Probabilistic enrichment of phosphopeptides by their mass defect

被引:23
作者
Bruce, Can [1 ]
Shifman, Mark A. [1 ]
Miller, Perry [1 ]
Gulcicek, Erol E. [1 ]
机构
[1] Yale Univ, Ctr Med Informat, WM Keck Fdn Biotechnol Resource Lab, New Haven, CT 06511 USA
关键词
D O I
10.1021/ac060046w
中图分类号
O65 [分析化学];
学科分类号
070302 ; 081704 ;
摘要
The mass defect, that is, the difference between the nominal and actual monoisotopic masses, of a phosphorus in a phosphate group is greater than for most other atoms present in proteins. When the mass defects of tryptic peptides derived from the human proteome are plotted against their masses, phosphopeptides tend to fall off the regression line. By calculating the masses of all potential tryptic peptides from the human proteome, we show that regions of higher phosphorylation probability exist on such a plot. We developed a transformation function to estimate the mass defect of a peptide from its monoisotopic mass and empirically defined a simple formula for a user-selectable discriminant line that categorizes a peptide mass according to its probability of being phosphorylated. Our method performs similarly well on phosphopeptides derived from a database of experimentally validated phosphoproteins. The method is relatively insensitive to mass measurement error of up to 20 ppm. The approach can be used with a tandem mass spectrometer in real time to rapidly select and rank order the possible phosphopeptides from a mixture of unmodified peptides for subsequent phosphorylation site mapping and peptide sequence analysis.
引用
收藏
页码:4374 / 4382
页数:9
相关论文
共 41 条
[21]   The International Protein Index: An integrated database for proteomics experiments [J].
Kersey, PJ ;
Duarte, J ;
Williams, A ;
Karavidopoulou, Y ;
Birney, E ;
Apweiler, R .
PROTEOMICS, 2004, 4 (07) :1985-1988
[22]   Identification of black carbon derived structures in a volcanic ash soil humic acid by Fourier transform ion cyclotron resonance mass spectrometry [J].
Kramer, RW ;
Kujawinski, EB ;
Hatcher, PG .
ENVIRONMENTAL SCIENCE & TECHNOLOGY, 2004, 38 (12) :3387-3395
[23]   Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns [J].
Larsen, MR ;
Thingholm, TE ;
Jensen, ON ;
Roepstorff, P ;
Jorgensen, TJD .
MOLECULAR & CELLULAR PROTEOMICS, 2005, 4 (07) :873-886
[24]   Unique scanning capabilities of a new hybrid linear ion trap mass spectrometer (Q TRAP) used for high sensitivity proteomics applications [J].
Le Blanc, JCY ;
Hager, JW ;
Ilisiu, AMP ;
Hunter, C ;
Zhong, F ;
Chu, I .
PROTEOMICS, 2003, 3 (06) :859-869
[25]   Petroleomics: The next grand challenge for chemical analysis [J].
Marshall, AG ;
Rodgers, RP .
ACCOUNTS OF CHEMICAL RESEARCH, 2004, 37 (01) :53-59
[26]   Improved β-elimination-based affinity purification strategy for enrichment of phosphopeptides [J].
McLachlin, DT ;
Chait, BT .
ANALYTICAL CHEMISTRY, 2003, 75 (24) :6826-6836
[27]   Signaling through scaffold, anchoring, and adaptor proteins [J].
Pawson, T ;
Scott, JD .
SCIENCE, 1997, 278 (5346) :2075-2080
[28]   Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-nanoLC-ESI-MS/MS and titanium oxide precolumns [J].
Pinkse, MWH ;
Uitto, PM ;
Hilhorst, MJ ;
Ooms, B ;
Heck, AJR .
ANALYTICAL CHEMISTRY, 2004, 76 (14) :3935-3943
[29]   Immobilized gallium(III) affinity chromatography of phosphopeptides [J].
Posewitz, MC ;
Tempst, P .
ANALYTICAL CHEMISTRY, 1999, 71 (14) :2883-2892
[30]   Phosphoprotein isotope-coded solid-phase tag approach for enrichment and quantitative analysis of phosphopeptides from complex mixtures [J].
Qian, WJ ;
Gosche, MB ;
Camp, DG ;
Yu, LR ;
Tang, KQ ;
Smith, RD .
ANALYTICAL CHEMISTRY, 2003, 75 (20) :5441-5450