Research Articles

1.Pinto, S. M., Nirujogi, R. S., Rojas, P. L., Patil, A. H., Manda, S. S., Subbannayya, Y., Roa, J. C., Chatterjee, A., Prasad, T. S. K. and Pandey, A.  Quantitative phosphoproteomic analysis of IL-33 mediated signaling. Proteomics. 2014. [PubMed]
2.Kim, M. S., Zhong, Y., Yachida, S., Rajeshkumar, N. V., Abel, M. L., Marimuthu, A., Mudgal, K., Hruban, R. H., Poling, J. S., Tyner, J. W., Maitra, A., Iacobuzio-Donahue, C. A. and Pandey, A.  Heterogeneity of pancreatic cancer metastases in a single patient revealed by quantitative proteomics. Molecular & Cellular Proteomics : MCP. 2014. 13, 2803-2811. [PubMed]
3.Dowell, J. A. and Johnson, J. A.  Mechanisms of Nrf2 protection in astrocytes as identified by quantitative proteomics and siRNA screening. PloS One. 2013. 8, e70163. [PubMed]
4.Scheibe, M., Arnoult, N., Kappei, D., Buchholz, F., Decottignies, A., Butter, F. and Mann, M.  Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators. Genome Research. 2013. 23, 2149-2157. [PubMed]
5.Skorupa, A., Urbach, S., Vigy, O., King, M. A., Chaumont-Dubel, S., Prehn, J. H. and Marin, P.  Angiogenin induces modifications in the astrocyte secretome: relevance to amyotrophic lateral sclerosis. Journal of Proteomics. 2013. 91, 274-285. [PubMed]
6.Schweppe, D. K., Rigas, J. R. and Gerber, S. A.  Quantitative phosphoproteomic profiling of human non-small cell lung cancer tumors. Journal of Proteomics. 2013. 91, 286-296. [PubMed]
7.Wu, Q., Xu, W., Cao, L., Li, X., He, T., Wu, Z. and Li, W.  SAHA treatment reveals the link between histone lysine acetylation and proteome in nonsmall cell lung cancer A549 Cells. Journal of Proteome Research. 2013. 12, 4064-4073. [PubMed]
8.Hekmat, O., Munk, S., Fogh, L., Yadav, R., Francavilla, C., Horn, H., Wurtz, S. O., Schrohl, A. S., Damsgaard, B., Romer, M. U., Belling, K. C., Jensen, N. F., Gromova, I., Bekker-Jensen, D. B., Moreira, J. M., Jensen, L. J., Gupta, R., Lademann, U., Brunner, N., Olsen, J. V. and Stenvang, J.  TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells. Journal of Proteome Research. 2013. 12, 4136-4151. [PubMed]
9.Oppermann, F. S., Klammer, M., Bobe, C., Cox, J., Schaab, C., Tebbe, A. and Daub, H.  Comparison of SILAC and mTRAQ quantification for phosphoproteomics on a quadrupole orbitrap mass spectrometer. Journal of Proteome Research. 2013. 12, 4089-4100. [PubMed]
10.Syred, H. M., Welburn, J., Rappsilber, J. and Ohkura, H.  Cell cycle regulation of microtubule interactomes: multi-layered regulation is critical for the interphase/mitosis transition. Molecular & Cellular Proteomics : MCP. 2013. 12, 3135-3147. [PubMed]
11.Wang, J., Zhang, X., Ma, D., Lee, W. N., Xiao, J., Zhao, Y., Go, V. L., Wang, Q., Yen, Y., Recker, R. and Xiao, G. G.  Inhibition of transketolase by oxythiamine altered dynamics of protein signals in pancreatic cancer cells. Experimental Hematology & Oncology. 2013. 2, 18. [PubMed]
12.Zhao, Y., Fang, X., Wang, Y., Zhang, J., Jiang, S., Liu, Z., Ma, Z., Xu, L., Li, E. and Zhang, K.  Comprehensive analysis for histone acetylation of human colon cancer cells treated with a novel HDAC inhibitor. Current Pharmaceutical Design. 2014. 20, 1866-1873. [PubMed]
13.Xia, L., Wang, T. D., Shen, S. M., Zhao, M., Sun, H., He, Y., Xie, L., Wu, Z. X., Han, S. F., Wang, L. S. and Chen, G. Q.  Phosphoproteomics study on the activated PKCdelta-induced cell death. Journal of Proteome Research. 2013. 12, 4280-4301. [PubMed]
14.Barrero, C. A., Datta, P. K., Sen, S., Deshmane, S., Amini, S., Khalili, K. and Merali, S.  HIV-1 Vpr modulates macrophage metabolic pathways: a SILAC-based quantitative analysis. PloS One. 2013. 8, e68376. [PubMed]
15.Chen, J. T., Ho, C. W., Chi, L. M., Chien, K. Y., Hsieh, Y. J., Lin, S. J. and Yu, J. S.  Identification of the lamin A/C phosphoepitope recognized by the antibody P-STM in mitotic HeLa S3 cells. BMC Biochemistry. 2013. 14, 18. [PubMed]
16.Bard-Chapeau, E. A., Gunaratne, J., Kumar, P., Chua, B. Q., Muller, J., Bard, F. A., Blackstock, W., Copeland, N. G. and Jenkins, N. A.  EVI1 oncoprotein interacts with a large and complex network of proteins and integrates signals through protein phosphorylation. Proceedings of the National Academy of Sciences of the United States of America. 2013. 110, E2885-94. [PubMed]
17.Konvalinka, A., Zhou, J., Dimitromanolakis, A., Drabovich, A. P., Fang, F., Gurley, S., Coffman, T., John, R., Zhang, S. L., Diamandis, E. P. and Scholey, J. W.  Determination of an angiotensin II-regulated proteome in primary human kidney cells by stable isotope labeling of amino acids in cell culture (SILAC). The Journal of Biological Chemistry. 2013. 288, 24834-24847. [PubMed]
18.Rezgui, V. A., Tyagi, K., Ranjan, N., Konevega, A. L., Mittelstaet, J., Rodnina, M. V., Peter, M. and Pedrioli, P. G.  tRNA tKUUU, tQUUG, and tEUUC wobble position modifications fine-tune protein translation by promoting ribosome A-site binding. Proceedings of the National Academy of Sciences of the United States of America. 2013. 110, 12289-12294. [PubMed]
19.Kim, J. Y., Welsh, E. A., Oguz, U., Fang, B., Bai, Y., Kinose, F., Bronk, C., Remsing, R. i. x., Beg, A. A., Rix, U., Eschrich, S. A., Koomen, J. M. and Haura, E. B.  Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells. Proceedings of the National Academy of Sciences of the United States of America. 2013. 110, 12414-12419. [PubMed]
20.Reales-Calderon, J. A., Sylvester, M., Strijbis, K., Jensen, O. N., Nombela, C., Molero, G. and Gil, C.  Candida albicans induces pro-inflammatory and anti-apoptotic signals in macrophages as revealed by quantitative proteomics and phosphoproteomics. Journal of Proteomics. 2013. 91, 106-135. [PubMed]
21.Yan, L. B., Shi, K., Bing, Z. T., Sun, Y. L. and Shen, Y.  Proteomic analysis of energy metabolism and signal transduction in irradiated melanoma cells. International Journal of Ophthalmology. 2013. 6, 286-294. [PubMed]
22.Zhang, Y., Kweon, H. K., Shively, C., Kumar, A. and Andrews, P. C.  Towards systematic discovery of signaling networks in budding yeast filamentous growth stress response using interventional phosphorylation data. PLoS Computational Biology. 2013. 9, e1003077. [PubMed]
23.Chen, Y., Yang, L. N., Cheng, L., Tu, S., Guo, S. J., Le, H. Y., Xiong, Q., Mo, R., Li, C. Y., Jeong, J. S., Jiang, L., Blackshaw, S., Bi, L. J., Zhu, H., Tao, S. C. and Ge, F.  Bcl2-associated athanogene 3 interactome analysis reveals a new role in modulating proteasome activity. Molecular & Cellular Proteomics : MCP. 2013. 12, 2804-2819. [PubMed]
24.Bottermann, K., Reinartz, M., Barsoum, M., Kotter, S. and Godecke, A.  Systematic Analysis Reveals Elongation Factor 2 and alpha-Enolase as Novel Interaction Partners of AKT2. PloS One. 2013. 8, e66045. [PubMed]
25.Berghoff, B. A., Konzer, A., Mank, N. N., Looso, M., Rische, T., Forstner, K. U., Kruger, M. and Klug, G.  Integrative "omics"-approach discovers dynamic and regulatory features of bacterial stress responses. PLoS Genetics. 2013. 9, e1003576. [PubMed]
26.Ma, Y., Bao, J., Zhao, X., Shen, H., Lv, J., Ma, S., Zhang, X., Li, Z., Wang, S., Wang, Q. and Ji, J.  Activated cyclin-dependent kinase 5 promotes microglial phagocytosis of fibrillar beta-amyloid by up-regulating lipoprotein lipase expression. Molecular & Cellular Proteomics : MCP. 2013. 12, 2833-2844. [PubMed]
27.Coombs K. M.  HeLa cell response proteome alterations induced by mammalian reovirus T3D infection. Virology Journal. 2013. 10, 202. [PubMed]
28.Kolawa, N., Sweredoski, M. J., Graham, R. L., Oania, R., Hess, S. and Deshaies, R. J.  Perturbations to the ubiquitin conjugate proteome in yeast deltaubx mutants identify Ubx2 as a regulator of membrane lipid composition. Molecular & Cellular Proteomics : MCP. 2013. 12, 2791-2803. [PubMed]
29.Plasman, K., Maurer-Stroh, S., Ahmad, J., Hao, H., Kaiserman, D., Sirota, F. L., Jonckheere, V., Bird, P. I., Gevaert, K. and Van, D.  Conservation of the extended substrate specificity profiles among homologous granzymes across species. Molecular & Cellular Proteomics : MCP. 2013. 12, 2921-2934. [PubMed]
30.Wickman, G. R., Julian, L., Mardilovich, K., Schumacher, S., Munro, J., Rath, N., Zander, S. A., Mleczak, A., Sumpton, D., Morrice, N., Bienvenut, W. V. and Olson, M. F.  Blebs produced by actin-myosin contraction during apoptosis release damage-associated molecular pattern proteins before secondary necrosis occurs. Cell Death and Differentiation. 2013. 20, 1293-1305. [PubMed]
31.Alves, R. D., Eijken, M., Bezstarosti, K., Demmers, J. A. and van, L.  Activin A suppresses osteoblast mineralization capacity by altering extracellular matrix (ECM) composition and impairing matrix vesicle (MV) production. Molecular & Cellular Proteomics : MCP. 2013. 12, 2890-2900. [PubMed]
32.Aten, T. M., Redmond, M. M., Weaver, S. O., Love, C. C., Joy, R. M., Lapp, A. S., Rivera, O. D., Hinkle, K. L. and Ballif, B. A.  Tyrosine phosphorylation of the orphan receptor ESDN/DCBLD2 serves as a scaffold for the signaling adaptor CrkL. FEBS Letters. 2013. 587, 2313-2318. [PubMed]
33.Kroeker, A. L., Ezzati, P., Coombs, K. M. and Halayko, A. J.  Influenza A infection of primary human airway epithelial cells up-regulates proteins related to purine metabolism and ubiquitin-related signaling. Journal of Proteome Research. 2013. 12, 3139-3151. [PubMed]
34.Zeng, X., Yang, P., Chen, B., Jin, X., Liu, Y., Zhao, X. and Liang, S.  Quantitative secretome analysis reveals the interactions between epithelia and tumor cells by in vitro modulating colon cancer microenvironment. Journal of Proteomics. 2013. 89, 51-70. [PubMed]
35.Wang, D., Xue, P., Chen, X. L., Xie, Z. S., Yang, F. Q., Zheng, L. and Xu, T.  Angiotensin IV upregulates the activity of protein phosphatase 1alpha in Neura-2A cells. Protein & Cell. 2013. 4, 520-528. [PubMed]
36.Zhai, L., Chang, C., Li, N., Duong, D. M., Chen, H., Deng, Z., Yang, J., Hong, X., Zhu, Y. and Xu, P.  Systematic research on the pretreatment of peptides for quantitative proteomics using a C(1)(8) microcolumn. Proteomics. 2013. 13, 2229-2237. [PubMed]
37.Sprenger, A., Weber, S., Zarai, M., Engelke, R., Nascimento, J. M., Gretzmeier, C., Hilpert, M., Boerries, M., Has, C., Busch, H., Bruckner-Tuderman, L. and Dengjel, J.  Consistency of the proteome in primary human keratinocytes with respect to gender, age, and skin localization. Molecular & Cellular Proteomics : MCP. 2013. 12, 2509-2521. [PubMed]
38.Holmberg, C., Ghesquiere, B., Impens, F., Gevaert, K., Kumar, J. D., Cash, N., Kandola, S., Hegyi, P., Wang, T. C., Dockray, G. J. and Varro, A.  Mapping proteolytic processing in the secretome of gastric cancer-associated myofibroblasts reveals activation of MMP-1, MMP-2, and MMP-3. Journal of Proteome Research. 2013. 12, 3413-3422. [PubMed]
39.Ma, J., Li, W., Lv, Y., Chang, C., Wu, S., Song, L., Ding, C., Wei, H., He, F., Jiang, Y. and Zhu, Y.  A new insight into the impact of different proteases on SILAC quantitative proteome of the mouse liver. Proteomics. 2013. 13, 2238-2242. [PubMed]
40.Wrann, C. D. and Rosen, E. D.  New insights into adipocyte-specific leptin gene expression. Adipocyte. 2012. 1, 168-172. [PubMed]
41.David, C., Koch, J., Oeljeklaus, S., Laernsack, A., Melchior, S., Wiese, S., Schummer, A., Erdmann, R., Warscheid, B. and Brocard, C.  A combined approach of quantitative interaction proteomics and live-cell imaging reveals a regulatory role for endoplasmic reticulum (ER) reticulon homology proteins in peroxisome biogenesis. Molecular & Cellular Proteomics : MCP. 2013. 12, 2408-2425. [PubMed]
42.Kappei, D., Butter, F., Benda, C., Scheibe, M., Draskovic, I., Stevense, M., Novo, C. L., Basquin, C., Araki, M., Araki, K., Krastev, D. B., Kittler, R., Jessberger, R., Londono-Vallejo, J. A., Mann, M. and Buchholz, F.  HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment. The EMBO Journal. 2013. 32, 1681-1701. [PubMed]
43.Gokhale, A., Perez-Cornejo, P., Duran, C., Hartzell, H. C. and Faundez, V.  A comprehensive strategy to identify stoichiometric membrane protein interactomes. Cellular Logistics. 2012. 2, 189-196. [PubMed]
44.Cohen, L. D., Zuchman, R., Sorokina, O., Muller, A., Dieterich, D. C., Armstrong, J. D., Ziv, T. and Ziv, N. E.  Metabolic turnover of synaptic proteins: kinetics, interdependencies and implications for synaptic maintenance. PloS One. 2013. 8, e63191. [PubMed]
45.Bennetzen, M. V., Larsen, D. H., Dinant, C., Watanabe, S., Bartek, J., Lukas, J. and Andersen, J. S.  Acetylation dynamics of human nuclear proteins during the ionizing radiation-induced DNA damage response. Cell Cycle. 2013. 12, 1688-1695. [PubMed]
46.Qiu, H., Jiang, J. L., Liu, M., Huang, X., Ding, S. J. and Wang, L.  Quantitative phosphoproteomics analysis reveals broad regulatory role of heparan sulfate on endothelial signaling. Molecular & Cellular Proteomics : MCP. 2013. 12, 2160-2173. [PubMed]
47.Zhang, L. K., Chai, F., Li, H. Y., Xiao, G. and Guo, L.  Identification of host proteins involved in Japanese encephalitis virus infection by quantitative proteomics analysis. Journal of Proteome Research. 2013. 12, 2666-2678. [PubMed]
48.Emmott, E., Munday, D., Bickerton, E., Britton, P., Rodgers, M. A., Whitehouse, A., Zhou, E. M. and Hiscox, J. A.  The cellular interactome of the coronavirus infectious bronchitis virus nucleocapsid protein and functional implications for virus biology. Journal of Virology. 2013. 87, 9486-9500. [PubMed]
49.Hersch, S. J., Wang, M., Zou, S. B., Moon, K. M., Foster, L. J., Ibba, M. and Navarre, W. W.  Divergent protein motifs direct elongation factor P-mediated translational regulation in Salmonella enterica and Escherichia coli. mBio. 2013. 4, e00180-13. [PubMed]
50.Halbach, S., Rigbolt, K. T., Wohrle, F. U., Diedrich, B., Gretzmeier, C., Brummer, T. and Dengjel, J.  Alterations of Gab2 signalling complexes in imatinib and dasatinib treated chronic myeloid leukaemia cells. Cell Communication and Signaling : CCS. 2013. 11, 30. [PubMed]
51.Yakulov, T., Raggioli, A., Franz, H. and Kemler, R.  Wnt3a-dependent and -independent protein interaction networks of chromatin-bound beta-catenin in mouse embryonic stem cells. Molecular & Cellular Proteomics : MCP. 2013. 12, 1980-1994. [PubMed]
