Systems Analysis of Arrestin Pathway Functions - Progress in Molecular Biology and Translational Science - page 451

121. Pinkse MW, Uitto PM, Hilhorst MJ, Ooms B, Heck AJ. Selective isolation
at the femtomole level of phosphopeptides from proteolytic digests using
2D - nanoLC - ESI- MS/MS and titanium oxide precolumns. Anal Chem . 2004;76:
3935- 3943.
122. Jensen SS, Larsen MR. Evaluation of the impact of some experimental procedures on
different phosphopeptide enrichment techniques. Rapid Commun Mass Spectrom .

2007;21:3635- 3645.
123. Olsen JV, Vermeulen M, Santamaria A, et al. Quantitative phosphoproteomics reveals
widespread full phosphorylation site occupancy during mitosis. Sci Signal . 2010;3:ra3.
124. Olsen JV, Blagoev B, Gnad F, et al. Global, in vivo, and site-specific phosphorylation
dynamics in signaling networks. Cell . 2006;127:635 - 648.
125. Davidson L, Pawson AJ, L ´ pez de Maturana R, et al. Gonadotropin-releasing
hormone-induced activation of diacylglycerol kinase-zeta and its association with
active c-src. J Biol Chem . 2004;279:11906- 11916.
126. Heck AJ. Native mass spectrometry: a bridge between interactomics and structural biol-
ogy. Nat Methods . 2008;5:927 - 933.
127. Zhong Y, Hyung SJ, Ruotolo BT. Ion mobility-mass spectrometry for structural pro-
teomics. Expert Rev Proteomics . 2012;9:47 - 58.
128. Zhou Y, Yi T, Park SS, et al. Rapid and enhanced proteolytic digestion using electric
field-oriented enzyme reactor. J Proteomics . 2011;74:1030 - 1035.
129. Zhong J, Chaerkady R, Kandasamy K, Gucek M, Cole RN, Pandey A. The inter-
actome of a PTB domain-containing adapter protein, Odin, revealed by SILAC.
J Proteomics . 2011;74:294 - 303.
130. Martinez-Ferrando I, Chaerkady R, Zhong J, et al. Identification of targets of c-Src
tyrosine kinase by chemical complementation and phosphoproteomics. Mol Cell Prote-
omics . 2012;11:355 - 369.
131. Gong S, Yoon G, Jang I, et al. PSIbase: a database of protein sructural interactome map
(PSIMAP). Bioinformatics . 2005;21:2541- 2543.
132. Venkatesan K, Rual JF, Vazquez A, et al. An empirical framework for binary inter-
actome mapping. Nat Methods . 2009;6:83- 90.
133. Lievens S, Peelman F, De Bosscher K, Lemmens I, Tavernier J. MAPPIT: a protein
interaction toolbox built on insights in cytokine receptor signaling. Cytokine Growth
Factor Rev . 2011;22:321 - 329.
134. Yang CY, Chang CH, Yu YL, et al. PhosphoPOINT: a comprehensive human kinase
interactome and phospho-protein database. Bioinformatics . 2008;24:14 - 20.
135. Hvidsten TR, Komorowski J, Sandvik AK, Laegreid A. Predicting gene function from
gene expressions and ontologies. Pac Symp Biocomput . 2010;6:299 - 310.
136. Adams MD, Celniker SE, Holt RA, et al. The genome sequence of Drosophila mela-
nogaster. Science . 2000;287:2185 - 2195.
137. Liu M, Liberzon A, Kong SW, et al. Network-based analysis of affected biological pro-
cesses in type 2 diabetes models. PLoS Genet . 2007;3:e96.
138. Hirschman L, Yeh A, Blaschke C, Valencia A. Overview of BioCreAtIvE: critical
assessment of information extraction for biology. BMC Bioinformatics . 2005;6:S1.
139. Dressman HK, Muramoto GG, Chao NJ, et al. Gene expression signatures that predict
radiation exposure in mice and humans. PLoS Med . 2007;4:e106.
140. Chadwick W, Boyle JP, Zhou Y, et al. Multiple oxygen tension environments reveal
diverse patterns of transcriptional regulation in primary astrocytes. PLoS One . 2011;6:
e21638.
141. Chadwick W, Zhou Y, Park SS, et al. Minimal peroxide exposure of neuronal cells
induces multifaceted adaptive responses. PLoS One . 2010;5:e14352.
142. Kim S-Y, Volsky DJ. PAGE: parametric analysis of geneset enrichment. BMC Bioin-
formatics . 2005;6:144 - 156.