Systematic comparison of a two-dimensional ion trap and a three-dimensional ion trap mass spectrometer in proteomics

被引:45
作者
Mayya, V [1 ]
Rezaul, K [1 ]
Cong, YS [1 ]
Han, D [1 ]
机构
[1] Univ Connecticut, Ctr Hlth, Ctr Vasc Biol, Dept Cell Biol, Farmington, CT 06030 USA
关键词
D O I
10.1074/mcp.T400015-MCP200
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The utility and advantages of the recently introduced two-dimensional quadrupole ion trap mass spectrometer in proteomics over the traditional three-dimensional ion trap mass spectrometer have not been systematically characterized. Here we rigorously compared the performance of these two platforms by using over 100,000 tandem mass spectra acquired with identical complex peptide mixtures and acquisition parameters. Specifically we compared four factors that are critical for a successful proteomic study: 1) the number of proteins identified, 2) sequence coverage or the number of peptides identified for every protein, 3) the data base matching SEQUEST X-corr and S-p score, and 4) the quality of the fragment ion series of peptides. We found a 4-6-fold increase in the number of peptides and proteins identified on the two-dimensional ion trap mass spectrometer as a direct result of improvement in all the other parameters examined. Interestingly more than 70% of the doubly and triply charged peptides, but not the singly charged peptides, showed better quality of fragmentation spectra on the two-dimensional ion trap. These results highlight specific advantages of the two-dimensional ion trap over the conventional three-dimensional ion traps for protein identification in proteomic experiments.
引用
收藏
页码:214 / 223
页数:10
相关论文
共 29 条
[1]   Mass spectrometry in proteomics [J].
Aebersold, R ;
Goodlett, DR .
CHEMICAL REVIEWS, 2001, 101 (02) :269-295
[2]   Mass spectrometry-based proteomics [J].
Aebersold, R ;
Mann, M .
NATURE, 2003, 422 (6928) :198-207
[3]   Large-scale characterization of HeLa cell nuclear phosphoproteins [J].
Beausoleil, SA ;
Jedrychowski, M ;
Schwartz, D ;
Elias, JE ;
Villén, J ;
Li, JX ;
Cohn, MA ;
Cantley, LC ;
Gygi, SP .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (33) :12130-12135
[4]   Emerging tandem-mass-spectrometry techniques for the rapid identification of proteins [J].
Dongre, AR ;
Eng, JK ;
Yates, JR .
TRENDS IN BIOTECHNOLOGY, 1997, 15 (10) :418-425
[5]   Intensity-based protein identification by machine learning from a library of tandem mass spectra [J].
Elias, JE ;
Gibbons, FD ;
King, OD ;
Roth, FP ;
Gygi, SP .
NATURE BIOTECHNOLOGY, 2004, 22 (02) :214-219
[6]   AN APPROACH TO CORRELATE TANDEM MASS-SPECTRAL DATA OF PEPTIDES WITH AMINO-ACID-SEQUENCES IN A PROTEIN DATABASE [J].
ENG, JK ;
MCCORMACK, AL ;
YATES, JR .
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 1994, 5 (11) :976-989
[7]   A proteomic view of the Plasmodium falciparum life cycle [J].
Florens, L ;
Washburn, MP ;
Raine, JD ;
Anthony, RM ;
Grainger, M ;
Haynes, JD ;
Moch, JK ;
Muster, N ;
Sacci, JB ;
Tabb, DL ;
Witney, AA ;
Wolters, D ;
Wu, YM ;
Gardner, MJ ;
Holder, AA ;
Sinden, RE ;
Yates, JR ;
Carucci, DJ .
NATURE, 2002, 419 (6906) :520-526
[8]   Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography microspray and nanospray mass spectrometry [J].
Gatlin, CL ;
Kleemann, GR ;
Hays, LG ;
Link, AJ ;
Yates, JR .
ANALYTICAL BIOCHEMISTRY, 1998, 263 (01) :93-101
[9]   Protein identification with a single accurate mass of a cysteine-containing peptide and constrained database searching [J].
Goodlett, DR ;
Bruce, JE ;
Anderson, GA ;
Rist, B ;
Pasa-Tolic, L ;
Fiehn, O ;
Smith, RD ;
Aebersold, R .
ANALYTICAL CHEMISTRY, 2000, 72 (06) :1112-1118
[10]   Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry [J].
Han, DK ;
Eng, J ;
Zhou, HL ;
Aebersold, R .
NATURE BIOTECHNOLOGY, 2001, 19 (10) :946-951