52.Guan, X., Rastogi, N., Parthun, M. R. and Freitas, M. A.  Discovery of histone modification crosstalk networks by stable isotope labeling of amino acids in cell culture mass spectrometry (SILAC MS). Molecular & Cellular Proteomics : MCP. 2013. 12, 2048-2059. [PubMed]
53.Soares, N. C., Spat, P., Krug, K. and Macek, B.  Global dynamics of the Escherichia coli proteome and phosphoproteome during growth in minimal medium. Journal of Proteome Research. 2013. 12, 2611-2621. [PubMed]
54.Paul, D., Kumar, A., Gajbhiye, A., Santra, M. K. and Srikanth, R.  Mass spectrometry-based proteomics in molecular diagnostics: discovery of cancer biomarkers using tissue culture. BioMed Research International. 2013. 2013, 783131. [PubMed]
55.Muller, P. J., Rigbolt, K. T., Paterok, D., Piehler, J., Vanselow, J., Lasonder, E., Andersen, J. S., Schaper, F. and Sobota, R. M.  Protein tyrosine phosphatase SHP2/PTPN11 mistargeting as a consequence of SH2-domain point mutations associated with Noonan Syndrome and leukemia. Journal of Proteomics. 2013. 84, 132-147. [PubMed]
56.Zhang, F., Chen, L., Liu, C., Qiu, P., Wang, A., Li, L. and Wang, H.  Up-regulation of protein tyrosine nitration in methamphetamine-induced neurotoxicity through DDAH/ADMA/NOS pathway. Neurochemistry International. 2013. 62, 1055-1064. [PubMed]
57.Taga, Y., Kusubata, M., Ogawa-Goto, K. and Hattori, S.  Site-specific quantitative analysis of overglycosylation of collagen in osteogenesis imperfecta using hydrazide chemistry and SILAC. Journal of Proteome Research. 2013. 12, 2225-2232. [PubMed]
58.Milner, E., Gutter-Kapon, L., Bassani-Strenberg, M., Barnea, E., Beer, I. and Admon, A.  The effect of proteasome inhibition on the generation of the human leukocyte antigen (HLA) peptidome. Molecular & Cellular Proteomics : MCP. 2013. 12, 1853-1864. [PubMed]
59.Chang, Y. C., Tang, H. W., Liang, S. Y., Pu, T. H., Meng, T. C., Khoo, K. H. and Chen, G. C.  Evaluation of Drosophila metabolic labeling strategies for in vivo quantitative proteomic analyses with applications to early pupa formation and amino acid starvation. Journal of Proteome Research. 2013. 12, 2138-2150. [PubMed]
60.Wang, H., Dong, D., Tang, S., Chen, X. and Gao, Q.  PPE38 of Mycobacterium marinum triggers the cross-talk of multiple pathways involved in the host response, as revealed by subcellular quantitative proteomics. Journal of Proteome Research. 2013. 12, 2055-2066. [PubMed]
61.Caceres, N. E., Aerts, M., Marquez, B., Mingeot-Leclercq, M. P., Tulkens, P. M., Devreese, B. and Van, B.  Analysis of the membrane proteome of ciprofloxacin-resistant macrophages by stable isotope labeling with amino acids in cell culture (SILAC). PloS One. 2013. 8, e58285. [PubMed]
62.Bell-Temin, H., Zhang, P., Chaput, D., King, M. A., You, M., Liu, B. and Stevens, S. M.  Quantitative proteomic characterization of ethanol-responsive pathways in rat microglial cells. Journal of Proteome Research. 2013. 12, 2067-2077. [PubMed]
63.Urbaniak, M. D., Martin, D. M. and Ferguson, M. A.  Global quantitative SILAC phosphoproteomics reveals differential phosphorylation is widespread between the procyclic and bloodstream form lifecycle stages of Trypanosoma brucei. Journal of Proteome Research. 2013. 12, 2233-2244. [PubMed]
64.Barderas, R., Mendes, M., Torres, S., Bartolome, R. A., Lopez-Lucendo, M., Villar-Vazquez, R., Pelaez-Garcia, A., Fuente, E., Bonilla, F. and Casal, J. I.  In-depth characterization of the secretome of colorectal cancer metastatic cells identifies key proteins in cell adhesion, migration, and invasion. Molecular & Cellular Proteomics : MCP. 2013. 12, 1602-1620. [PubMed]
65.Saraon, P., Cretu, D., Musrap, N., Karagiannis, G. S., Batruch, I., Drabovich, A. P., van, d. e. r., Mizokami, A., Morrissey, C., Jarvi, K. and Diamandis, E. P.  Quantitative proteomics reveals that enzymes of the ketogenic pathway are associated with prostate cancer progression. Molecular & Cellular Proteomics : MCP. 2013. 12, 1589-1601. [PubMed]
66.Foster, M. W., Thompson, J. W., Forrester, M. T., Sha, Y., McMahon, T. J., Bowles, D. E., Moseley, M. A. and Marshall, H. E.  Proteomic analysis of the NOS2 interactome in human airway epithelial cells. Nitric Oxide : Biology and Chemistry / Official Journal of the Nitric Oxide Society. 2013. 34, 37-46. [PubMed]
67.Geiger, T., Velic, A., Macek, B., Lundberg, E., Kampf, C., Nagaraj, N., Uhlen, M., Cox, J. and Mann, M.  Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse. Molecular & Cellular Proteomics : MCP. 2013. 12, 1709-1722. [PubMed]
68.Cao, X. J., Zee, B. M. and Garcia, B. A.  Heavy methyl-SILAC labeling coupled with liquid chromatography and high-resolution mass spectrometry to study the dynamics of site-specific histone methylation. Methods in Molecular Biology. 2013. 977, 299-313. [PubMed]
69.Konzer, A., Ruhs, A., Braun, H., Jungblut, B., Braun, T. and Kruger, M.  Stable isotope labeling in zebrafish allows in vivo monitoring of cardiac morphogenesis. Molecular & Cellular Proteomics : MCP. 2013. 12, 1502-1512. [PubMed]
70.Zeiser, J., Gerhard, R., Just, I. and Pich, A.  Substrate specificity of clostridial glucosylating toxins and their function on colonocytes analyzed by proteomics techniques. Journal of Proteome Research. 2013. 12, 1604-1618. [PubMed]
71.Yamada, K., Ono, M., Perkins, N. D., Rocha, S. and Lamond, A. I.  Identification and functional characterization of FMN2, a regulator of the cyclin-dependent kinase inhibitor p21. Molecular Cell. 2013. 49, 922-933. [PubMed]
72.Zanivan, S., Meves, A., Behrendt, K., Schoof, E. M., Neilson, L. J., Cox, J., Tang, H. R., Kalna, G., van, R. e. e., van, D., Trempus, C. S., Machesky, L. M., Linding, R., Wickstrom, S. A., Fassler, R. and Mann, M.  In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis. Cell Reports. 2013. 3, 552-566. [PubMed]
73.Pan, X., Whitten, D. A., Wu, M., Chan, C., Wilkerson, C. G. and Pestka, J. J.  Global protein phosphorylation dynamics during deoxynivalenol-induced ribotoxic stress response in the macrophage. Toxicology and Applied Pharmacology. 2013. 268, 201-211. [PubMed]
74.Duguez, S., Duddy, W., Johnston, H., Laine, J., Le, B., Brown, K. J., Bigot, A., Hathout, Y., Butler-Browne, G. and Partridge, T.  Dystrophin deficiency leads to disturbance of LAMP1-vesicle-associated protein secretion. Cellular and Molecular Life Sciences : CMLS. 2013. 70, 2159-2174. [PubMed]
75.Mulvey, C. M., Tudzarova, S., Crawford, M., Williams, G. H., Stoeber, K. and Godovac-Zimmermann, J.  Subcellular proteomics reveals a role for nucleo-cytoplasmic trafficking at the DNA replication origin activation checkpoint. Journal of Proteome Research. 2013. 12, 1436-1453. [PubMed]
76.Stoehr, G., Schaab, C., Graumann, J. and Mann, M.  A SILAC-based approach identifies substrates of caspase-dependent cleavage upon TRAIL-induced apoptosis. Molecular & Cellular Proteomics : MCP. 2013. 12, 1436-1450. [PubMed]
77.Grau, L., Luque-Garcia, J. L., Gonzalez-Peramato, P., Theodorescu, D., Palou, J., Fernandez-Gomez, J. M. and Sanchez-Carbayo, M.  A quantitative proteomic analysis uncovers the relevance of CUL3 in bladder cancer aggressiveness. PloS One. 2013. 8, e53328. [PubMed]
78.Choudhury, N. R., de, L., de, A., Graf, T., Caceres, J. F., Rappsilber, J. and Michlewski, G.  Tissue-specific control of brain-enriched miR-7 biogenesis. Genes & Development. 2013. 27, 24-38. [PubMed]
79.Schulz, M., Brandner, S., Eberhagen, C., Eckardt-Schupp, F., Larsen, M. R. and Andrae, U.  Quantitative phosphoproteomic analysis of early alterations in protein phosphorylation by 2,3,7,8-tetrachlorodibenzo-p-dioxin. Journal of Proteome Research. 2013. 12, 866-882. [PubMed]
80.Rayavarapu, S., Coley, W., Cakir, E., Jahnke, V., Takeda, S., Aoki, Y., Grodish-Dressman, H., Jaiswal, J. K., Hoffman, E. P., Brown, K. J., Hathout, Y. and Nagaraju, K.  Identification of disease specific pathways using in vivo SILAC proteomics in dystrophin deficient mdx mouse. Molecular & Cellular Proteomics : MCP. 2013. 12, 1061-1073. [PubMed]
81.Acosta, J. C., Snijders, A. P. and Gil, J.  Unbiased characterization of the senescence-associated secretome using SILAC-based quantitative proteomics. Methods in Molecular Biology. 2013. 965, 175-184. [PubMed]
82.Batsukh, T., Schulz, Y., Wolf, S., Rabe, T. I., Oellerich, T., Urlaub, H., Schaefer, I. M. and Pauli, S.  Identification and characterization of FAM124B as a novel component of a CHD7 and CHD8 containing complex. PloS One. 2012. 7, e52640. [PubMed]
83.Lai, W., Wu, J., Zou, X., Xie, J., Zhang, L., Zhao, X., Zhao, M., Wang, Q. and Ji, J.  Secretome analyses of Abeta(1-42) stimulated hippocampal astrocytes reveal that CXCL10 is involved in astrocyte migration. Journal of Proteome Research. 2013. 12, 832-843. [PubMed]
84.Villarreal, L., Mendez, O., Salvans, C., Gregori, J., Baselga, J. and Villanueva, J.  Unconventional secretion is a major contributor of cancer cell line secretomes. Molecular & Cellular Proteomics : MCP. 2013. 12, 1046-1060. [PubMed]
85.Larance, M., Ahmad, Y., Kirkwood, K. J., Ly, T. and Lamond, A. I.  Global subcellular characterization of protein degradation using quantitative proteomics. Molecular & Cellular Proteomics : MCP. 2013. 12, 638-650. [PubMed]
86.Bosshard, F., Armand, F., Hamelin, R. and Kohn, T.  Mechanisms of human adenovirus inactivation by sunlight and UVC light as examined by quantitative PCR and quantitative proteomics. Applied and Environmental Microbiology. 2013. 79, 1325-1332. [PubMed]
87.Berard, A. R., Cortens, J. P., Krokhin, O., Wilkins, J. A., Severini, A. and Coombs, K. M.  Quantification of the host response proteome after mammalian reovirus T1L infection. PloS One. 2012. 7, e51939. [PubMed]
88.Ferrar, T., Chamousset, D., De, W., Nimick, M., Andersen, J., Trinkle-Mulcahy, L. and Moorhead, G. B.  Taperin (c9orf75), a mutated gene in nonsyndromic deafness, encodes a vertebrate specific, nuclear localized protein phosphatase one alpha (PP1alpha) docking protein. Biology Open. 2012. 1, 128-139. [PubMed]
89.Ye, Y., Yan, G., Luo, Y., Tong, T., Liu, X., Xin, C., Liao, M. and Fan, H.  Quantitative proteomics by amino acid labeling in foot-and-mouth disease virus (FMDV)-infected cells. Journal of Proteome Research. 2013. 12, 363-377. [PubMed]
90.Jarboui, M. A., Bidoia, C., Woods, E., Roe, B., Wynne, K., Elia, G., Hall, W. W. and Gautier, V. W.  Nucleolar protein trafficking in response to HIV-1 Tat: rewiring the nucleolus. PloS One. 2012. 7, e48702. [PubMed]
91.Chaput, D., Kirouac, L. H., Bell-Temin, H., Stevens, S. M. and Padmanabhan, J.  SILAC-based proteomic analysis to investigate the impact of amyloid precursor protein expression in neuronal-like B103 cells. Electrophoresis. 2012. 33, 3728-3737. [PubMed]
92.Marimuthu, A., Subbannayya, Y., Sahasrabuddhe, N. A., Balakrishnan, L., Syed, N., Sekhar, N. R., Katte, T. V., Pinto, S. M., Srikanth, S. M., Kumar, P., Pawar, H., Kashyap, M. K., Maharudraiah, J., Ashktorab, H., Smoot, D. T., Ramaswamy, G., Kumar, R. V., Cheng, Y., Meltzer, S. J., Roa, J. C., Chaerkady, R., Prasad, T. S., Harsha, H. C., Chatterjee, A. and Pandey, A.  SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics. Clinical Applications. 2013. 7, 355-366. [PubMed]
93.Li, Y., Liu, N., Huang, D., Zhang, Z., Peng, Z., Duan, C., Tang, X., Tan, G., Yan, G., Mei, W. and Tang, F.  Proteomic analysis on N, N'-dinitrosopiperazine-mediated metastasis of nasopharyngeal carcinoma 6-10B cells. BMC Biochemistry. 2012. 13, 25. [PubMed]
94.Cai, X., Ramalingam, R., Wong, H. S., Cheng, J., Ajuh, P., Cheng, S. H. and Lam, Y. W.  Characterization of carbon nanotube protein corona by using quantitative proteomics. Nanomedicine : Nanotechnology, Biology, and Medicine. 2013. 9, 583-593. [PubMed]
95.Boersema, P. J., Geiger, T., Wisniewski, J. R. and Mann, M.  Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples. Molecular & Cellular Proteomics : MCP. 2013. 12, 158-171. [PubMed]
96.Mausbacher, N., Schreiber, T. B., Machatti, M., Schaab, C. and Daub, H.  Proteome-wide analysis of temporal phosphorylation dynamics in lysophosphatidic acid-induced signaling. Proteomics. 2012. 12, 3485-3498. [PubMed]
97.Kimura, M., Kose, S., Okumura, N., Imai, K., Furuta, M., Sakiyama, N., Tomii, K., Horton, P., Takao, T. and Imamoto, N.  Identification of cargo proteins specific for the nucleocytoplasmic transport carrier transportin by combination of an in vitro transport system and stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics. Molecular & Cellular Proteomics : MCP. 2013. 12, 145-157. [PubMed]
98.Gaetani, M., Matafora, V., Saare, M., Spiliotopoulos, D., Mollica, L., Quilici, G., Chignola, F., Mannella, V., Zucchelli, C., Peterson, P., Bachi, A. and Musco, G.  AIRE-PHD fingers are structural hubs to maintain the integrity of chromatin-associated interactome. Nucleic Acids Research. 2012. 40, 11756-11768. [PubMed]
99.Gunasekera, K., Wuthrich, D., Braga-Lagache, S., Heller, M. and Ochsenreiter, T.  Proteome remodelling during development from blood to insect-form Trypanosoma brucei quantified by SILAC and mass spectrometry. BMC Genomics. 2012. 13, 556. [PubMed]
100.Schmollinger, S., Strenkert, D., Offeddu, V., Nordhues, A., Sommer, F. and Schroda, M.  A protocol for the identification of protein-protein interactions based on 15N metabolic labeling, immunoprecipitation, quantitative mass spectrometry and affinity modulation. Journal of Visualized Experiments : JoVE. 2012. [PubMed]
101.Thiede, B., Koehler, C. J., Strozynski, M., Treumann, A., Stein, R., Zimny-Arndt, U., Schmid, M. and Jungblut, P. R.  High resolution quantitative proteomics of HeLa cells protein species using stable isotope labeling with amino acids in cell culture(SILAC), two-dimensional gel electrophoresis(2DE) and nano-liquid chromatograpohy coupled to an LTQ-OrbitrapMass spectrometer. Molecular & Cellular Proteomics : MCP. 2013. 12, 529-538. [PubMed]
102.Calamia, V., Lourido, L., Fernandez-Puente, P., Mateos, J., Rocha, B., Montell, E., Verges, J., Ruiz-Romero, C. and Blanco, F. J.  Secretome analysis of chondroitin sulfate-treated chondrocytes reveals anti-angiogenic, anti-inflammatory and anti-catabolic properties. Arthritis Research & Therapy. 2012. 14, R202. [PubMed]
103.Ren, Y. R., Chaerkady, R., Hu, S., Wan, J., Qian, J., Zhu, H., Pandey, A. and Kern, S. E.  Unbiased discovery of interactions at a control locus driving expression of the cancer-specific therapeutic and diagnostic target, mesothelin. Journal of Proteome Research. 2012. 11, 5301-5310. [PubMed]
