Factorial experimental designs elucidate significant variables affecting data acquisition on a quadrupole orbitrap mass spectrometer

Journal of the American Society for Mass Spectrometry

Volumn 24, Issue 10, 2013, Pages 1501-1512

  Randall, Shan M ^a   Cardasis, Helene L ^b   Muddiman, David C ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b Thermo Fisher Scientific   (United States)

Author keywords

Data dependent acquisition; Design of experiments; FTMS; Proteome coverage; Q Exactive

Indexed keywords

AUTOMATIC GAIN CONTROL; DATA DEPENDENT; EFFECTIVE APPROACHES; FACTORIAL EXPERIMENTAL DESIGN; FTMS; OPTIMIZING PARAMETERS; Q EXACTIVE; SIGNIFICANT VARIABLES;

DATA ACQUISITION; DESIGN OF EXPERIMENTS; GAIN CONTROL; MASS SPECTROMETERS; OPTIMIZATION; PEPTIDES;

IONS;

ARTICLE; AUTOMATIC GAIN CONTROL; CLINICAL EFFECTIVENESS; CONTROLLED STUDY; DATA ANALYSIS; EXPERIMENTAL DESIGN; FACTORIAL ANALYSIS; FACTORIAL DESIGN; MASS SPECTROMETRY; MEDICAL PARAMETERS; NONHUMAN; NORMALIZED COLLISION ENERGY; PEPTIDE ANALYSIS; PHYSICAL PHENOMENA; PREDICTION; QUADRUPOLE ORBITRAP MASS SPECTROMETRY; QUALITY CONTROL; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; TANDEM MASS SPECTROMETRY;

MODELS, CHEMICAL; PROTEOME; PROTEOMICS; RESEARCH DESIGN; SACCHAROMYCES CEREVISIAE PROTEINS; TANDEM MASS SPECTROMETRY;

EID: 84884583449     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-013-0693-y     Document Type: Article

References (25)

