HCD-only fragmentation method balances peptide identification and quantitation of TMT-labeled samples in hybrid linear ion trap/orbitrap mass spectrometers

Journal of Proteomics

Volumn 96, Issue , 2014, Pages 263-270

  Chiva, Cristina ^a,b   Sabidó, Eduard ^a,b  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

Collision energy; Mass spectrometry; Protein quantitation; TMT

Indexed keywords

ESCHERICHIA COLI PROTEIN; PEPTIDE; PEPTIDE FRAGMENT;

ACCURACY; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; ENERGY; FRAGMENTATION REACTION; HIGH ENERGY COLLISION DISSOCIATION; ION TRAP MASS SPECTROMETRY; PEPTIDE ANALYSIS; PRIORITY JOURNAL; SIGNAL NOISE RATIO;

COLLISION ENERGY; MASS SPECTROMETRY; PROTEIN QUANTITATION; TMT;

ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MASS SPECTROMETRY; PEPTIDES;

EID: 84890145824     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.11.013     Document Type: Article

References (18)

1. Boersema P.J., Raijmakers R., Lemeer S., Mohammed S., Heck A.J.R. Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat Protoc 2009, 4:484-494.
2. Schmidt A., Kellermann J., Lottspeich F. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 2005, 5:4-15.
3. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17:994-999.
4. Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3:1154-1169.
5. Dayon L., Hainard A., Licker V., Turck N., Kuhn K., Hochstrasser D.F., et al. Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal Chem 2008, 80:2921-2931.
6. Thompson A., Schäfer J., Kuhn K., Kienle S., Schwarz J., Schmidt G., et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 2003, 75:1895-1904.
7. Bantscheff M., Boesche M., Eberhard D., Matthieson T., Sweetman G., Kuster B. Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer. Mol Cell Proteomics 2008, 7:1702-1713.
8. Griffin T.J., Xie H., Bandhakavi S., Popko J., Mohan A., Carlis J.V., et al. iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer. J Proteome Res 2007, 6:4200-4209.
9. Olsen J.V., Macek B., Lange O., Makarov A., Horning S., Mann M. Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods 2007, 4:709-712.
10. Köcher T., Pichler P., Schutzbier M., Stingl C., Kaul A., Teucher N., et al. High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all. J Proteome Res 2009, 8:4743-4752.
11. Pichler P., Köcher T., Holzmann J., Möhring T., Ammerer G., Mechtler K. Improved precision of iTRAQ and TMT quantification by an axial extraction field in an Orbitrap HCD cell. Anal Chem 2011, 83:1469-1474.
12. Zhang Y., Ficarro S.B., Li S., Marto J.A. Optimized Orbitrap HCD for quantitative analysis of phosphopeptides. J Am Soc Mass Spectrom 2009, 20:1425-1434.
13. Olsen J.V., Schwartz J.C., Griep-Raming J., Nielsen M.L., Damoc E., Denisov E., et al. A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics 2009, 8:2759-2769.
14. Dayon L., Pasquarello C., Hoogland C., Sanchez J.-C., Scherl A. Combining low- and high-energy tandem mass spectra for optimized peptide quantification with isobaric tags. J Proteomics 2010, 73:769-777.
15. Altelaar A.F.M., Frese C.K., Preisinger C., Hennrich M.L., Schram A.W., Timmers H.T.M., et al. Benchmarking stable isotope labeling based quantitative proteomics. J Proteomics 2013, 88:14-26.
16. Ting L., Rad R., Gygi S.P., Haas W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods 2011, 8:937-940.
17. Wang H., Alvarez S., Hicks L.M. Comprehensive comparison of iTRAQ and label-free LC-based quantitative proteomics approaches using two Chlamydomonas reinhardtii strains of interest for biofuels engineering. J Proteome Res 2012, 11:487-501.
18. Yang Q., Peng J., Lu S.-B., Guo Q.-Y., Zhao B., Zhang L., et al. Evaluation of an extracellular matrix-derived acellular biphasic scaffold/cell construct in the repair of a large articular high-load-bearing osteochondral defect in a canine model. Chin Med J (Engl) 2011, 124:3930-3938.