104.Sirvent, A., Vigy, O., Orsetti, B., Urbach, S. and Roche, S.  Analysis of SRC oncogenic signaling in colorectal cancer by stable isotope labeling with heavy amino acids in mouse xenografts. Molecular & Cellular Proteomics : MCP. 2012. 11, 1937-1950. [PubMed]
105.Hughes, C., Radan, L., Chang, W. Y., Stanford, W. L., Betts, D. H., Postovit, L. M. and Lajoie, G. A.  Mass spectrometry-based proteomic analysis of the matrix microenvironment in pluripotent stem cell culture. Molecular & Cellular Proteomics : MCP. 2012. 11, 1924-1936. [PubMed]
106.Lee, N., Pimienta, G. and Steitz, J. A.  AUF1/hnRNP D is a novel protein partner of the EBER1 noncoding RNA of Epstein-Barr virus. RNA. 2012. 18, 2073-2082. [PubMed]
107.Thouvenot, E., Urbach, S., Vigy, O., Seveno, M., Galeotti, N., Nguyen, G., Bockaert, J. and Marin, P.  Quantitative proteomic analysis reveals protein expression changes in the murine neuronal secretome during apoptosis. Journal of Proteomics. 2012. 77, 394-405. [PubMed]
108.Thome, C. H., dos, S., Ferreira, G. A., Scheucher, P. S., Izumi, C., Leopoldino, A. M., Simao, A. M., Ciancaglini, P., de, O., Chin, A., Hanash, S. M., Falcao, R. P., Rego, E. M., Greene, L. J. and Faca, V. M.  Linker for activation of T-cell family member2 (LAT2) a lipid raft adaptor protein for AKT signaling, is an early mediator of alkylphospholipid anti-leukemic activity. Molecular & Cellular Proteomics : MCP. 2012. 11, 1898-1912. [PubMed]
109.Rocha, B., Calamia, V., Mateos, J., Fernandez-Puente, P., Blanco, F. J. and Ruiz-Romero, C.  Metabolic labeling of human bone marrow mesenchymal stem cells for the quantitative analysis of their chondrogenic differentiation. Journal of Proteome Research. 2012. 11, 5350-5361. [PubMed]
110.Goettsch, C., Kliemt, S., Sinningen, K., von, B., Hofbauer, L. C. and Kalkhof, S.  Quantitative proteomics reveals novel functions of osteoclast-associated receptor in STAT signaling and cell adhesion in human endothelial cells. Journal of Molecular and Cellular Cardiology. 2012. 53, 829-837. [PubMed]
111.Chen, C., Wu, D., Zhang, L., Zhao, Y. and Guo, L.  Comparative phosphoproteomics studies of macrophage response to bacterial virulence effectors. Journal of Proteomics. 2012. 77, 251-261. [PubMed]
112.Omerovic, J., Hammond, D. E., Prior, I. A. and Clague, M. J.  Global snapshot of the influence of endocytosis upon EGF receptor signaling output. Journal of Proteome Research. 2012. 11, 5157-5166. [PubMed]
113.Somasekharan, S. P., Stoynov, N., Rotblat, B., Leprivier, G., Galpin, J. D., Ahern, C. A., Foster, L. J. and Sorensen, P. H.  Identification and quantification of newly synthesized proteins translationally regulated by YB-1 using a novel Click-SILAC approach. Journal of Proteomics. 2012. 77, e1-10. [PubMed]
114.Bargaje, R., Gupta, S., Sarkeshik, A., Park, R., Xu, T., Sarkar, M., Halimani, M., Roy, S. S., Yates, J. and Pillai, B.  Identification of novel targets for miR-29a using miRNA proteomics. PloS One. 2012. 7, e43243. [PubMed]
115.Kozuka-Hata, H., Nasu-Nishimura, Y., Koyama-Nasu, R., Ao-Kondo, H., Tsumoto, K., Akiyama, T. and Oyama, M.  Phosphoproteome of human glioblastoma initiating cells reveals novel signaling regulators encoded by the transcriptome. PloS One. 2012. 7, e43398. [PubMed]
116.Barbi, d. e., Vincent, G., Fayewicz, S. L., Bateman, N. W., Hood, B. L., Sun, M., Suhan, J., Duensing, S., Yin, Y., Sander, C., Kirkwood, J. M., Becker, D., Conrads, T. P., Van, H. and Moschos, S. J.  Mitochondrial respiration--an important therapeutic target in melanoma. PloS One. 2012. 7, e40690. [PubMed]
117.Choi, S., Srivas, R., Fu, K. Y., Hood, B. L., Dost, B., Gibson, G. A., Watkins, S. C., Van, H., Bandeira, N., Conrads, T. P., Ideker, T. and Bakkenist, C. J.  Quantitative proteomics reveal ATM kinase-dependent exchange in DNA damage response complexes. Journal of Proteome Research. 2012. 11, 4983-4991. [PubMed]
118.Wang, H., Tipthara, P., Zhu, L., Poon, S. Y., Tang, K. and Liu, J.  Chromatin-Associated Proteins Revealed by SILAC-Proteomic Analysis Exhibit a High Likelihood of Requirement for Growth Fitness under DNA Damage Stress. International Journal of Proteomics. 2012. 2012, 630409. [PubMed]
119.Bauer, K. M. and Hummon, A. B.  Effects of the miR-143/-145 microRNA cluster on the colon cancer proteome and transcriptome. Journal of Proteome Research. 2012. 11, 4744-4754. [PubMed]
120.Scheibe, M., Butter, F., Hafner, M., Tuschl, T. and Mann, M.  Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions. Nucleic Acids Research. 2012. 40, 9897-9902. [PubMed]
121.Kristensen, L. P., Chen, L., Nielsen, M. O., Qanie, D. W., Kratchmarova, I., Kassem, M. and Andersen, J. S.  Temporal profiling and pulsed SILAC labeling identify novel secreted proteins during ex vivo osteoblast differentiation of human stromal stem cells. Molecular & Cellular Proteomics : MCP. 2012. 11, 989-1007. [PubMed]
122.Dammer, E. B., Fallini, C., Gozal, Y. M., Duong, D. M., Rossoll, W., Xu, P., Lah, J. J., Levey, A. I., Peng, J., Bassell, G. J. and Seyfried, N. T.  Coaggregation of RNA-binding proteins in a model of TDP-43 proteinopathy with selective RGG motif methylation and a role for RRM1 ubiquitination. PloS One. 2012. 7, e38658. [PubMed]
123.Bull, V. H. and Thiede, B.  Proteome analysis of tunicamycin-induced ER stress. Electrophoresis. 2012. 33, 1814-1823. [PubMed]
124.Phillips, N. J., Steichen, C. T., Schilling, B., Post, D. M., Niles, R. K., Bair, T. B., Falsetta, M. L., Apicella, M. A. and Gibson, B. W.  Proteomic analysis of Neisseria gonorrhoeae biofilms shows shift to anaerobic respiration and changes in nutrient transport and outermembrane proteins. PloS One. 2012. 7, e38303. [PubMed]
125.Perez-Cornejo, P., Gokhale, A., Duran, C., Cui, Y., Xiao, Q., Hartzell, H. C. and Faundez, V.  Anoctamin 1 (Tmem16A) Ca2+-activated chloride channel stoichiometrically interacts with an ezrin-radixin-moesin network. Proceedings of the National Academy of Sciences of the United States of America. 2012. 109, 10376-10381. [PubMed]
126.Gagne, J. P., Pic, E., Isabelle, M., Krietsch, J., Ethier, C., Paquet, E., Kelly, I., Boutin, M., Moon, K. M., Foster, L. J. and Poirier, G. G.  Quantitative proteomics profiling of the poly(ADP-ribose)-related response to genotoxic stress. Nucleic Acids Research. 2012. 40, 7788-7805. [PubMed]
127.Mastrobuoni, G., Irgang, S., Pietzke, M., Assmus, H. E., Wenzel, M., Schulze, W. X. and Kempa, S.  Proteome dynamics and early salt stress response of the photosynthetic organism Chlamydomonas reinhardtii. BMC Genomics. 2012. 13, 215. [PubMed]
128.Tilghman, R. W., Blais, E. M., Cowan, C. R., Sherman, N. E., Grigera, P. R., Jeffery, E. D., Fox, J. W., Blackman, B. R., Tschumperlin, D. J., Papin, J. A. and Parsons, J. T.  Matrix rigidity regulates cancer cell growth by modulating cellular metabolism and protein synthesis. PloS One. 2012. 7, e37231. [PubMed]
129.Lund, R. R., Terp, M. G., Laenkholm, A. V., Jensen, O. N., Leth-Larsen, R. and Ditzel, H. J.  Quantitative proteomics of primary tumors with varying metastatic capabilities using stable isotope-labeled proteins of multiple histogenic origins. Proteomics. 2012. 12, 2139-2148. [PubMed]
130.Merl, J., Ueffing, M., Hauck, S. M. and von, T.  Direct comparison of MS-based label-free and SILAC quantitative proteome profiling strategies in primary retinal Muller cells. Proteomics. 2012. 12, 1902-1911. [PubMed]
131.Park, S. S., Wu, W. W., Zhou, Y., Shen, R. F., Martin, B. and Maudsley, S.  Effective correction of experimental errors in quantitative proteomics using stable isotope labeling by amino acids in cell culture (SILAC). Journal of Proteomics. 2012. 75, 3720-3732. [PubMed]
132.Urbaniak, M. D., Guther, M. L. and Ferguson, M. A.  Comparative SILAC proteomic analysis of Trypanosoma brucei bloodstream and procyclic lifecycle stages. PloS One. 2012. 7, e36619. [PubMed]
133.Schvartz, D., Brunner, Y., Coute, Y., Foti, M., Wollheim, C. B. and Sanchez, J. C.  Improved characterization of the insulin secretory granule proteomes. Journal of Proteomics. 2012. 75, 4620-4631. [PubMed]
134.Lamoureux, F., Gastinel, L. N., Mestre, E., Marquet, P. and Essig, M.  Mapping cyclosporine-induced changes in protein secretion by renal cells using stable isotope labeling with amino acids in cell culture (SILAC). Journal of Proteomics. 2012. 75, 3674-3687. [PubMed]
135.Jourdan, S. S., Osorio, F. and Hiscox, J. A.  An interactome map of the nucleocapsid protein from a highly pathogenic North American porcine reproductive and respiratory syndrome virus strain generated using SILAC-based quantitative proteomics. Proteomics. 2012. 12, 1015-1023. [PubMed]
136.Bennetzen, M. V., Marino, G., Pultz, D., Morselli, E., Faergeman, N. J., Kroemer, G. and Andersen, J. S.  Phosphoproteomic analysis of cells treated with longevity-related autophagy inducers. Cell Cycle. 2012. 11, 1827-1840. [PubMed]
137.Zhao, M., An, M., Wang, Q., Liu, X., Lai, W., Zhao, X., Wei, S. and Ji, J.  Quantitative proteomic analysis of human osteoblast-like MG-63 cells in response to bioinert implant material titanium and polyetheretherketone. Journal of Proteomics. 2012. 75, 3560-3573. [PubMed]
138.He, P., Ng, B. G., Losfeld, M. E., Zhu, W. and Freeze, H. H.  Identification of intercellular cell adhesion molecule 1 (ICAM-1) as a hypoglycosylation marker in congenital disorders of glycosylation cells. The Journal of Biological Chemistry. 2012. 287, 18210-18217. [PubMed]
139.Krogager, T. P., Nielsen, L. V., Bak, S., Young, C., Ferreri, C., Jensen, O. N., Hojrup, P., Thoma, V., Thogersen, I. B. and Enghild, J. J.  Identification of a potential biomarker panel for the intake of the common dietary trans fat elaidic acid (trans9-C18:1). Journal of Proteomics. 2012. 75, 2685-2696. [PubMed]
140.Borner, G. H., Antrobus, R., Hirst, J., Bhumbra, G. S., Kozik, P., Jackson, L. P., Sahlender, D. A. and Robinson, M. S.  Multivariate proteomic profiling identifies novel accessory proteins of coated vesicles. The Journal of Cell Biology. 2012. 197, 141-160. [PubMed]
141.Schwertman, P., Lagarou, A., Dekkers, D. H., Raams, A., van, d. e. r., Laffeber, C., Hoeijmakers, J. H., Demmers, J. A., Fousteri, M., Vermeulen, W. and Marteijn, J. A.  UV-sensitive syndrome protein UVSSA recruits USP7 to regulate transcription-coupled repair. Nature Genetics. 2012. 44, 598-602. [PubMed]
142.Gui, Y. X., Wang, X. Y., Kang, W. Y., Zhang, Y. J., Zhang, Y., Zhou, Y., Quinn, T. J., Liu, J. and Chen, S. D.  Extracellular signal-regulated kinase is involved in alpha-synuclein-induced mitochondrial dynamic disorders by regulating dynamin-like protein 1. Neurobiology of Aging. 2012. 33, 2841-2854. [PubMed]
143.Deeb, S. J., D'Souza, R. C., Cox, J., Schmidt-Supprian, M. and Mann, M.  Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles. Molecular & Cellular Proteomics : MCP. 2012. 11, 77-89. [PubMed]
144.Huo, Y., Iadevaia, V., Yao, Z., Kelly, I., Cosulich, S., Guichard, S., Foster, L. J. and Proud, C. G.  Stable isotope-labelling analysis of the impact of inhibition of the mammalian target of rapamycin on protein synthesis. The Biochemical Journal. 2012. 444, 141-151. [PubMed]
145.Schvartz, D., Coute, Y., Brunner, Y., Wollheim, C. B. and Sanchez, J. C.  Modulation of neuronal pentraxin 1 expression in rat pancreatic beta-cells submitted to chronic glucotoxic stress. Molecular & Cellular Proteomics : MCP. 2012. 11, 244-254. [PubMed]
146.Gokhale, A., Larimore, J., Werner, E., So, L., Moreno-De-Luca, A., Lese-Martin, C., Lupashin, V. V., Smith, Y. and Faundez, V.  Quantitative proteomic and genetic analyses of the schizophrenia susceptibility factor dysbindin identify novel roles of the biogenesis of lysosome-related organelles complex 1. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 2012. 32, 3697-3711. [PubMed]
147.Samant, R. S., Clarke, P. A. and Workman, P.  The expanding proteome of the molecular chaperone HSP90. Cell Cycle. 2012. 11, 1301-1308. [PubMed]
148.Seyfried, N. T., Gozal, Y. M., Donovan, L. E., Herskowitz, J. H., Dammer, E. B., Xia, Q., Ku, L., Chang, J., Duong, D. M., Rees, H. D., Cooper, D. S., Glass, J. D., Gearing, M., Tansey, M. G., Lah, J. J., Feng, Y., Levey, A. I. and Peng, J.  Quantitative analysis of the detergent-insoluble brain proteome in frontotemporal lobar degeneration using SILAC internal standards. Journal of Proteome Research. 2012. 11, 2721-2738. [PubMed]
149.Geiger, T., Madden, S. F., Gallagher, W. M., Cox, J. and Mann, M.  Proteomic portrait of human breast cancer progression identifies novel prognostic markers. Cancer Research. 2012. 72, 2428-2439. [PubMed]
150.Zhang, L., Zhao, H., Blagg, B. S. and Dobrowsky, R. T.  C-terminal heat shock protein 90 inhibitor decreases hyperglycemia-induced oxidative stress and improves mitochondrial bioenergetics in sensory neurons. Journal of Proteome Research. 2012. 11, 2581-2593. [PubMed]
151.Kani, K., Faca, V. M., Hughes, L. D., Zhang, W., Fang, Q., Shahbaba, B., Luethy, R., Erde, J., Schmidt, J., Pitteri, S. J., Zhang, Q., Katz, J. E., Gross, M. E., Plevritis, S. K., McIntosh, M. W., Jain, A., Hanash, S., Agus, D. B. and Mallick, P.  Quantitative proteomic profiling identifies protein correlates to EGFR kinase inhibition. Molecular Cancer Therapeutics. 2012. 11, 1071-1081. [PubMed]
152.Foster, M. W., Yang, Z., Gooden, D. M., Thompson, J. W., Ball, C. H., Turner, M. E., Hou, Y., Pi, J., Moseley, M. A. and Que, L. G.  Proteomic characterization of the cellular response to nitrosative stress mediated by s-nitrosoglutathione reductase inhibition. Journal of Proteome Research. 2012. 11, 2480-2491. [PubMed]
153.Oeljeklaus, S., Reinartz, B. S., Wolf, J., Wiese, S., Tonillo, J., Podwojski, K., Kuhlmann, K., Stephan, C., Meyer, H. E., Schliebs, W., Brocard, C., Erdmann, R. and Warscheid, B.  Identification of core components and transient interactors of the peroxisomal importomer by dual-track stable isotope labeling with amino acids in cell culture analysis. Journal of Proteome Research. 2012. 11, 2567-2580. [PubMed]
154.Sriharshan, A., Boldt, K., Sarioglu, H., Barjaktarovic, Z., Azimzadeh, O., Hieber, L., Zitzelsberger, H., Ueffing, M., Atkinson, M. J. and Tapio, S.  Proteomic analysis by SILAC and 2D-DIGE reveals radiation-induced endothelial response: four key pathways. Journal of Proteomics. 2012. 75, 2319-2330. [PubMed]
