Multidimensional separations-based shotgun proteomics

被引:142
作者
Fournier, Marjorie L. [1 ]
Gilmore, Joshua M. [1 ]
Martin-Brown, Skylar A. [1 ]
Washburn, Michael P. [1 ]
机构
[1] Stowers Inst Med Res, Kansas City, MO 64110 USA
关键词
D O I
10.1021/cr068279a
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
A review focusing on the development of multidimensional chromatography coupled to tandem mass spectrometry (MS)for shotgun proteomics analysis is presented. Proteomics analyses are frequently performed to obtain information ranging from simple protein identification to more complex post-translational modification studies and have extended to dynamic studies in response to various stimuli. The coupling of different chromatographic techniques like strong cation exchange/reversed phase liquid chromatography separations with the addition of affinity chromatography has granted a view into a realm previously unknown. The human serum proteome is likely to span >10 orders of magnitude for the dynamic range. Highly abundant proteins such as albumin and transferrin must be removed from the serum through affinity methods and fractionation techniques. Another way to increase the number of theoretical plates in a chromatography analysis is to have smaller particle size which then requires higher pressures for analysis. Ultrahigh-pressure reversed phase liquid chromatography has become active in this area. The implementation of UHPLC in shotgun proteomics system is now possible, but further research is needed in small particle and high-pressure resistant strong cation exchange to fully integrate such application. Moreover, advances in mass spectrometry such as coupling of linear ion trap (LTQ) to Fourier transform (FT-MS) has improved analyses of prostate cancer and of histone phosphorylation. The implementation of all these technological advances and others into shotgun proteomics will continue enabling biological discoveries.
引用
收藏
页码:3654 / 3686
页数:33
相关论文
共 372 条
[1]   Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project [J].
Adamski, M ;
Blackwell, T ;
Menon, R ;
Martens, L ;
Hermjakob, H ;
Taylor, C ;
Omenn, GS ;
States, DJ .
PROTEOMICS, 2005, 5 (13) :3246-3261
[2]   Toward a human blood serum proteome - Analysis by multidimensional separation coupled with mass spectrometry [J].
Adkins, JN ;
Varnum, SM ;
Auberry, KJ ;
Moore, RJ ;
Angell, NH ;
Smith, RD ;
Springer, DL ;
Pounds, JG .
MOLECULAR & CELLULAR PROTEOMICS, 2002, 1 (12) :947-955
[3]  
Allison WT, 2006, MOL VIS, V12, P655
[4]   Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].
Altschul, SF ;
Madden, TL ;
Schaffer, AA ;
Zhang, JH ;
Zhang, Z ;
Miller, W ;
Lipman, DJ .
NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402
[5]   Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC-MS [J].
America, AHP ;
Cordewener, JHG ;
van Geffen, MHA ;
Lommen, A ;
Vissers, JPC ;
Bino, RJ ;
Hall, RD .
PROTEOMICS, 2006, 6 (02) :641-653
[6]   The human plasma proteome - History, character, and diagnostic prospects [J].
Anderson, NL ;
Anderson, NG .
MOLECULAR & CELLULAR PROTEOMICS, 2002, 1 (11) :845-867
[7]  
[Anonymous], 2001, Bioinformatics
[8]   The Trypanosoma cruzi proteome [J].
Atwood, JA ;
Weatherly, DB ;
Minning, TA ;
Bundy, B ;
Cavola, C ;
Opperdoes, FR ;
Orlando, R ;
Tarleton, RL .
SCIENCE, 2005, 309 (5733) :473-476
[9]   Glycoproteomics of Trypanosoma cruzi trypomastigotes using subcellular fractionation, lectin affinity, and stable isotope labeling [J].
Atwood, James A., III ;
Minning, Todd ;
Ludolf, Fernanda ;
Nuccio, Arthur ;
Weatherly, Daniel B. ;
Alvarez-Manilla, Gerardo ;
Tarleton, Rick ;
Orlando, Ron .
JOURNAL OF PROTEOME RESEARCH, 2006, 5 (12) :3376-3384
[10]   Phosphoproteomic analysis of the developing mouse brain [J].
Ballif, BA ;
Villén, J ;
Beausoleil, SA ;
Schwartz, D ;
Gygi, SP .
MOLECULAR & CELLULAR PROTEOMICS, 2004, 3 (11) :1093-1101