1. Cravatt, B.F.; Simon, G.M.; Yates, J.R.: The biological impact of mass-spectrometry-based proteomics. Nature 450, 991-1000 (2007) (Pubitemid 350273629)
2. Bantscheff, M.; Lemeer, S.; Savitski, M.M.; Kuster, B.: Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal. Bioanal. Chem. 404, 939-965 (2012)
3. Hu, Q.Z.; Noll, R.J.; Li, H.Y.; Makarov, A.; Hardman, M.; Cooks, R.G.: The Orbitrap: a new mass spectrometer. J. Mass Spectrom. 40, 430-443 (2005) (Pubitemid 40637866)
4. Michalski, A.; Damoc, E.; Hauschild, J. P.; Lange, O.; Wieghaus, A.; Makarov, A.; Nagaraj, N.; Cox, J.; Mann, M.; Horning, S.: Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole orbitrap mass spectrometer. Mol. Cell. Proteom. 10, (2011). doi: 10.1074/mcp.M111.011015
5. Kelstrup, C.D.; Young, C.; Lavallee, R.; Nielsen, M.L.; Olsen, J.V.: Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer. J. Proteome Res. 11, 3487-3497 (2012)
6. Vining, B.A.; Bossio, R.E.; Marshall, A.G.: Phase correction for collision model analysis and enhanced resolving power of Fourier transform ion cyclotron resonance mass spectra. Anal. Chem. 71, 460-467 (1999) (Pubitemid 29042725)
7. Second, T.P.; Blethrow, J.D.; Schwartz, J.C.; Merrihew, G.E.; MacCoss, M.J.; Swaney, D.L.; Russell, J.D.; Coon, J.J.; Zabrouskov, V.: Dual-Pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal. Chem. 81, 7757-7765 (2009)
8. Olsen, J.V.; Macek, B.; Lange, O.; Makarov, A.; Horning, S.; Mann, M.: Higher-energy C-trap dissociation for peptide modification analysis. Nat. Methods 4, 709-712 (2007) (Pubitemid 47338163)
9. Sun, L.L.; Zhu, G.J.; Dovichi, N.J.: Comparison of the LTQ-Orbitrap Velos and the Q-Exactive for proteomic analysis of 1-1000 ng RAW 264.7 cell lysate digests. Rapid Commun. Mass Spectrom. 27, 157-162 (2013)
10. Fisher, R.A.: The Design of Experiments. Oliver and Boyd, Edinburgh, Scotland (1935)
11. Shuford, C.M.; Li, Q.Z.; Sun, Y.H.; Chen, H.C.; Wang, J.; Shi, R.; Sederoff, R.R.; Chiang, V.L.; Muddiman, D.C.: Comprehensive quantification of monolignol-pathway enzymes in Populus trichocarpa by Protein Cleavage Isotope Dilution Mass Spectrometry. J. Proteome Res. 11, 3390-3404 (2012)
12. Robichaud, G.; Dixon, R.B.; Potturi, A.S.; Cassidy, D.; Edwards, J.R.; Sohn, A.; Dow, T.A.; Muddiman, D.C.: Design, modeling, fabrication, and evaluation of the air amplifier for improved detection of biomolecules by electrospray ionization mass spectrometry. Int. J. Mass Spectrom. 300, 99-107 (2011)
13. Walker, S.H.; Papas, B.N.; Comins, D.L.; Muddiman, D.C.: Interplay of permanent charge and hydrophobicity in the electrospray ionization of glycans. Anal. Chem. 82, 6636-6642 (2010)
14. Barry, J.A.; Muddiman, D.C.: Global optimization of the infrared matrix-assisted laser desorption electrospray ionization (IR MALDESI) source for mass spectrometry using statistical design of experiments. Rapid Commun. Mass Spectrom. 25, 3527-3536 (2011)
15. Andrews, G.L.; Dean, R.A.; Hawkridge, A.M.; Muddiman, D.C.: Improving proteome coverage on a LTQ-Orbitrap using design of experiments. J. Am. Soc. Mass Spectrom. 22, 773-783 (2011)
16. Montgomery, D.C.: Design and Analysis of Experiments. John Wiley and Sons, Inc.; Hoboken, NJ (2005)
17. Riter, L.S.; Vitek, O.; Gooding, K.M.; Hodge, B.D.; Julian, R.K.: Statistical design of experiments as a tool in mass spectrometry. J. Mass Spectrom. 40, 565-579 (2005) (Pubitemid 40733314)
18. Eliasson, M.; Rannar, S.; Madsen, R.; Donten, M.A.; Marsden-Edwards, E.; Moritz, T.; Shockcor, J.P.; Johansson, E.; Trygg, J.: Strategy for optimizing LC-MS data processing in metabolomics: a design of experiments approach. Anal. Chem. 84, 6869-6876 (2012)
19. Telford, J.K.: A Brief introduction to design of experiments. Johns Hopkins APL Tech. Dig. 27, 224-232 (2007) (Pubitemid 351652795)
20. Perkins, D.N.; Pappin, D.J.C.; Creasy, D.M.; Cottrell, J.S.: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567 (1999) (Pubitemid 30007252)
21. Weatherly, D.B.; Atwood, J.A.; Minning, T.A.; Cavola, C.; Tarleton, R.L.; Orlando, R.: A heuristic method for assigning a false-discovery rate for protein identifications from mascot database search results. Mol. Cell. Proteom. 4, 762-772 (2005) (Pubitemid 40873005)
22. JMP Version 9. SAS Institute Inc.; Cary, NC, 1989-2013.
23. JMP Design of Experiments. SAS Institute Inc. Cary, NC (2013)
24. Jedrychowski, M.P.; Huttlin, E.L.; Haas, W.; Sowa, M.E.; Rad, R.; Gygi, S.P.: Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics. Mol. Cell. Proteom. 10, (2011). doi: 10.1074/mcp.M111.009910
25. Elias, J.E.; Gygi, S.P.: Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214 (2007) (Pubitemid 46358868)