155.Prins, J. M. and Wang, Y.  Quantitative proteomic analysis revealed 4-(methylnitrosamino)-1-(3-pyridinyl)-1-butanone-induced up-regulation of 20S proteasome in cultured human fibroblast cells. Journal of Proteome Research. 2012. 11, 2347-2354. [PubMed]
156.Schreiber, T. B., Mausbacher, N., Soroka, J., Wandinger, S. K., Buchner, J. and Daub, H.  Global analysis of phosphoproteome regulation by the Ser/Thr phosphatase Ppt1 in Saccharomyces cerevisiae. Journal of Proteome Research. 2012. 11, 2397-2408. [PubMed]
157.Azimifar, S. B., Bottcher, R. T., Zanivan, S., Grashoff, C., Kruger, M., Legate, K. R., Mann, M. and Fassler, R.  Induction of membrane circular dorsal ruffles requires co-signalling of integrin-ILK-complex and EGF receptor. Journal of Cell Science. 2012. 125, 435-448. [PubMed]
158.Zhong, J., Kim, M. S., Chaerkady, R., Wu, X., Huang, T. C., Getnet, D., Mitchell, C. J., Palapetta, S. M., Sharma, J., O'Meally, R. N., Cole, R. N., Yoda, A., Moritz, A., Loriaux, M. M., Rush, J., Weinstock, D. M., Tyner, J. W. and Pandey, A.  TSLP signaling network revealed by SILAC-based phosphoproteomics. Molecular & Cellular Proteomics : MCP. 2012. 11, M112.017764. [PubMed]
159.Haines, D. S., Lee, J. E., Beauparlant, S. L., Kyle, D. B., den, B., Sweredoski, M. J., Graham, R. L., Hess, S. and Deshaies, R. J.  Protein interaction profiling of the p97 adaptor UBXD1 points to a role for the complex in modulating ERGIC-53 trafficking. Molecular & Cellular Proteomics : MCP. 2012. 11, M111.016444. [PubMed]
160.Xiong, Q., Zhong, Q., Zhang, J., Yang, M., Li, C., Zheng, P., Bi, L. J. and Ge, F.  Identification of novel miR-21 target proteins in multiple myeloma cells by quantitative proteomics. Journal of Proteome Research. 2012. 11, 2078-2090. [PubMed]
161.Huang, T. C., Sahasrabuddhe, N. A., Kim, M. S., Getnet, D., Yang, Y., Peterson, J. M., Ghosh, B., Chaerkady, R., Leach, S. D., Marchionni, L., Wong, G. W. and Pandey, A.  Regulation of lipid metabolism by Dicer revealed through SILAC mice. Journal of Proteome Research. 2012. 11, 2193-2205. [PubMed]
162.Feng, Y., Chien, K. Y., Chen, H. L. and Chiu, C. H.  Pseudogene recoding revealed from proteomic analysis of salmonella serovars. Journal of Proteome Research. 2012. 11, 1715-1719. [PubMed]
163.Weekes, M. P., Antrobus, R., Talbot, S., Hor, S., Simecek, N., Smith, D. L., Bloor, S., Randow, F. and Lehner, P. J.  Proteomic plasma membrane profiling reveals an essential role for gp96 in the cell surface expression of LDLR family members, including the LDL receptor and LRP6. Journal of Proteome Research. 2012. 11, 1475-1484. [PubMed]
164.Grigera, P. R., Ma, L., Borgman, C. A., Pinto, A. F., Sherman, N. E., Parsons, J. T. and Fox, J. W.  Mass spectrometric analysis identifies a cortactin-RCC2/TD60 interaction in mitotic cells. Journal of Proteomics. 2012. 75, 2153-2159. [PubMed]
165.Migliori, V., Muller, J., Phalke, S., Low, D., Bezzi, M., Mok, W. C., Sahu, S. K., Gunaratne, J., Capasso, P., Bassi, C., Cecatiello, V., De, M., Blackstock, W., Kuznetsov, V., Amati, B., Mapelli, M. and Guccione, E.  Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance. Nature Structural & Molecular Biology. 2012. 19, 136-144. [PubMed]
166.Drexler, H. C., Ruhs, A., Konzer, A., Mendler, L., Bruckskotten, M., Looso, M., Gunther, S., Boettger, T., Kruger, M. and Braun, T.  On marathons and Sprints: an integrated quantitative proteomics and transcriptomics analysis of differences between slow and fast muscle fibers. Molecular & Cellular Proteomics : MCP. 2012. 11, M111.010801. [PubMed]
167.Calamia, V., Fernandez-Puente, P., Mateos, J., Lourido, L., Rocha, B., Montell, E., Verges, J., Ruiz-Romero, C. and Blanco, F. J.  Pharmacoproteomic study of three different chondroitin sulfate compounds on intracellular and extracellular human chondrocyte proteomes. Molecular & Cellular Proteomics : MCP. 2012. 11, M111.013417. [PubMed]
168.Oppermann, F. S., Grundner-Culemann, K., Kumar, C., Gruss, O. J., Jallepalli, P. V. and Daub, H.  Combination of chemical genetics and phosphoproteomics for kinase signaling analysis enables confident identification of cellular downstream targets. Molecular & Cellular Proteomics : MCP. 2012. 11, O111.012351. [PubMed]
169.Chen, C. Y., Chi, L. M., Chi, H. C., Tsai, M. M., Tsai, C. Y., Tseng, Y. H., Lin, Y. H., Chen, W. J., Huang, Y. H. and Lin, K. H.  Stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomics study of a thyroid hormone-regulated secretome in human hepatoma cells. Molecular & Cellular Proteomics : MCP. 2012. 11, M111.011270. [PubMed]
170.Tasso, R., Gaetani, M., Molino, E., Cattaneo, A., Monticone, M., Bachi, A. and Cancedda, R.  The role of bFGF on the ability of MSC to activate endogenous regenerative mechanisms in an ectopic bone formation model. Biomaterials. 2012. 33, 2086-2096. [PubMed]
171.Sharma, K., Vabulas, R. M., Macek, B., Pinkert, S., Cox, J., Mann, M. and Hartl, F. U.  Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response. Molecular & Cellular Proteomics : MCP. 2012. 11, M111.014654. [PubMed]
172.Ma, D., Wang, J., Zhao, Y., Lee, W. N., Xiao, J., Go, V. L., Wang, Q., Recker, R. R. and Xiao, G. G.  Inhibition of glycogen phosphorylation induces changes in cellular proteome and signaling pathways in MIA pancreatic cancer cells. Pancreas. 2012. 41, 397-408. [PubMed]
173.Cao, R., Chen, K., Song, Q., Zang, Y., Li, J., Wang, X., Chen, P. and Liang, S.  Quantitative proteomic analysis of membrane proteins involved in astroglial differentiation of neural stem cells by SILAC labeling coupled with LC-MS/MS. Journal of Proteome Research. 2012. 11, 829-838. [PubMed]
174.Fan, H., Ye, Y., Luo, Y., Tong, T., Yan, G. and Liao, M.  Quantitative proteomics using stable isotope labeling with amino acids in cell culture reveals protein and pathway regulation in porcine circovirus type 2 infected PK-15 cells. Journal of Proteome Research. 2012. 11, 995-1008. [PubMed]
175.Zhang, X. X., Chan, C. S., Bao, H., Fang, Y., Foster, L. J. and Duong, F.  Nanodiscs and SILAC-based mass spectrometry to identify a membrane protein interactome. Journal of Proteome Research. 2012. 11, 1454-1459. [PubMed]
176.Austin, R. J., Smidansky, H. M., Holstein, C. A., Chang, D. K., Epp, A., Josephson, N. C. and Martin, D. B.  Proteomic analysis of the androgen receptor via MS-compatible purification of biotinylated protein on streptavidin resin. Proteomics. 2012. 12, 43-53. [PubMed]
177.Weber, C., Schreiber, T. B. and Daub, H.  Dual phosphoproteomics and chemical proteomics analysis of erlotinib and gefitinib interference in acute myeloid leukemia cells. Journal of Proteomics. 2012. 75, 1343-1356. [PubMed]
178.Chan, C. Y., McDermott, J. C. and Siu, K. W.  Secretome Analysis of Skeletal Myogenesis Using SILAC and Shotgun Proteomics. International Journal of Proteomics. 2011. 2011, 329467. [PubMed]
179.Yang, W., Thompson, J. W., Wang, Z., Wang, L., Sheng, H., Foster, M. W., Moseley, M. A. and Paschen, W.  Analysis of oxygen/glucose-deprivation-induced changes in SUMO3 conjugation using SILAC-based quantitative proteomics. Journal of Proteome Research. 2012. 11, 1108-1117. [PubMed]
180.Zheng, P., Zhong, Q., Xiong, Q., Yang, M., Zhang, J., Li, C., Bi, L. J. and Ge, F.  QUICK identification and SPR validation of signal transducers and activators of transcription 3 (Stat3) interacting proteins. Journal of Proteomics. 2012. 75, 1055-1066. [PubMed]
181.Stephanowitz, H., Lange, S., Lang, D., Freund, C. and Krause, E.  Improved two-dimensional reversed phase-reversed phase LC-MS/MS approach for identification of peptide-protein interactions. Journal of Proteome Research. 2012. 11, 1175-1183. [PubMed]
182.Cambridge, S. B., Gnad, F., Nguyen, C., Bermejo, J. L., Kruger, M. and Mann, M.  Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover. Journal of Proteome Research. 2011. 10, 5275-5284. [PubMed]
183.Chawla, B., Jhingran, A., Panigrahi, A., Stuart, K. D. and Madhubala, R.  Paromomycin affects translation and vesicle-mediated trafficking as revealed by proteomics of paromomycin -susceptible -resistant Leishmania donovani. PloS One. 2011. 6, e26660. [PubMed]
184.Carinhas, N., Robitaille, A. M., Moes, S., Carrondo, M. J., Jenoe, P., Oliveira, R. and Alves, P. M.  Quantitative proteomics of Spodoptera frugiperda cells during growth and baculovirus infection. PloS One. 2011. 6, e26444. [PubMed]
185.Busk, O. L., Frizzell, C., Verhaegen, S., Uhlig, S., Connolly, L., Ropstad, E. and Sorlie, M.  Cytosol protein regulation in H295R steroidogenesis model induced by the zearalenone metabolites, alpha- and beta-zearalenol. Toxicon : Official Journal of the International Society On Toxinology. 2012. 59, 17-24. [PubMed]
186.Zhang, G. and Neubert, T. A.  Comparison of three quantitative phosphoproteomic strategies to study receptor tyrosine kinase signaling. Journal of Proteome Research. 2011. 10, 5454-5462. [PubMed]
187.Hilger, M. and Mann, M.  Triple SILAC to determine stimulus specific interactions in the Wnt pathway. Journal of Proteome Research. 2012. 11, 982-994. [PubMed]
188.Pines, A., Kelstrup, C. D., Vrouwe, M. G., Puigvert, J. C., Typas, D., Misovic, B., de, G., von, S., van, d. e., Danen, E. H., Vrieling, H., Mullenders, L. H. and Olsen, J. V.  Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells. Molecular and Cellular Biology. 2011. 31, 4964-4977. [PubMed]
189.Bartels, S. J., Spruijt, C. G., Brinkman, A. B., Jansen, P. W., Vermeulen, M. and Stunnenberg, H. G.  A SILAC-based screen for Methyl-CpG binding proteins identifies RBP-J as a DNA methylation and sequence-specific binding protein. PloS One. 2011. 6, e25884. [PubMed]
190.Xie, N., Huang, K., Zhang, T., Lei, Y., Liu, R., Wang, K., Zhou, S., Li, J., Wu, J., Wu, H., Deng, C., Zhao, X., Nice, E. C. and Huang, C.  Comprehensive proteomic analysis of host cell lipid rafts modified by HBV infection. Journal of Proteomics. 2012. 75, 725-739. [PubMed]
191.Nebl, T., Prieto, J. H., Kapp, E., Smith, B. J., Williams, M. J., Yates, J. R., Cowman, A. F. and Tonkin, C. J.  Quantitative in vivo analyses reveal calcium-dependent phosphorylation sites and identifies a novel component of the Toxoplasma invasion motor complex. PLoS Pathogens. 2011. 7, e1002222. [PubMed]
192.Dong, X., Xiao, Y., Jiang, X. and Wang, Y.  Quantitative proteomic analysis revealed lovastatin-induced perturbation of cellular pathways in HL-60 cells. Journal of Proteome Research. 2011. 10, 5463-5471. [PubMed]
193.Zeiler, M., Straube, W. L., Lundberg, E., Uhlen, M. and Mann, M.  A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines. Molecular & Cellular Proteomics : MCP. 2012. 11, O111.009613. [PubMed]
194.Lamoureux, F., Mestre, E., Essig, M., Sauvage, F. L., Marquet, P. and Gastinel, L. N.  Quantitative proteomic analysis of cyclosporine-induced toxicity in a human kidney cell line and comparison with tacrolimus. Journal of Proteomics. 2011. 75, 677-694. [PubMed]
195.Yan, G. R., Yin, X. F., Xiao, C. L., Tan, Z. L., Xu, S. H. and He, Q. Y.  Identification of novel signaling components in genistein-regulated signaling pathways by quantitative phosphoproteomics. Journal of Proteomics. 2011. 75, 695-707. [PubMed]
196.Akimov, V., Rigbolt, K. T., Nielsen, M. M. and Blagoev, B.  Characterization of ubiquitination dependent dynamics in growth factor receptor signaling by quantitative proteomics. Molecular BioSystems. 2011. 7, 3223-3233. [PubMed]
197.Wojcechowskyj, J. A., Lee, J. Y., Seeholzer, S. H. and Doms, R. W.  Quantitative phosphoproteomics of CXCL12 (SDF-1) signaling. PloS One. 2011. 6, e24918. [PubMed]
198.Austin, R. J., Kuestner, R. E., Chang, D. K., Madden, K. R. and Martin, D. B.  SILAC compatible strain of Pichia pastoris for expression of isotopically labeled protein standards and quantitative proteomics. Journal of Proteome Research. 2011. 10, 5251-5259. [PubMed]
199.Vogels, M. W., van, B., Heck, A. J., de, H., Rottier, P. J., Batenburg, J. J., Kaloyanova, D. V. and Helms, J. B.  Quantitative proteomic identification of host factors involved in the Salmonella typhimurium infection cycle. Proteomics. 2011. 11, 4477-4491. [PubMed]
200.Busk, O. L., Ndossi, D., Verhaegen, S., Connolly, L., Eriksen, G., Ropstad, E. and Sorlie, M.  Relative quantification of the proteomic changes associated with the mycotoxin zearalenone in the H295R steroidogenesis model. Toxicon : Official Journal of the International Society On Toxinology. 2011. 58, 533-542. [PubMed]
201.Westman-Brinkmalm, A., Abramsson, A., Pannee, J., Gang, C., Gustavsson, M. K., von, O., Blennow, K., Brinkmalm, G., Heumann, H. and Zetterberg, H.  SILAC zebrafish for quantitative analysis of protein turnover and tissue regeneration. Journal of Proteomics. 2011. 75, 425-434. [PubMed]
202.Nikolov, M., Stutzer, A., Mosch, K., Krasauskas, A., Soeroes, S., Stark, H., Urlaub, H. and Fischle, W.  Chromatin affinity purification and quantitative mass spectrometry defining the interactome of histone modification patterns. Molecular & Cellular Proteomics : MCP. 2011. 10, M110.005371. [PubMed]
203.Kar, B., Liu, B., Zhou, Z. and Lam, Y. W.  Quantitative nucleolar proteomics reveals nuclear re-organization during stress- induced senescence in mouse fibroblast. BMC Cell Biology. 2011. 12, 33. [PubMed]
204.Lossner, C., Meier, J., Warnken, U., Rogers, M. A., Lichter, P., Pscherer, A. and Schnolzer, M.  Quantitative proteomics identify novel miR-155 target proteins. PloS One. 2011. 6, e22146. [PubMed]
205.Christofk, H. R., Wu, N., Cantley, L. C. and Asara, J. M.  Proteomic screening method for phosphopeptide motif binding proteins using peptide libraries. Journal of Proteome Research. 2011. 10, 4158-4164. [PubMed]
206.Wang, H. X., Kolesnikova, T. V., Denison, C., Gygi, S. P. and Hemler, M. E.  The C-terminal tail of tetraspanin protein CD9 contributes to its function and molecular organization. Journal of Cell Science. 2011. 124, 2702-2710. [PubMed]
207.Flavin, P., Redmond, A., McBryan, J., Cocchiglia, S., Tibbitts, P., Fahy-Browne, P., Kay, E., Treumann, A., Perrem, K., McIlroy, M., Hill, A. D. and Young, L. S.  RuvBl2 cooperates with Ets2 to transcriptionally regulate hTERT in colon cancer. FEBS Letters. 2011. 585, 2537-2544. [PubMed]
