The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS

Proteomics

Volumn 9, Issue 6, 2009, Pages 1683-1695

  Geromanos, Scott J ^a   Vissers, Johannes P C ^a   Silva, Jeffrey C ^a,b   Dorschel, Craig A ^a   Li, Guo Zhong ^a   Gorenstein, Marc V ^a   Bateman, Robert H ^a   Langridge, James I ^a  

^a WATERS CORPORATION   (United States)

^b CELL SIGNALING TECHNOLOGY   (United States)

Author keywords

Biomarker discovery; Data independent LC MS; Multiplexed LC MS; Shotgun sequencing; Time resolved mass spectrometry

Indexed keywords

ION; ISOTOPE; PROTEIN PRECURSOR;

ANALYZER; ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; DATA ANALYSIS; ENERGY; ESCHERICHIA COLI; LIQUID CHROMATOGRAPHY; MASS SPECTROMETER; PRIORITY JOURNAL; PROTEIN ANALYSIS; TANDEM MASS SPECTROMETRY;

AMINO ACID SEQUENCE; CHROMATOGRAPHY, LIQUID; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEINS; REPRODUCIBILITY OF RESULTS; TIME FACTORS; TRYPSIN;

ESCHERICHIA COLI;

EID: 63049084861     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800562     Document Type: Article

References (32)

1. Strupat, K., Karas, M., Hillenkamp, F., Eckerskorn, C., Lottspeich, F., Matrix-assisted laser desorption ionization mass spectrometry of proteins electroblotted after polyacrylamide gel electrophoresis. Anal. Chem. 1994, 66, 464-470.
2. Mann, M., Hojrup, P., Roepstorff, P., Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol. Mass Spectrom. 1993, 22, 338-345.
3. McCormack, A. L., Schieltz, D., Eng, J. K., Goode, B. et al., Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low femtomole level. Anal. Chem. 1997, 69, 767-776.
4. Washburn, M. P., Wolters, D., Yates, III, J. R., Large scale analysis of the yeast proteome via multidimensional protein identification technology, Nat. Biotech. 2001, 19, 242-247.
5. Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., Gygi, S. P., Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J. Proteome Res. 2003, 2, 43-50.
6. Ishihama, Y., Oda, Y., Tabata, T., Sato, T. et al., Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 2005, 4, 1265-1272.
7. Geromanos, S., Freckleton, G., Tempst, P., Tuning of an electrospray ionization source for maximum peptide-ion transmission into a mass spectrometer. Anal. Chem. 2000, 72, 777-790.
8. Hoopmann, M. R., Finney, G. L., MacCoss, M. J., High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. Anal. Chem. 2007, 79, 5620-5632.
9. Luethy, R., Kessner, D. E., Katz, J. E., MacLean, B. et al., Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. J. Proteome Res. 2008, 7, 4031-4039
10. Carr, S., Aebersold, R., Baldwin, M., Burlingame, A. et al., The need for guidelines in publication of peptide and protein identification data: Working Group on publication guidelines for peptide and protein identification data, Mol. Cell. Proteomics 2004, 3, 531-533.
11. Wilkins, M. R., Appel, R. D., Van Eyk, J. E., Chung, M. C. M. et al., Guidelines for the next 10 years of proteomics, Proteomics 2006, 6, 4-8.
12. Chamrad, D., Meyer, H. E., Valid data from large-scale proteomics studies, Nat. Methods 2005, 2, 647-648.
13. Anderson, N. L., Polanski, M., Pieper, R., Gatlin, T. et al., The Human plasma proteome - A nonredundant list developed by combination of four separate sources, Mol. Cell Proteomics 2004, 3, 311-326.
14. Miyamoto, M., Yoshida, Y., Taguchi, I., Nagasaka, Y. et al., Indepth proteomic profiling of the normal human kidney glomerulus using two-dimensional protein prefractionation in combination with liquid chromatography-tandem mass spectrometry. J. Proteome Res. 2007, 6, 3680-3690.
15. Bateman, R. H., Carruthers, R., Hoyes, J. B., Jones, C. et al., A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-Flight (Q-TOF) mass spectrometer for studying protein phosphorylation. J. Am. Soc. Mass Spectrom. 2002, 13, 792-803.
16. Silva, J. C., Denny, R., Dorschel, C. A., Gorenstein, M. V. et al., Quantitative proteomic analysis by accurate mass retention time pairs. Anal. Chem. 2005, 77, 2187-2200.
17. Williams, E. R., Loh, S. Y., McLafferty, F. W., Cody, R. B., Hadamard transform measurement of tandem fourier-transform mass spectra. Anal. Chem. 1990, 62, 698-703.
18. Masselon, C., Anderson, G. A., Harkewicz, R., Bruce, J. E. et al., Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures. Anal. Chem. 2000, 72, 1918-1924.
19. Wilson, J., Vachet, R. W., Multiplexed MS/MS in a Quadrupole Ion Trap Mass Spectrometer. Anal. Chem. 2004, 76, 7346-7353.
20. Venable, J. D., Dong, M.-Q., Wohlschlegel, J., Dillin, A., Yates, III, J. R., Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 2004, 1, 39-45.
21. Purvine, S., Eppel, J.-T., Yi, E. C., Goodlett, D. R., Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 2003, 3, 847-850.
22. Hoaglund-Hyzer, C. S., Li, J., Clemmer, D. E., Mobility labeling for parallel CID of ion mixtures. Anal. Chem. 2000, 72, 2737-2740.
23. Ramos, A. A., Yang, H., Rosen, L. E., Yao, X., Tandem parallel fragmentation of peptides for mass spectrometry. Anal. Chem. 2006, 78, 6391-6397.
24. Silva, J. C., Denny, R., Dorschel, C. A., Gorenstein, M. V. et al., Simultaneous qualitative and quantitative analysis of the E. coli proteome: A sweet tale. Mol. Cell. Proteomics 2006, 5, 589-607.
25. Hughes, M., Silva, J. C., Geromanos, S. J., Townsend, C. A., Quantitative proteomic analysis of drug-induced changes in mycobacteria. J. Proteome Res. 2006, 5, 54-63.
26. Vissers, J. P. C., Langridge, J. I., Aerts, J. M. F. G., Analysis and quantification diagnostic serum markers and protein signatures for gaucher disease. Mol. Cell. Proteomics 2007, 5, 755-766.
27. Kraemer-Albers, E.-M., Bretz, N., Tenzer, S., Winterstein, C. et al., Oligodendrocytes secrete exosomes containing major myelin and stress-protective proteins: Trophic support for axons? Proteomics Clin. Appl. 2007, 1, 1446-1461.
28. Skilling, J., Denny, R., Richardson, K., Young, P. et al., Prob-Seq-A fragmentation model for interpretation of electrospray tandem mass spectrometry data. Comp. Funct. Genom. 2004, 5, 61-68.
29. Li, G.-Z., Vissers, J. P. C., Silva, J. C., Golick, D. et al., Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures. Proteomics, 2009, 9, 1696-1719.
30. E: A virtue of parallel MS acquisition. Mol. Cell. Proteomics 2006, 5, 144-156.
31. Masselon, C., Pasa-Tolic, L., Lee, S.-W., Li, L. et al., Identification of tryptic peptides from large databases using multiplexed tandem mass spectrometry: Simulations and experimental results. Proteomics 2003, 3, 1279-1286.
32. Zubarev, R., Mann, M., On the proper use of mass accuracy in proteomics. Mol. Cell. Proteomics 2006, 6, 377-381.