; SOFTWARE;

EID: 67650388498     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr801122b     Document Type: Article

References (22)

1. Arnott, D.; Kishiyama, A.; Luis, E. A.; Ludlum, S. G.; Marsters, J. C., Jr.; Stults, J. T. Selective detection of membrane proteins without antibodies: a mass spectrometric version of the Western blot. Mol. Cell. Proteomics 2002, 1 (2), 148-156.
2. Anderson, L.; Hunter, C. L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 2006, 5 (4), 573-588.
3. Kostiainen, R.; Kotiaho, T.; Kuuranne, T.; Auriola, S. Liquid chromatography/atmospheric pressure ionization-mass spectrometry in drug metabolism studies. J. Mass Spectrom. 2003, 38 (4), 357-372.
4. Sannino, A.; Bolzoni, L.; Bandini, M. Application of liquid chromatography with electrospray tandem mass spectrometry to the determination of a new generation of pesticides in processed fruits and vegetables. J. Chromatogr., A 2004, 1036 (2), 161-169.
5. Tai, S. S.; Bunk, D. M.; White, E. t.; Welch, M. J. Development and evaluation of a reference measurement procedure for the determination of total 3,3′,5-triiodothyronine in human serum using isotope-dilution liquid chromatography-tandem mass spectrometry. Anal. Chem. 2004, 76 (17), 5092-5096.
6. Lee, M. S.; Kerns, E. H. LC/MS applications in drug development. Mass Spectrom. Rev. 1999, 18 (3-4), 187-279.
7. Tiller, P. R.; Cunniff, J.; Land, A. P.; Schwartz, J.; Jardine, I.; Wakefield, M.; Lopez, L.; Newton, J. F.; Burton, R. D.; Folk, B. M.; Buhrman, D. L.; Price, P.; Wu, D. Drug quantitation on a benchtop liquid chromatography-tandem mass spectrometry system. J. Chromatogr., A 1997, 771 (1-2), 119-125.
8. Wolf-Yadlin, A.; Hautaniemi, S.; Lauffenburger, D. A.; White, F. M. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc. Natl. Acad. Sci. U.S.A. 2007, 104 (14), 5860-5865.
9. Keshishian, H.; Addona, T.; Burgess, M.; Kuhn, E.; Carr, S. A. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 2007, 6 (12), 2212-2229.
10. Stahl-Zeng, J.; Lange, V.; Ossola, R.; Eckhardt, K.; Krek, W.; Aebersold, R.; Domon, B. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 2007, 6 (10), 1809-1817.
11. Lange, V.; Picotti, P.; Domon, B.; Aebersold, R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 2008, 4, 222.
12. Martin, D. B.; Holzman, T.; May, D.; Peterson, A.; Eastham, A.; Eng, J.; McIntosh, M. MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol. Cell. Proteomics 2008, 7 (11), 2270-2278.
13. Huang, Y.; Triscari, J. M.; Tseng, G. C.; Pasa-Tolic, L.; Lipton, M. S.; Smith, R. D.; Wysocki, V. H. Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal. Chem. 2005, 77 (18), 5800-5813.
14. Dongre, A. R.; Jones, J. L.; Somogyi, A.; Wysocki, V. H. Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: evidence for the mobile proton model. J. Am. Chem. Soc. 1996, 118 (35), 8365-8374.
15. Kapp, E. A.; Schutz, F.; Reid, G. E.; Eddes, J. S.; Moritz, R. L.; O'Hair, R. A.; Speed, T. P.; Simpson, R. J. Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal. Chem. 2003, 75 (22), 6251-6264.
16. Wysocki, V. H.; Tsaprailis, G.; Smith, L. L.; Breci, L. A. Mobile and localized protons: a framework for understanding peptide dissociation. J. Mass Spectrom. 2000, 35 (12), 1399-1406.
17. Paizs, B.; Suhai, S. Towards understanding the tandem mass spectra of protonated oligopeptides. 1: mechanism of amide bond cleavage. J. Am. Soc. Mass Spectrom. 2004, 15 (1), 103-113.
18. Paizs, B.; Suhai, S. Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 2005, 24, 508-548.
19. Klimek, J.; Eddes, J. S.; Hohmann, L.; Jackson, J.; Peterson, A.; Letarte, S.; Gafken, P. R.; Katz, J. E.; Mallick, P.; Lee, H.; Schmidt, A.; Ossola, R.; Eng, J. K.; Aebersold, R.; Martin, D. B. The standard protein mix database: a diverse data set to assist in the production of improved peptide and protein identification software tools. J. Proteome Res. 2008, 7, 96-103.
20. Keller, A.; Eng, J.; Zhang, N.; Li, X. J.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005, 1, 2005.0017.
21. Lam, H.; Deutsch, E. W.; Eddes, J. S.; Eng, J. K.; King, N.; Stein, S. E.; Aebersold, R. Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 2007, 7 (5), 655-667.
22. Lam, H.; Deutsch, E. W.; Eddes, J. S.; Eng, J. K.; Stein, S. E.; Aebersold, R. Building consensus spectral libraries for peptide identification in proteomics. Nat. Methods 2008, 5, 873-875.