208.Ali, N. A. and Molloy, M. P.  Quantitative phosphoproteomics of transforming growth factor-beta signaling in colon cancer cells. Proteomics. 2011. 11, 3390-3401. [PubMed]
209.Phillips, C. M., Iavarone, A. T. and Marletta, M. A.  Quantitative proteomic approach for cellulose degradation by Neurospora crassa. Journal of Proteome Research. 2011. 10, 4177-4185. [PubMed]
210.Osinalde, N., Moss, H., Arrizabalaga, O., Omaetxebarria, M. J., Blagoev, B., Zubiaga, A. M., Fullaondo, A., Arizmendi, J. M. and Kratchmarova, I.  Interleukin-2 signaling pathway analysis by quantitative phosphoproteomics. Journal of Proteomics. 2011. 75, 177-191. [PubMed]
211.Holland, C., Schmid, M., Zimny-Arndt, U., Rohloff, J., Stein, R., Jungblut, P. R. and Meyer, T. F.  Quantitative phosphoproteomics reveals link between Helicobacter pylori infection and RNA splicing modulation in host cells. Proteomics. 2011. 11, 2798-2811. [PubMed]
212.Calamia, V., Rocha, B., Mateos, J., Fernandez-Puente, P., Ruiz-Romero, C. and Blanco, F. J.  Metabolic labeling of chondrocytes for the quantitative analysis of the interleukin-1-beta-mediated modulation of their intracellular and extracellular proteomes. Journal of Proteome Research. 2011. 10, 3701-3711. [PubMed]
213.Westman, B. J. and Lamond, A. I.  A role for SUMOylation in snoRNP biogenesis revealed by quantitative proteomics. Nucleus. 2011. 2, 30-37. [PubMed]
214.Chavez, J. D., Hoopmann, M. R., Weisbrod, C. R., Takara, K. and Bruce, J. E.  Quantitative proteomic and interaction network analysis of cisplatin resistance in HeLa cells. PloS One. 2011. 6, e19892. [PubMed]
215.Dolai, S., Xu, Q., Liu, F. and Molloy, M. P.  Quantitative chemical proteomics in small-scale culture of phorbol ester stimulated basal breast cancer cells. Proteomics. 2011. 11, 2683-2692. [PubMed]
216.Thomas, S. N., Wan, Y., Liao, Z., Hanson, P. I. and Yang, A. J.  Stable isotope labeling with amino acids in cell culture based mass spectrometry approach to detect transient protein interactions using substrate trapping. Analytical Chemistry. 2011. 83, 5511-5518. [PubMed]
217.Agyeman, A. S., Chaerkady, R., Shaw, P. G., Davidson, N. E., Visvanathan, K., Pandey, A. and Kensler, T. W.  Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane-treated human breast epithelial cells reveals common expression profiles. Breast Cancer Research and Treatment. 2012. 132, 175-187. [PubMed]
218.Formolo, C. A., Williams, R., Gordish-Dressman, H., MacDonald, T. J., Lee, N. H. and Hathout, Y.  Secretome signature of invasive glioblastoma multiforme. Journal of Proteome Research. 2011. 10, 3149-3159. [PubMed]
219.Kaller, M., Liffers, S. T., Oeljeklaus, S., Kuhlmann, K., Roh, S., Hoffmann, R., Warscheid, B. and Hermeking, H.  Genome-wide characterization of miR-34a induced changes in protein and mRNA expression by a combined pulsed SILAC and microarray analysis. Molecular & Cellular Proteomics : MCP. 2011. 10, M111.010462. [PubMed]
220.Auweter, S. D., Bhavsar, A. P., de, H., Li, Y., Chan, Y. A., van, d. e. r., Lowden, M. J., Coombes, B. K., Rogers, L. D., Stoynov, N., Foster, L. J. and Finlay, B. B.  Quantitative mass spectrometry catalogues Salmonella pathogenicity island-2 effectors and identifies their cognate host binding partners. The Journal of Biological Chemistry. 2011. 286, 24023-24035. [PubMed]
221.Yu, J. L. and Guo, L.  Quantitative proteomic analysis of Salmonella enterica serovar Typhimurium under PhoP/PhoQ activation conditions. Journal of Proteome Research. 2011. 10, 2992-3002. [PubMed]
222.Gu, T. L., Nardone, J., Wang, Y., Loriaux, M., Villen, J., Beausoleil, S., Tucker, M., Kornhauser, J., Ren, J., MacNeill, J., Gygi, S. P., Druker, B. J., Heinrich, M. C., Rush, J. and Polakiewicz, R. D.  Survey of activated FLT3 signaling in leukemia. PloS One. 2011. 6, e19169. [PubMed]
223.Guerrera, I. C., Ollero, M., Vieu, D. L. and Edelman, A.  Quantitative differential proteomics of cystic fibrosis cell models by SILAC (stable isotope labelling in cell culture). Methods in Molecular Biology. 2011. 742, 213-225. [PubMed]
224.Ebner, O. A. and Selbach, M.  Whole cell proteome regulation by microRNAs captured in a pulsed SILAC mass spectrometry approach. Methods in Molecular Biology. 2011. 725, 315-331. [PubMed]
225.Kelstrup, C. D., Hekmat, O., Francavilla, C. and Olsen, J. V.  Pinpointing phosphorylation sites: Quantitative filtering and a novel site-specific x-ion fragment. Journal of Proteome Research. 2011. 10, 2937-2948. [PubMed]
226.Kubota, T., Hiraga, S., Yamada, K., Lamond, A. I. and Donaldson, A. D.  Quantitative proteomic analysis of chromatin reveals that Ctf18 acts in the DNA replication checkpoint. Molecular & Cellular Proteomics : MCP. 2011. 10, M110.005561. [PubMed]
227.Gunaratne, J., Goh, M. X., Swa, H. L., Lee, F. Y., Sanford, E., Wong, L. M., Hogue, K. A., Blackstock, W. P. and Okumura, K.  Protein interactions of phosphatase and tensin homologue (PTEN) and its cancer-associated G20E mutant compared by using stable isotope labeling by amino acids in cell culture-based parallel affinity purification. The Journal of Biological Chemistry. 2011. 286, 18093-18103. [PubMed]
228.Mandal, N., Heegaard, S., Prause, J. U., Honore, B. and Vorum, H.  Ocular proteomics with emphasis on two-dimensional gel electrophoresis and mass spectrometry. Biological Procedures Online. 2009. 12, 56-88. [PubMed]
229.Jakobsen, L., Vanselow, K., Skogs, M., Toyoda, Y., Lundberg, E., Poser, I., Falkenby, L. G., Bennetzen, M., Westendorf, J., Nigg, E. A., Uhlen, M., Hyman, A. A. and Andersen, J. S.  Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods. The EMBO Journal. 2011. 30, 1520-1535. [PubMed]
230.Marcilla, M., Alpizar, A., Paradela, A. and Albar, J. P.  A systematic approach to assess amino acid conversions in SILAC experiments. Talanta. 2011. 84, 430-436. [PubMed]
231.Zhang, G., Deinhardt, K., Chao, M. V. and Neubert, T. A.  Study of neurotrophin-3 signaling in primary cultured neurons using multiplex stable isotope labeling with amino acids in cell culture. Journal of Proteome Research. 2011. 10, 2546-2554. [PubMed]
232.Hart, J. R., Liao, L., Ueno, L., Yates, J. R. and Vogt, P. K.  Protein expression profiles of C3H 10T1/2 murine fibroblasts and of isogenic cells transformed by the H1047R mutant of phosphoinositide 3-kinase (PI3K). Cell Cycle. 2011. 10, 971-976. [PubMed]
233.Denis, N., Palmer-Smith, H., Elisma, F., Busuttil, A., Wright, T. G., Bou, K., Prat, A., Seidah, N. G., Chretien, M., Mayne, J. and Figeys, D.  Quantitative proteomic analysis of PCSK9 gain of function in human hepatic HuH7 cells. Journal of Proteome Research. 2011. 10, 2011-2026. [PubMed]
234.Quan, H., Peng, X., Liu, S., Bo, F., Yang, L., Huang, Z., Li, H., Chen, X. and Di, W.  Differentially expressed protein profile of renal tubule cell stimulated by elevated uric acid using SILAC coupled to LC-MS. Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology. 2011. 27, 91-98. [PubMed]
235.Tsai, B. P., Wang, X., Huang, L. and Waterman, M. L.  Quantitative profiling of in vivo-assembled RNA-protein complexes using a novel integrated proteomic approach. Molecular & Cellular Proteomics : MCP. 2011. 10, M110.007385. [PubMed]
236.Yan, G. R., Xu, S. H., Tan, Z. L., Liu, L. and He, Q. Y.  Global identification of miR-373-regulated genes in breast cancer by quantitative proteomics. Proteomics. 2011. 11, 912-920. [PubMed]
237.Basu, S. S., Mesaros, C., Gelhaus, S. L. and Blair, I. A.  Stable isotope labeling by essential nutrients in cell culture for preparation of labeled coenzyme A and its thioesters. Analytical Chemistry. 2011. 83, 1363-1369. [PubMed]
238.Lossner, C., Warnken, U., Pscherer, A. and Schnolzer, M.  Preventing arginine-to-proline conversion in a cell-line-independent manner during cell cultivation under stable isotope labeling by amino acids in cell culture (SILAC) conditions. Analytical Biochemistry. 2011. 412, 123-125. [PubMed]
239.Gunawardena, H. P., Huang, Y., Kenjale, R., Wang, H., Xie, L. and Chen, X.  Unambiguous characterization of site-specific phosphorylation of leucine-rich repeat Fli-I-interacting protein 2 (LRRFIP2) in Toll-like receptor 4 (TLR4)-mediated signaling. The Journal of Biological Chemistry. 2011. 286, 10897-10910. [PubMed]
240.Liu, H., Ong, S. E., Badu-Nkansah, K., Schindler, J., White, F. M. and Hynes, R. O.  CUB-domain-containing protein 1 (CDCP1) activates Src to promote melanoma metastasis. Proceedings of the National Academy of Sciences of the United States of America. 2011. 108, 1379-1384. [PubMed]
241.Wilde, I. B., Brack, M., Winget, J. M. and Mayor, T.  Proteomic characterization of aggregating proteins after the inhibition of the ubiquitin proteasome system. Journal of Proteome Research. 2011. 10, 1062-1072. [PubMed]
242.Brockmeyer, C., Paster, W., Pepper, D., Tan, C. P., Trudgian, D. C., McGowan, S., Fu, G., Gascoigne, N. R., Acuto, O. and Salek, M.  T cell receptor (TCR)-induced tyrosine phosphorylation dynamics identifies THEMIS as a new TCR signalosome component. The Journal of Biological Chemistry. 2011. 286, 7535-7547. [PubMed]
243.Zee, B. M., Levin, R. S., Dimaggio, P. A. and Garcia, B. A.  Global turnover of histone post-translational modifications and variants in human cells. Epigenetics & Chromatin. 2010. 3, 22. [PubMed]
244.Zhong, J., Chaerkady, R., Kandasamy, K., Gucek, M., Cole, R. N. and Pandey, A.  The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. Journal of Proteomics. 2011. 74, 294-303. [PubMed]
245.Ge, F., Zhang, L., Tao, S. C., Kitazato, K., Zhang, Z. P., Zhang, X. E. and Bi, L. J.  Quantitative proteomic analysis of tumor reversion in multiple myeloma cells. Journal of Proteome Research. 2011. 10, 845-855. [PubMed]
246.Hong, D., Chen, H. X., Yu, H. Q., Wang, C., Deng, H. T., Lian, Q. Q. and Ge, R. S.  Quantitative proteomic analysis of dexamethasone-induced effects on osteoblast differentiation, proliferation, and apoptosis in MC3T3-E1 cells using SILAC. Osteoporosis International : A Journal Established As Result of Cooperation Between the European Foundation For Osteoporosis and the National Osteoporosis. 2011. 22, 2175-2186. [PubMed]
247.Knowlton, M. L., Selfors, L. M., Wrobel, C. N., Gu, T. L., Ballif, B. A., Gygi, S. P., Polakiewicz, R. and Brugge, J. S.  Profiling Y561-dependent and -independent substrates of CSF-1R in epithelial cells. PloS One. 2010. 5, e13587. [PubMed]
248.Plasman, K., Van, D., Kaiserman, D., Impens, F., Demeyer, K., Helsens, K., Goethals, M., Bird, P. I., Vandekerckhove, J. and Gevaert, K.  Probing the efficiency of proteolytic events by positional proteomics. Molecular & Cellular Proteomics : MCP. 2011. 10, M110.003301. [PubMed]
249.Walther, D. M. and Mann, M.  Accurate quantification of more than 4000 mouse tissue proteins reveals minimal proteome changes during aging. Molecular & Cellular Proteomics : MCP. 2011. 10, M110.004523. [PubMed]
250.Bartke, T., Vermeulen, M., Xhemalce, B., Robson, S. C., Mann, M. and Kouzarides, T.  Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell. 2010. 143, 470-484. [PubMed]
251.Chen, H., Pimienta, G., Gu, Y., Sun, X., Hu, J., Kim, M. S., Chaerkady, R., Gucek, M., Cole, R. N., Sukumar, S. and Pandey, A.  Proteomic characterization of Her2/neu-overexpressing breast cancer cells. Proteomics. 2010. 10, 3800-3810. [PubMed]
252.Lee, K. K., Todorova, K. and Mandinova, A.  Maximizing early detection of esophageal squamous cell carcinoma via SILAC-proteomics. Cancer Biology & Therapy. 2010. 10, 811-813. [PubMed]
253.Xiong, L., Zhang, J., Yuan, B., Dong, X., Jiang, X. and Wang, Y.  Global proteome quantification for discovering imatinib-induced perturbation of multiple biological pathways in K562 human chronic myeloid leukemia cells. Journal of Proteome Research. 2010. 9, 6007-6015. [PubMed]
254.Khositseth, S., Pisitkun, T., Slentz, D. H., Wang, G., Hoffert, J. D., Knepper, M. A. and Yu, M. J.  Quantitative protein and mRNA profiling shows selective post-transcriptional control of protein expression by vasopressin in kidney cells. Molecular & Cellular Proteomics : MCP. 2011. 10, M110.004036. [PubMed]
255.Ge, F., Xiao, C. L., Bi, L. J., Tao, S. C., Xiong, S., Yin, X. F., Li, L. P., Lu, C. H., Jia, H. T. and He, Q. Y.  Quantitative phosphoproteomics of proteasome inhibition in multiple myeloma cells. PloS One. 2010. 5. [PubMed]
256.Wagner, W., Ajuh, P., Lower, J. and Wessler, S.  Quantitative phosphoproteomic analysis of prion-infected neuronal cells. Cell Communication and Signaling : CCS. 2010. 8, 28. [PubMed]
257.Sotoca, A. M., Gelpke, M. D., Boeren, S., Strom, A., Gustafsson, J. A., Murk, A. J., Rietjens, I. M. and Vervoort, J.  Quantitative proteomics and transcriptomics addressing the estrogen receptor subtype-mediated effects in T47D breast cancer cells exposed to the phytoestrogen genistein. Molecular & Cellular Proteomics : MCP. 2011. 10, M110.002170. [PubMed]
258.Ge, F., Li, W. L., Bi, L. J., Tao, S. C., Zhang, Z. P. and Zhang, X. E.  Identification of novel 14-3-3zeta interacting proteins by quantitative immunoprecipitation combined with knockdown (QUICK). Journal of Proteome Research. 2010. 9, 5848-5858. [PubMed]
259.Akude, E., Zherebitskaya, E., Chowdhury, S. K., Smith, D. R., Dobrowsky, R. T. and Fernyhough, P.  Diminished superoxide generation is associated with respiratory chain dysfunction and changes in the mitochondrial proteome of sensory neurons from diabetic rats. Diabetes. 2011. 60, 288-297. [PubMed]
260.Breitkopf, S. B., Oppermann, F. S., Keri, G., Grammel, M. and Daub, H.  Proteomics analysis of cellular imatinib targets and their candidate downstream effectors. Journal of Proteome Research. 2010. 9, 6033-6043. [PubMed]
261.Collier, T. S., Sarkar, P., Franck, W. L., Rao, B. M., Dean, R. A. and Muddiman, D. C.  Direct comparison of stable isotope labeling by amino acids in cell culture and spectral counting for quantitative proteomics. Analytical Chemistry. 2010. 82, 8696-8702. [PubMed]
262.Emmott, E., Smith, C., Emmett, S. R., Dove, B. K. and Hiscox, J. A.  Elucidation of the avian nucleolar proteome by quantitative proteomics using SILAC and changes in cells infected with the coronavirus infectious bronchitis virus. Proteomics. 2010. 10, 3558-3562. [PubMed]
263.Cuomo, A. and Bonaldi, T.  Systems biology "on-the-fly": SILAC-based quantitative proteomics and RNAi approach in Drosophila melanogaster. Methods in Molecular Biology. 2010. 662, 59-78. [PubMed]
264.Dong, X., Xiong, L., Jiang, X. and Wang, Y.  Quantitative proteomic analysis reveals the perturbation of multiple cellular pathways in jurkat-T cells induced by doxorubicin. Journal of Proteome Research. 2010. 9, 5943-5951. [PubMed]
265.Westman, B. J., Verheggen, C., Hutten, S., Lam, Y. W., Bertrand, E. and Lamond, A. I.  A proteomic screen for nucleolar SUMO targets shows SUMOylation modulates the function of Nop5/Nop58. Molecular Cell. 2010. 39, 618-631. [PubMed]
266.Matsumura, T., Oyama, M., Kozuka-Hata, H., Ishikawa, K., Inoue, T., Muta, T., Semba, K. and Inoue, J.  Identification of BCAP-(L) as a negative regulator of the TLR signaling-induced production of IL-6 and IL-10 in macrophages by tyrosine phosphoproteomics. Biochemical and Biophysical Research Communications. 2010. 400, 265-270. [PubMed]
267.Mulvey, C., Tudzarova, S., Crawford, M., Williams, G. H., Stoeber, K. and Godovac-Zimmermann, J.  Quantitative proteomics reveals a "poised quiescence" cellular state after triggering the DNA replication origin activation checkpoint. Journal of Proteome Research. 2010. 9, 5445-5460. [PubMed]
268.Coombs, K. M., Berard, A., Xu, W., Krokhin, O., Meng, X., Cortens, J. P., Kobasa, D., Wilkins, J. and Brown, E. G.  Quantitative proteomic analyses of influenza virus-infected cultured human lung cells. Journal of Virology. 2010. 84, 10888-10906. [PubMed]
269.Emmott, E., Wise, H., Loucaides, E. M., Matthews, D. A., Digard, P. and Hiscox, J. A.  Quantitative proteomics using SILAC coupled to LC-MS/MS reveals changes in the nucleolar proteome in influenza A virus-infected cells. Journal of Proteome Research. 2010. 9, 5335-5345. [PubMed]
270.Ash, M. R., Faelber, K., Kosslick, D., Albert, G. I., Roske, Y., Kofler, M., Schuemann, M., Krause, E. and Freund, C.  Conserved beta-hairpin recognition by the GYF domains of Smy2 and GIGYF2 in mRNA surveillance and vesicular transport complexes. Structure. 2010. 18, 944-954. [PubMed]
271.Benhar, M., Thompson, J. W., Moseley, M. A. and Stamler, J. S.  Identification of S-nitrosylated targets of thioredoxin using a quantitative proteomic approach. Biochemistry. 2010. 49, 6963-6969. [PubMed]
272.Kashyap, M. K., Harsha, H. C., Renuse, S., Pawar, H., Sahasrabuddhe, N. A., Kim, M. S., Marimuthu, A., Keerthikumar, S., Muthusamy, B., Kandasamy, K., Subbannayya, Y., Prasad, T. S., Mahmood, R., Chaerkady, R., Meltzer, S. J., Kumar, R. V., Rustgi, A. K. and Pandey, A.  SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biology & Therapy. 2010. 10, 796-810. [PubMed]
273.Xiao, K., Sun, J., Kim, J., Rajagopal, S., Zhai, B., Villen, J., Haas, W., Kovacs, J. J., Shukla, A. K., Hara, M. R., Hernandez, M., Lachmann, A., Zhao, S., Lin, Y., Cheng, Y., Mizuno, K., Ma'ayan, A., Gygi, S. P. and Lefkowitz, R. J.  Global phosphorylation analysis of beta-arrestin-mediated signaling downstream of a seven transmembrane receptor (7TMR). Proceedings of the National Academy of Sciences of the United States of America. 2010. 107, 15299-15304. [PubMed]
274.Sylvester, M., Kliche, S., Lange, S., Geithner, S., Klemm, C., Schlosser, A., Grossmann, A., Stelzl, U., Schraven, B., Krause, E. and Freund, C.  Adhesion and degranulation promoting adapter protein (ADAP) is a central hub for phosphotyrosine-mediated interactions in T cells. PloS One. 2010. 5, e11708. [PubMed]
275.Sommer, U., Petersen, J., Pfeiffer, M., Schrotz-King, P. and Morsczeck, C.  Comparison of surface proteomes of enterotoxigenic (ETEC) and commensal Escherichia coli strains. Journal of Microbiological Methods. 2010. 83, 13-19. [PubMed]
276.Mausbacher, N., Schreiber, T. B. and Daub, H.  Glycoprotein capture and quantitative phosphoproteomics indicate coordinated regulation of cell migration upon lysophosphatidic acid stimulation. Molecular & Cellular Proteomics : MCP. 2010. 9, 2337-2353. [PubMed]
277.Cuomo, A., Moretti, S., Minucci, S. and Bonaldi, T.  SILAC-based proteomic analysis to dissect the "histone modification signature" of human breast cancer cells. Amino Acids. 2011. 41, 387-399. [PubMed]
278.Kannan, L., Rath, N. C., Liyanage, R. and Lay, J. O.  Effect of toll-like receptor activation on thymosin beta-4 production by chicken macrophages. Molecular and Cellular Biochemistry. 2010. 344, 55-63. [PubMed]
279.Hjelle, S. M., Forthun, R. B., Haaland, I., Reikvam, H., Sjoholt, G., Bruserud, O. and Gjertsen, B. T.  Clinical proteomics of myeloid leukemia. Genome Medicine. 2010. 2, 41. [PubMed]
280.Lange, S., Sylvester, M., Schumann, M., Freund, C. and Krause, E.  Identification of phosphorylation-dependent interaction partners of the adapter protein ADAP using quantitative mass spectrometry: SILAC vs (18)O-labeling. Journal of Proteome Research. 2010. 9, 4113-4122. [PubMed]
281.Yang, Y., Chaerkady, R., Kandasamy, K., Huang, T. C., Selvan, L. D., Dwivedi, S. B., Kent, O. A., Mendell, J. T. and Pandey, A.  Identifying targets of miR-143 using a SILAC-based proteomic approach. Molecular BioSystems. 2010. 6, 1873-1882. [PubMed]
282.Li, J., Liu, R., Lei, Y., Wang, K., Lau, Q. C., Xie, N., Zhou, S., Nie, C., Chen, L., Wei, Y. and Huang, C.  Proteomic analysis revealed association of aberrant ROS signaling with suberoylanilide hydroxamic acid-induced autophagy in Jurkat T-leukemia cells. Autophagy. 2010. 6, 711-724. [PubMed]
283.Yee, J. C., Jacob, N. M., Jayapal, K. P., Kok, Y. J., Philp, R., Griffin, T. J. and Hu, W. S.  Global assessment of protein turnover in recombinant antibody producing myeloma cells. Journal of Biotechnology. 2010. 148, 182-193. [PubMed]
284.Tian, R., Wang, S., Elisma, F., Li, L., Zhou, H., Wang, L. and Figeys, D.  Rare cell proteomic reactor applied to stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics study of human embryonic stem cell differentiation. Molecular & Cellular Proteomics : MCP. 2011. 10, M110.000679. [PubMed]
285.Sury, M. D., Chen, J. X. and Selbach, M.  The SILAC fly allows for accurate protein quantification in vivo. Molecular & Cellular Proteomics : MCP. 2010. 9, 2173-2183. [PubMed]
286.Spruijt, C. G., Bartels, S. J., Brinkman, A. B., Tjeertes, J. V., Poser, I., Stunnenberg, H. G. and Vermeulen, M.  CDK2AP1/DOC-1 is a bona fide subunit of the Mi-2/NuRD complex. Molecular BioSystems. 2010. 6, 1700-1706. [PubMed]
287.Soufi, B., Kumar, C., Gnad, F., Mann, M., Mijakovic, I. and Macek, B.  Stable isotope labeling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Bacillus subtilis. Journal of Proteome Research. 2010. 9, 3638-3646. [PubMed]
288.Ostasiewicz, P., Zielinska, D. F., Mann, M. and Wisniewski, J. R.  Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. Journal of Proteome Research. 2010. 9, 3688-3700. [PubMed]
289.Emmott, E., Rodgers, M. A., Macdonald, A., McCrory, S., Ajuh, P. and Hiscox, J. A.  Quantitative proteomics using stable isotope labeling with amino acids in cell culture reveals changes in the cytoplasmic, nuclear, and nucleolar proteomes in Vero cells infected with the coronavirus infectious bronchitis virus. Molecular & Cellular Proteomics : MCP. 2010. 9, 1920-1936. [PubMed]
290.Hah, N., Kolkman, A., Ruhl, D. D., Pijnappel, W. W., Heck, A. J., Timmers, H. T. and Kraus, W. L.  A role for BAF57 in cell cycle-dependent transcriptional regulation by the SWI/SNF chromatin remodeling complex. Cancer Research. 2010. 70, 4402-4411. [PubMed]
291.Bicho, C. C., de, L., Chen, Z. A., Rappsilber, J. and Sawin, K. E.  A genetic engineering solution to the "arginine conversion problem" in stable isotope labeling by amino acids in cell culture (SILAC). Molecular & Cellular Proteomics : MCP. 2010. 9, 1567-1577. [PubMed]
292.Imamura, H., Yachie, N., Saito, R., Ishihama, Y. and Tomita, M.  Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. BMC Bioinformatics. 2010. 11, 232. [PubMed]
293.Dilworth, D. J., Saleem, R. A., Rogers, R. S., Mirzaei, H., Boyle, J. and Aitchison, J. D.  QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments. Journal of the American Society For Mass Spectrometry. 2010. 21, 1417-1422. [PubMed]
294.Yang, W., Cai, Q., Lui, V. W., Everley, P. A., Kim, J., Bhola, N., Quesnelle, K. M., Zetter, B. R., Steen, H., Freeman, M. R. and Grandis, J. R.  Quantitative proteomics analysis reveals molecular networks regulated by epidermal growth factor receptor level in head and neck cancer. Journal of Proteome Research. 2010. 9, 3073-3082. [PubMed]
295.Xu, B. J., Yan, W., Jovanovic, B., An, A. Q., Cheng, N., Aakre, M. E., Yi, Y., Eng, J., Link, A. J. and Moses, H. L.  Quantitative analysis of the secretome of TGF-beta signaling-deficient mammary fibroblasts. Proteomics. 2010. 10, 2458-2470. [PubMed]
296.Ren, F., Wu, H., Lei, Y., Zhang, H., Liu, R., Zhao, Y., Chen, X., Zeng, D., Tong, A., Chen, L., Wei, Y. and Huang, C.  Quantitative proteomics identification of phosphoglycerate mutase 1 as a novel therapeutic target in hepatocellular carcinoma. Molecular Cancer. 2010. 9, 81. [PubMed]
297.Zhang, L., Zhang, Z. P., Zhang, X. E., Lin, F. S. and Ge, F.  Quantitative proteomics analysis reveals BAG3 as a potential target to suppress severe acute respiratory syndrome coronavirus replication. Journal of Virology. 2010. 84, 6050-6059. [PubMed]
298.Zhou, X., Han, P., Li, J., Zhang, X., Huang, B., Ruan, H. Q. and Chen, C.  ESNOQ, proteomic quantification of endogenous S-nitrosation. PloS One. 2010. 5, e10015. [PubMed]
299.Schmidt, F., Dahlmann, B., Hustoft, H. K., Koehler, C. J., Strozynski, M., Kloss, A., Zimny-Arndt, U., Jungblut, P. R. and Thiede, B.  Quantitative proteome analysis of the 20S proteasome of apoptotic Jurkat T cells. Amino Acids. 2011. 41, 351-361. [PubMed]
300.Geiger, T., Cox, J., Ostasiewicz, P., Wisniewski, J. R. and Mann, M.  Super-SILAC mix for quantitative proteomics of human tumor tissue. Nature Methods. 2010. 7, 383-385. [PubMed]
301.Christensen, G. L., Kelstrup, C. D., Lyngso, C., Sarwar, U., Bogebo, R., Sheikh, S. P., Gammeltoft, S., Olsen, J. V. and Hansen, J. L.  Quantitative phosphoproteomics dissection of seven-transmembrane receptor signaling using full and biased agonists. Molecular & Cellular Proteomics : MCP. 2010. 9, 1540-1553. [PubMed]
302.Shen, G., Liang, S., Xu, Z., Zhou, L., Xiao, S., Xia, X., Li, R., Liao, Y., You, C. and Wei, Y.  Downregulated expression of HSP27 in human low-grade glioma tissues discovered by a quantitative proteomic analysis. Proteome Science. 2010. 8, 17. [PubMed]
303.Duan, X., Kelsen, S. G., Clarkson, A. B., Ji, R. and Merali, S.  SILAC analysis of oxidative stress-mediated proteins in human pneumocytes: new role for treacle. Proteomics. 2010. 10, 2165-2174. [PubMed]
304.Liu, J., Shi, M., Hong, Z., Zhang, J., Bradner, J., Quinn, T., Beyer, R. P., Mcgeer, P. L., Chen, S. and Zhang, J.  Identification of ciliary neurotrophic factor receptor alpha as a mediator of neurotoxicity induced by alpha-synuclein. Proteomics. 2010. 10, 2138-2150. [PubMed]
305.Greco, T. M., Seeholzer, S. H., Mak, A., Spruce, L. and Ischiropoulos, H.  Quantitative mass spectrometry-based proteomics reveals the dynamic range of primary mouse astrocyte protein secretion. Journal of Proteome Research. 2010. 9, 2764-2774. [PubMed]
306.Skiba, M., Glowinski, F., Koczan, D., Mettenleiter, T. C. and Karger, A.  Gene expression profiling of Pseudorabies virus (PrV) infected bovine cells by combination of transcript analysis and quantitative proteomic techniques. Veterinary Microbiology. 2010. 143, 14-20. [PubMed]
307.Cunningham, D. L., Sweet, S. M., Cooper, H. J. and Heath, J. K.  Differential phosphoproteomics of fibroblast growth factor signaling: identification of Src family kinase-mediated phosphorylation events. Journal of Proteome Research. 2010. 9, 2317-2328. [PubMed]
308.Sharma, K., Kumar, C., Keri, G., Breitkopf, S. B., Oppermann, F. S. and Daub, H.  Quantitative analysis of kinase-proximal signaling in lipopolysaccharide-induced innate immune response. Journal of Proteome Research. 2010. 9, 2539-2549. [PubMed]
309.Hammond, D. E., Hyde, R., Kratchmarova, I., Beynon, R. J., Blagoev, B. and Clague, M. J.  Quantitative analysis of HGF and EGF-dependent phosphotyrosine signaling networks. Journal of Proteome Research. 2010. 9, 2734-2742. [PubMed]
310.An, E., Sen, S., Park, S. K., Gordish-Dressman, H. and Hathout, Y.  Identification of novel substrates for the serine protease HTRA1 in the human RPE secretome. Investigative Ophthalmology & Visual Science. 2010. 51, 3379-3386. [PubMed]
311.Collier, T. S., Sarkar, P., Rao, B. and Muddiman, D. C.  Quantitative top-down proteomics of SILAC labeled human embryonic stem cells. Journal of the American Society For Mass Spectrometry. 2010. 21, 879-889. [PubMed]
312.Jayapal, K. P., Sui, S., Philp, R. J., Kok, Y. J., Yap, M. G., Griffin, T. J. and Hu, W. S.  Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems. Journal of Proteome Research. 2010. 9, 2087-2097. [PubMed]
313.Imami, K., Sugiyama, N., Tomita, M. and Ishihama, Y.  Quantitative proteome and phosphoproteome analyses of cultured cells based on SILAC labeling without requirement of serum dialysis. Molecular BioSystems. 2010. 6, 594-602. [PubMed]
314.Agard, N. J., Maltby, D. and Wells, J. A.  Inflammatory stimuli regulate caspase substrate profiles. Molecular & Cellular Proteomics : MCP. 2010. 9, 880-893. [PubMed]
315.Kaake, R. M., Milenkovic, T., Przulj, N., Kaiser, P. and Huang, L.  Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy. Journal of Proteome Research. 2010. 9, 2016-2029. [PubMed]
316.Lee, J. H., Kim, B. G., Ahn, J. M., Park, H. J., Park, S. K., Yoo, J. S., Yates, J. R. and Cho, J. Y.  Role of PI3K on the regulation of BMP2-induced beta-Catenin activation in human bone marrow stem cells. Bone. 2010. 46, 1522-1532. [PubMed]
317.Du, R., Long, J., Yao, J., Dong, Y., Yang, X., Tang, S., Zuo, S., He, Y. and Chen, X.  Subcellular quantitative proteomics reveals multiple pathway cross-talk that coordinates specific signaling and transcriptional regulation for the early host response to LPS. Journal of Proteome Research. 2010. 9, 1805-1821. [PubMed]
318.Looso, M., Borchardt, T., Kruger, M. and Braun, T.  Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry. Molecular & Cellular Proteomics : MCP. 2010. 9, 1157-1166. [PubMed]
319.Rinschen, M. M., Yu, M. J., Wang, G., Boja, E. S., Hoffert, J. D., Pisitkun, T. and Knepper, M. A.  Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor-dependent signaling pathways in renal collecting duct cells. Proceedings of the National Academy of Sciences of the United States of America. 2010. 107, 3882-3887. [PubMed]
320.Polacek, M., Bruun, J. A., Johansen, O. and Martinez, I.  Differences in the secretome of cartilage explants and cultured chondrocytes unveiled by SILAC technology. Journal of Orthopaedic Research : Official Publication of the Orthopaedic Research Society. 2010. 28, 1040-1049. [PubMed]
321.Parker, S. J., Halligan, B. D. and Greene, A. S.  Quantitative analysis of SILAC data sets using spectral counting. Proteomics. 2010. 10, 1408-1415. [PubMed]
322.McGeer, E. G. and McGeer, P. L.  Neuroinflammation in Alzheimer's disease and mild cognitive impairment: a field in its infancy. Journal of Alzheimer's Disease : JAD. 2010. 19, 355-361. [PubMed]
323.Xiong, L. and Wang, Y.  Quantitative proteomic analysis reveals the perturbation of multiple cellular pathways in HL-60 cells induced by arsenite treatment. Journal of Proteome Research. 2010. 9, 1129-1137. [PubMed]
324.Zhou, Q., Chaerkady, R., Shaw, P. G., Kensler, T. W., Pandey, A. and Davidson, N. E.  Screening for therapeutic targets of vorinostat by SILAC-based proteomic analysis in human breast cancer cells. Proteomics. 2010. 10, 1029-1039. [PubMed]
325.Seyfried, N. T., Gozal, Y. M., Dammer, E. B., Xia, Q., Duong, D. M., Cheng, D., Lah, J. J., Levey, A. I. and Peng, J.  Multiplex SILAC analysis of a cellular TDP-43 proteinopathy model reveals protein inclusions associated with SUMOylation and diverse polyubiquitin chains. Molecular & Cellular Proteomics : MCP. 2010. 9, 705-718. [PubMed]
326.Deng, W., de, H., Yu, H. B., Li, Y., Croxen, M. A., Thomas, N. A., Puente, J. L., Foster, L. J. and Finlay, B. B.  A comprehensive proteomic analysis of the type III secretome of Citrobacter rodentium. The Journal of Biological Chemistry. 2010. 285, 6790-6800. [PubMed]
327.Pijnappel, W. P., Kolkman, A., Baltissen, M. P., Heck, A. and Timmers, H. M.  Quantitative mass spectrometry of TATA binding protein-containing complexes and subunit phosphorylations during the cell cycle. Proteome Science. 2009. 7, 46. [PubMed]
328.Li, M., Aliotta, J. M., Asara, J. M., Wu, Q., Dooner, M. S., Tucker, L. D., Wells, A., Quesenberry, P. J. and Ramratnam, B.  Intercellular transfer of proteins as identified by stable isotope labeling of amino acids in cell culture. The Journal of Biological Chemistry. 2010. 285, 6285-6297. [PubMed]
329.Boulon, S., Ahmad, Y., Trinkle-Mulcahy, L., Verheggen, C., Cobley, A., Gregor, P., Bertrand, E., Whitehorn, M. and Lamond, A. I.  Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners. Molecular & Cellular Proteomics : MCP. 2010. 9, 861-879. [PubMed]
330.Hsu, W. L. and Sung, T. Y.  Automated generic analysis tools for protein quantitation using stable isotope labeling. Methods in Molecular Biology. 2010. 604, 257-272. [PubMed]
331.Zee, B. M., Levin, R. S., Xu, B., LeRoy, G., Wingreen, N. S. and Garcia, B. A.  In vivo residue-specific histone methylation dynamics. The Journal of Biological Chemistry. 2010. 285, 3341-3350. [PubMed]
332.Zhang, L., Yu, C., Vasquez, F. E., Galeva, N., Onyango, I., Swerdlow, R. H. and Dobrowsky, R. T.  Hyperglycemia alters the schwann cell mitochondrial proteome and decreases coupled respiration in the absence of superoxide production. Journal of Proteome Research. 2010. 9, 458-471. [PubMed]
333.Emadali, A. and Gallagher-Gambarelli, M.  [Quantitative proteomics by SILAC: practicalities and perspectives for an evolving approach]. Medecine Sciences : M/S. 2009. 25, 835-842. [PubMed]
334.Wang, D. and Jang, D. J.  Protein kinase CK2 regulates cytoskeletal reorganization during ionizing radiation-induced senescence of human mesenchymal stem cells. Cancer Research. 2009. 69, 8200-8207. [PubMed]
335.Lam, Y. W., Evans, V. C., Heesom, K. J., Lamond, A. I. and Matthews, D. A.  Proteomics analysis of the nucleolus in adenovirus-infected cells. Molecular & Cellular Proteomics : MCP. 2010. 9, 117-130. [PubMed]
336.Kantardjieff, A., Jacob, N. M., Yee, J. C., Epstein, E., Kok, Y. J., Philp, R., Betenbaugh, M. and Hu, W. S.  Transcriptome and proteome analysis of Chinese hamster ovary cells under low temperature and butyrate treatment. Journal of Biotechnology. 2010. 145, 143-159. [PubMed]
337.Rangiah, K., Tippornwong, M., Sangar, V., Austin, D., Tetreault, M. P., Rustgi, A. K., Blair, I. A. and Yu, K. H.  Differential secreted proteome approach in murine model for candidate biomarker discovery in colon cancer. Journal of Proteome Research. 2009. 8, 5153-5164. [PubMed]
338.Pathak, S., De, S., Salte, T., Wiker, H. G. and Asjo, B.  HIV induces both a down-regulation of IRAK-4 that impairs TLR signalling and an up-regulation of the antibiotic peptide dermcidin in monocytic cells. Scandinavian Journal of Immunology. 2009. 70, 264-276. [PubMed]
339.Malik, R., Lenobel, R., Santamaria, A., Ries, A., Nigg, E. A. and Korner, R.  Quantitative analysis of the human spindle phosphoproteome at distinct mitotic stages. Journal of Proteome Research. 2009. 8, 4553-4563. [PubMed]
340.Kim, B. G., Lee, J. H., Ahn, J. M., Park, S. K., Cho, J. H., Hwang, D., Yoo, J. S., Yates, J. R., Ryoo, H. M. and Cho, J. Y.  'Two-stage double-technique hybrid (TSDTH)' identification strategy for the analysis of BMP2-induced transdifferentiation of premyoblast C2C12 cells to osteoblast. Journal of Proteome Research. 2009. 8, 4441-4454. [PubMed]
341.Pan, C., Olsen, J. V., Daub, H. and Mann, M.  Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics. Molecular & Cellular Proteomics : MCP. 2009. 8, 2796-2808. [PubMed]
342.Reeves, E. K., Gordish-Dressman, H., Hoffman, E. P. and Hathout, Y.  Proteomic profiling of glucocorticoid-exposed myogenic cells: Time series assessment of protein translocation and transcription of inactive mRNAs. Proteome Science. 2009. 7, 26. [PubMed]
343.Amanchy, R., Zhong, J., Hong, R., Kim, J. H., Gucek, M., Cole, R. N., Molina, H. and Pandey, A.  Identification of c-Src tyrosine kinase substrates in platelet-derived growth factor receptor signaling. Molecular Oncology. 2009. 3, 439-450. [PubMed]
344.Nguyen, V., Cao, L., Lin, J. T., Hung, N., Ritz, A., Yu, K., Jianu, R., Ulin, S. P., Raphael, B. J., Laidlaw, D. H., Brossay, L. and Salomon, A. R.  A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation. Molecular & Cellular Proteomics : MCP. 2009. 8, 2418-2431. [PubMed]
345.Kawase, H., Fujii, K., Miyamoto, M., Kubota, K. C., Hirano, S., Kondo, S. and Inagaki, F.  Differential LC-MS-based proteomics of surgical human cholangiocarcinoma tissues. Journal of Proteome Research. 2009. 8, 4092-4103. [PubMed]
346.Xu, P., Duong, D. M. and Peng, J.  Systematical optimization of reverse-phase chromatography for shotgun proteomics. Journal of Proteome Research. 2009. 8, 3944-3950. [PubMed]
347.Lohrberg, D., Krause, E., Schumann, M., Piontek, J., Winkler, L., Blasig, I. E. and Haseloff, R. F.  A strategy for enrichment of claudins based on their affinity to Clostridium perfringens enterotoxin. BMC Molecular Biology. 2009. 10, 61. [PubMed]
348.Schlundt, A., Sticht, J., Piotukh, K., Kosslick, D., Jahnke, N., Keller, S., Schuemann, M., Krause, E. and Freund, C.  Proline-rich sequence recognition: II. Proteomics analysis of Tsg101 ubiquitin-E2-like variant (UEV) interactions. Molecular & Cellular Proteomics : MCP. 2009. 8, 2474-2486. [PubMed]
349.Butter, F., Scheibe, M., Morl, M. and Mann, M.  Unbiased RNA-protein interaction screen by quantitative proteomics. Proceedings of the National Academy of Sciences of the United States of America. 2009. 106, 10626-10631. [PubMed]
350.Dreger, M., Leung, B. W., Brownlee, G. G. and Deng, T.  A quantitative strategy to detect changes in accessibility of protein regions to chemical modification on heterodimerization. Protein Science : A Publication of the Protein Society. 2009. 18, 1448-1458. [PubMed]
351.Hor, S., Ziv, T., Admon, A. and Lehner, P. J.  Stable isotope labeling by amino acids in cell culture and differential plasma membrane proteome quantitation identify new substrates for the MARCH9 transmembrane E3 ligase. Molecular & Cellular Proteomics : MCP. 2009. 8, 1959-1971. [PubMed]
352.Hilger, M., Bonaldi, T., Gnad, F. and Mann, M.  Systems-wide analysis of a phosphatase knock-down by quantitative proteomics and phosphoproteomics. Molecular & Cellular Proteomics : MCP. 2009. 8, 1908-1920. [PubMed]
353.Larive, R. M., Urbach, S., Poncet, J., Jouin, P., Mascre, G., Sahuquet, A., Mangeat, P. H., Coopman, P. J. and Bettache, N.  Phosphoproteomic analysis of Syk kinase signaling in human cancer cells reveals its role in cell-cell adhesion. Oncogene. 2009. 28, 2337-2347. [PubMed]
354.Gioia, M., Foster, L. J. and Overall, C. M.  Cell-based identification of natural substrates and cleavage sites for extracellular proteases by SILAC proteomics. Methods in Molecular Biology. 2009. 539, 131-153. [PubMed]
355.Oppermann, F. S., Gnad, F., Olsen, J. V., Hornberger, R., Greff, Z., Keri, G., Mann, M. and Daub, H.  Large-scale proteomics analysis of the human kinome. Molecular & Cellular Proteomics : MCP. 2009. 8, 1751-1764. [PubMed]
356.Lund, R., Leth-Larsen, R., Jensen, O. N. and Ditzel, H. J.  Efficient isolation and quantitative proteomic analysis of cancer cell plasma membrane proteins for identification of metastasis-associated cell surface markers. Journal of Proteome Research. 2009. 8, 3078-3090. [PubMed]
357.Aggelis, V., Craven, R. A., Peng, J., Harnden, P., Cairns, D. A., Maher, E. R., Tonge, R., Selby, P. J. and Banks, R. E.  Proteomic identification of differentially expressed plasma membrane proteins in renal cell carcinoma by stable isotope labelling of a von Hippel-Lindau transfectant cell line model. Proteomics. 2009. 9, 2118-2130. [PubMed]
358.Shah, S. J., Yu, K. H., Sangar, V., Parry, S. I. and Blair, I. A.  Identification and quantification of preterm birth biomarkers in human cervicovaginal fluid by liquid chromatography/tandem mass spectrometry. Journal of Proteome Research. 2009. 8, 2407-2417. [PubMed]
359.Chao, J. T., Foster, L. J. and Loewen, C. J.  Identification of protein complexes with quantitative proteomics in S. cerevisiae. Journal of Visualized Experiments : JoVE. 2009. [PubMed]
360.Ong, S. E., Schenone, M., Margolin, A. A., Li, X., Do, K., Doud, M. K., Mani, D. R., Kuai, L., Wang, X., Wood, J. L., Tolliday, N. J., Koehler, A. N., Marcaurelle, L. A., Golub, T. R., Gould, R. J., Schreiber, S. L. and Carr, S. A.  Identifying the proteins to which small-molecule probes and drugs bind in cells. Proceedings of the National Academy of Sciences of the United States of America. 2009. 106, 4617-4622. [PubMed]
361.Cui, Z., Chen, X., Lu, B., Park, S. K., Xu, T., Xie, Z., Xue, P., Hou, J., Hang, H., Yates, J. R. and Yang, F.  Preliminary quantitative profile of differential protein expression between rat L6 myoblasts and myotubes by stable isotope labeling with amino acids in cell culture. Proteomics. 2009. 9, 1274-1292. [PubMed]
362.Xu, Y., Liang, S., Shen, G., Xu, X., Liu, Q., Xu, Z., Gong, F., Tang, M. and Wei, Y.  Application of the SILAC (stable isotope labelling with amino acids in cell culture) technique in quantitative comparisons for tissue proteome expression. Biotechnology and Applied Biochemistry. 2009. 54, 11-20. [PubMed]
363.Ruiz, L., Coute, Y., Sanchez, B., de, l. o. s., Sanchez, J. C. and Margolles, A.  The cell-envelope proteome of Bifidobacterium longum in an in vitro bile environment. Microbiology. 2009. 155, 957-967. [PubMed]
364.Zhou, J., Liang, S., Fang, L., Chen, L., Tang, M., Xu, Y., Fu, A., Yang, J. and Wei, Y.  Quantitative proteomic analysis of HepG2 cells treated with quercetin suggests IQGAP1 involved in quercetin-induced regulation of cell proliferation and migration. Omics : A Journal of Integrative Biology. 2009. 13, 93-103. [PubMed]
365.Yu, K. H., Barry, C. G., Austin, D., Busch, C. M., Sangar, V., Rustgi, A. K. and Blair, I. A.  Stable isotope dilution multidimensional liquid chromatography-tandem mass spectrometry for pancreatic cancer serum biomarker discovery. Journal of Proteome Research. 2009. 8, 1565-1576. [PubMed]
366.Platt, M. D., Salicioni, A. M., Hunt, D. F. and Visconti, P. E.  Use of differential isotopic labeling and mass spectrometry to analyze capacitation-associated changes in the phosphorylation status of mouse sperm proteins. Journal of Proteome Research. 2009. 8, 1431-1440. [PubMed]
367.Prokhorova, T. A., Rigbolt, K. T., Johansen, P. T., Henningsen, J., Kratchmarova, I., Kassem, M. and Blagoev, B.  Stable isotope labeling by amino acids in cell culture (SILAC) and quantitative comparison of the membrane proteomes of self-renewing and differentiating human embryonic stem cells. Molecular & Cellular Proteomics : MCP. 2009. 8, 959-970. [PubMed]
368.Zhang, G., Fenyo, D. and Neubert, T. A.  Evaluation of the variation in sample preparation for comparative proteomics using stable isotope labeling by amino acids in cell culture. Journal of Proteome Research. 2009. 8, 1285-1292. [PubMed]
369.Zheng, Y. Z., Berg, K. B. and Foster, L. J.  Mitochondria do not contain lipid rafts, and lipid rafts do not contain mitochondrial proteins. Journal of Lipid Research. 2009. 50, 988-998. [PubMed]
370.Andersen, J. S., Matic, I. and Vertegaal, A. C.  Identification of SUMO target proteins by quantitative proteomics. Methods in Molecular Biology. 2009. 497, 19-31. [PubMed]
371.An, E., Gordish-Dressman, H. and Hathout, Y.  Effect of TNF-alpha on human ARPE-19-secreted proteins. Molecular Vision. 2008. 14, 2292-2303. [PubMed]
372.Shui, W., Gilmore, S. A., Sheu, L., Liu, J., Keasling, J. D. and Bertozzi, C. R.  Quantitative proteomic profiling of host-pathogen interactions: the macrophage response to Mycobacterium tuberculosis lipids. Journal of Proteome Research. 2009. 8, 282-289. [PubMed]
373.Cox, J. and Mann, M.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature Biotechnology. 2008. 26, 1367-1372. [PubMed]
374.Chen, N., Sun, W., Deng, X., Hao, Y., Chen, X., Xing, B., Jia, W., Ma, J., Wei, H., Zhu, Y., Qian, X., Jiang, Y. and He, F.  Quantitative proteome analysis of HCC cell lines with different metastatic potentials by SILAC. Proteomics. 2008. 8, 5108-5118. [PubMed]
375.Mittler, G., Butter, F. and Mann, M.  A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genome Research. 2009. 19, 284-293. [PubMed]
376.van, M., Lenferink, A. and Otto, C.  Noninvasive imaging of protein metabolic labeling in single human cells using stable isotopes and Raman microscopy. Analytical Chemistry. 2008. 80, 9576-9582. [PubMed]
377.Hanke, S. and Mann, M.  The phosphotyrosine interactome of the insulin receptor family and its substrates IRS-1 and IRS-2. Molecular & Cellular Proteomics : MCP. 2009. 8, 519-534. [PubMed]
378.Esselens, C. W., Malapeira, J., Colome, N., Moss, M., Canals, F. and Arribas, J.  Metastasis-associated C4.4A, a GPI-anchored protein cleaved by ADAM10 and ADAM17. Biological Chemistry. 2008. 389, 1075-1084. [PubMed]
379.Doherty, M. K., Hammond, D. E., Clague, M. J., Gaskell, S. J. and Beynon, R. J.  Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC. Journal of Proteome Research. 2009. 8, 104-112. [PubMed]
380.Pan, C., Kumar, C., Bohl, S., Klingmueller, U. and Mann, M.  Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type-specific functions. Molecular & Cellular Proteomics : MCP. 2009. 8, 443-450. [PubMed]
381.Molina, H., Yang, Y., Ruch, T., Kim, J. W., Mortensen, P., Otto, T., Nalli, A., Tang, Q. Q., Lane, M. D., Chaerkady, R. and Pandey, A.  Temporal profiling of the adipocyte proteome during differentiation using a five-plex SILAC based strategy. Journal of Proteome Research. 2009. 8, 48-58. [PubMed]
382.Trinkle-Mulcahy, L., Boulon, S., Lam, Y. W., Urcia, R., Boisvert, F. M., Vandermoere, F., Morrice, N. A., Swift, S., Rothbauer, U., Leonhardt, H. and Lamond, A.  Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. The Journal of Cell Biology. 2008. 183, 223-239. [PubMed]
383.Cockman, M. E., Webb, J. D., Kramer, H. B., Kessler, B. M. and Ratcliffe, P. J.  Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins. Molecular & Cellular Proteomics : MCP. 2009. 8, 535-546. [PubMed]
384.Fang, L., Wang, X., Yamoah, K., Chen, P. L., Pan, Z. Q. and Huang, L.  Characterization of the human COP9 signalosome complex using affinity purification and mass spectrometry. Journal of Proteome Research. 2008. 7, 4914-4925. [PubMed]
385.Pan, C., Gnad, F., Olsen, J. V. and Mann, M.  Quantitative phosphoproteome analysis of a mouse liver cell line reveals specificity of phosphatase inhibitors. Proteomics. 2008. 8, 4534-4546. [PubMed]
386.Hittel, D. S., Berggren, J. R., Shearer, J., Boyle, K. and Houmard, J. A.  Increased secretion and expression of myostatin in skeletal muscle from extremely obese women. Diabetes. 2009. 58, 30-38. [PubMed]
387.Liao, L., Park, S. K., Xu, T., Vanderklish, P. and Yates, J. R.  Quantitative proteomic analysis of primary neurons reveals diverse changes in synaptic protein content in fmr1 knockout mice. Proceedings of the National Academy of Sciences of the United States of America. 2008. 105, 15281-15286. [PubMed]
388.Harsha, H. C., Jimeno, A., Molina, H., Mihalas, A. B., Goggins, M. G., Hruban, R. H., Schulick, R. D., Kamath, U., Maitra, A., Hidalgo, M. and Pandey, A.  Activated epidermal growth factor receptor as a novel target in pancreatic cancer therapy. Journal of Proteome Research. 2008. 7, 4651-4658. [PubMed]
389.de, G., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Frohlich, F., Walther, T. C. and Mann, M.  Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature. 2008. 455, 1251-1254. [PubMed]
390.Nagashima, T., Oyama, M., Kozuka-Hata, H., Yumoto, N., Sakaki, Y. and Hatakeyama, M.  Phosphoproteome and transcriptome analyses of ErbB ligand-stimulated MCF-7 cells. Cancer Genomics & Proteomics. 2008. 5, 161-168. [PubMed]
391.Zhang, G., Fenyo, D. and Neubert, T. A.  Screening for EphB signaling effectors using SILAC with a linear ion trap-orbitrap mass spectrometer. Journal of Proteome Research. 2008. 7, 4715-4726. [PubMed]
392.Dhungana, S., Merrick, B. A., Tomer, K. B. and Fessler, M. B.  Quantitative proteomics analysis of macrophage rafts reveals compartmentalized activation of the proteasome and of proteasome-mediated ERK activation in response to lipopolysaccharide. Molecular & Cellular Proteomics : MCP. 2009. 8, 201-213. [PubMed]
393.Meierhofer, D., Wang, X., Huang, L. and Kaiser, P.  Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. Journal of Proteome Research. 2008. 7, 4566-4576. [PubMed]
394.Dengjel, J., Kristensen, A. R. and Andersen, J. S.  Ordered bulk degradation via autophagy. Autophagy. 2008. 4, 1057-1059. [PubMed]
395.Guha, U., Chaerkady, R., Marimuthu, A., Patterson, A. S., Kashyap, M. K., Harsha, H. C., Sato, M., Bader, J. S., Lash, A. E., Minna, J. D., Pandey, A. and Varmus, H. E.  Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proceedings of the National Academy of Sciences of the United States of America. 2008. 105, 14112-14117. [PubMed]
396.Bonaldi, T., Straub, T., Cox, J., Kumar, C., Becker, P. B. and Mann, M.  Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. Molecular Cell. 2008. 31, 762-772. [PubMed]
397.Ota, K., Kito, K., Okada, S. and Ito, T.  A proteomic screen reveals the mitochondrial outer membrane protein Mdm34p as an essential target of the F-box protein Mdm30p. Genes To Cells : Devoted To Molecular & Cellular Mechanisms. 2008. 13, 1075-1085. [PubMed]
398.Amanchy, R., Zhong, J., Molina, H., Chaerkady, R., Iwahori, A., Kalume, D. E., Gronborg, M., Joore, J., Cope, L. and Pandey, A.  Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. Journal of Proteome Research. 2008. 7, 3900-3910. [PubMed]
399.Park, K. S., Mohapatra, D. P. and Trimmer, J. S.  Proteomic analyses of K(v)2.1 channel phosphorylation sites determining cell background specific differences in function. Channels. 2007. 1, 59-61. [PubMed]
400.Song, H., Kong, W., Weatherspoon, N., Qin, G., Tyler, W., Turk, J., Curtiss, R. and Shi, Y.  Modulation of the regulatory activity of bacterial two-component systems by SlyA. The Journal of Biological Chemistry. 2008. 283, 28158-28168. [PubMed]
401.Dephoure, N., Zhou, C., Villen, J., Beausoleil, S. A., Bakalarski, C. E., Elledge, S. J. and Gygi, S. P.  A quantitative atlas of mitotic phosphorylation. Proceedings of the National Academy of Sciences of the United States of America. 2008. 105, 10762-10767. [PubMed]
402.Selbach, M., Schwanhausser, B., Thierfelder, N., Fang, Z., Khanin, R. and Rajewsky, N.  Widespread changes in protein synthesis induced by microRNAs. Nature. 2008. 455, 58-63. [PubMed]
403.Baek, D., Villen, J., Shin, C., Camargo, F. D., Gygi, S. P. and Bartel, D. P.  The impact of microRNAs on protein output. Nature. 2008. 455, 64-71. [PubMed]
404.Kruger, M., Moser, M., Ussar, S., Thievessen, I., Luber, C. A., Forner, F., Schmidt, S., Zanivan, S., Fassler, R. and Mann, M.  SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell. 2008. 134, 353-364. [PubMed]
405.Gu, S., Wang, T. and Chen, X.  Quantitative proteomic analysis of LPS-induced differential immune response associated with TLR4 Polymorphisms by multiplex amino acid coded mass tagging. Proteomics. 2008. 8, 3061-3070. [PubMed]
406.Skiba, M., Mettenleiter, T. C. and Karger, A.  Quantitative whole-cell proteome analysis of pseudorabies virus-infected cells. Journal of Virology. 2008. 82, 9689-9699. [PubMed]
407.Sun, Y., Mi, W., Cai, J., Ying, W., Liu, F., Lu, H., Qiao, Y., Jia, W., Bi, X., Lu, N., Liu, S., Qian, X. and Zhao, X.  Quantitative proteomic signature of liver cancer cells: tissue transglutaminase 2 could be a novel protein candidate of human hepatocellular carcinoma. Journal of Proteome Research. 2008. 7, 3847-3859. [PubMed]
408.Xue, Y., Yun, D., Esmon, A., Zou, P., Zuo, S., Yu, Y., He, F., Yang, P. and Chen, X.  Proteomic dissection of agonist-specific TLR-mediated inflammatory responses on macrophages at subcellular resolution. Journal of Proteome Research. 2008. 7, 3180-3193. [PubMed]
409.Luo, W., Slebos, R. J., Hill, S., Li, M., Brabek, J., Amanchy, R., Chaerkady, R., Pandey, A., Ham, A. J. and Hanks, S. K.  Global impact of oncogenic Src on a phosphotyrosine proteome. Journal of Proteome Research. 2008. 7, 3447-3460. [PubMed]
410.Rogers, L. D., Kristensen, A. R., Boyle, E. C., Robinson, D. P., Ly, R. T., Finlay, B. B. and Foster, L. J.  Identification of cognate host targets and specific ubiquitylation sites on the Salmonella SPI-1 effector SopB/SigD. Journal of Proteomics. 2008. 71, 97-108. [PubMed]
411.Georgianna, D. R., Hawkridge, A. M., Muddiman, D. C. and Payne, G. A.  Temperature-dependent regulation of proteins in Aspergillus flavus: whole organism stable isotope labeling by amino acids. Journal of Proteome Research. 2008. 7, 2973-2979. [PubMed]
412.Collier, T. S., Hawkridge, A. M., Georgianna, D. R., Payne, G. A. and Muddiman, D. C.  Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer. Analytical Chemistry. 2008. 80, 4994-5001. [PubMed]
413.Wisniewski, J. R., Zougman, A., Kruger, S., Ziolkowski, P., Pudelko, M., Bebenek, M. and Mann, M.  Constitutive and dynamic phosphorylation and acetylation sites on NUCKS, a hypermodified nuclear protein, studied by quantitative proteomics. Proteins. 2008. 73, 710-718. [PubMed]
414.Dreisbach, A., Otto, A., Becher, D., Hammer, E., Teumer, A., Gouw, J. W., Hecker, M. and Volker, U.  Monitoring of changes in the membrane proteome during stationary phase adaptation of Bacillus subtilis using in vivo labeling techniques. Proteomics. 2008. 8, 2062-2076. [PubMed]
415.Bendall, S. C., Hughes, C., Stewart, M. H., Doble, B., Bhatia, M. and Lajoie, G. A.  Prevention of amino acid conversion in SILAC experiments with embryonic stem cells. Molecular & Cellular Proteomics : MCP. 2008. 7, 1587-1597. [PubMed]
416.Mintz, M., Vanderver, A., Brown, K. J., Lin, J., Wang, Z., Kaneski, C., Schiffmann, R., Nagaraju, K., Hoffman, E. P. and Hathout, Y.  Time series proteome profiling to study endoplasmic reticulum stress response. Journal of Proteome Research. 2008. 7, 2435-2444. [PubMed]
417.Qiu, H. and Wang, Y.  Quantitative analysis of surface plasma membrane proteins of primary and metastatic melanoma cells. Journal of Proteome Research. 2008. 7, 1904-1915. [PubMed]
418.Liu, J., Hong, Z., Ding, J., Liu, J., Zhang, J. and Chen, S.  Predominant release of lysosomal enzymes by newborn rat microglia after LPS treatment revealed by proteomic studies. Journal of Proteome Research. 2008. 7, 2033-2049. [PubMed]
419.Dobreva, I., Fielding, A., Foster, L. J. and Dedhar, S.  Mapping the integrin-linked kinase interactome using SILAC. Journal of Proteome Research. 2008. 7, 1740-1749. [PubMed]
420.Klegeris, A., Li, J., Bammler, T. K., Jin, J., Zhu, D., Kashima, D. T., Pan, S., Hashioka, S., Maguire, J., McGeer, P. L. and Zhang, J.  Prolyl endopeptidase is revealed following SILAC analysis to be a novel mediator of human microglial and THP-1 cell neurotoxicity. Glia. 2008. 56, 675-685. [PubMed]
421.Hanke, S., Besir, H., Oesterhelt, D. and Mann, M.  Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level. Journal of Proteome Research. 2008. 7, 1118-1130. [PubMed]
422.Kruger, M., Kratchmarova, I., Blagoev, B., Tseng, Y. H., Kahn, C. R. and Mann, M.  Dissection of the insulin signaling pathway via quantitative phosphoproteomics. Proceedings of the National Academy of Sciences of the United States of America. 2008. 105, 2451-2456. [PubMed]
423.Spellman, D. S., Deinhardt, K., Darie, C. C., Chao, M. V. and Neubert, T. A.  Stable isotopic labeling by amino acids in cultured primary neurons: application to brain-derived neurotrophic factor-dependent phosphotyrosine-associated signaling. Molecular & Cellular Proteomics : MCP. 2008. 7, 1067-1076. [PubMed]
424.Zhang, G., Fenyo, D. and Neubert, T. A.  Use of DNA ladders for reproducible protein fractionation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for quantitative proteomics. Journal of Proteome Research. 2008. 7, 678-686. [PubMed]
425.Guo, A., Villen, J., Kornhauser, J., Lee, K. A., Stokes, M. P., Rikova, K., Possemato, A., Nardone, J., Innocenti, G., Wetzel, R., Wang, Y., MacNeill, J., Mitchell, J., Gygi, S. P., Rush, J., Polakiewicz, R. D. and Comb, M. J.  Signaling networks assembled by oncogenic EGFR and c-Met. Proceedings of the National Academy of Sciences of the United States of America. 2008. 105, 692-697. [PubMed]
426.Colzani, M., Schutz, F., Potts, A., Waridel, P. and Quadroni, M.  Relative protein quantification by isobaric SILAC with immonium ion splitting (ISIS). Molecular & Cellular Proteomics : MCP. 2008. 7, 927-937. [PubMed]
427.Ling, B., Liang, S. F., Xu, Y. H., Zhao, X. Y., Tang, M. H., Liu, X. Y., Zhao, X., Huang, C. H., Chen, L. J. and Wei, Y. Q.  Differential proteomic analysis of HeLa cells treated with Honokiol using a quantitative proteomic strategy. Amino Acids. 2008. 35, 115-122. [PubMed]
428.Mousson, F., Kolkman, A., Pijnappel, W. W., Timmers, H. T. and Heck, A. J.  Quantitative proteomics reveals regulation of dynamic components within TATA-binding protein (TBP) transcription complexes. Molecular & Cellular Proteomics : MCP. 2008. 7, 845-852. [PubMed]
429.Stokes, M. P., Rush, J., Macneill, J., Ren, J. M., Sprott, K., Nardone, J., Yang, V., Beausoleil, S. A., Gygi, S. P., Livingstone, M., Zhang, H., Polakiewicz, R. D. and Comb, M. J.  Profiling of UV-induced ATM/ATR signaling pathways. Proceedings of the National Academy of Sciences of the United States of America. 2007. 104, 19855-19860. [PubMed]
430.Graumann, J., Hubner, N. C., Kim, J. B., Ko, K., Moser, M., Kumar, C., Cox, J., Scholer, H. and Mann, M.  Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins. Molecular & Cellular Proteomics : MCP. 2008. 7, 672-683. [PubMed]
431.Schmidt, F., Hustoft, H. K., Strozynski, M., Dimmler, C., Rudel, T. and Thiede, B.  Quantitative proteome analysis of cisplatin-induced apoptotic Jurkat T cells by stable isotope labeling with amino acids in cell culture, SDS-PAGE, and LC-MALDI-TOF/TOF MS. Electrophoresis. 2007. 28, 4359-4368. [PubMed]
432.Schmidt, F., Strozynski, M., Salus, S. S., Nilsen, H. and Thiede, B.  Rapid determination of amino acid incorporation by stable isotope labeling with amino acids in cell culture (SILAC). Rapid Communications in Mass Spectrometry : RCM. 2007. 21, 3919-3926. [PubMed]
433.Wang, X. and Huang, L.  Identifying dynamic interactors of protein complexes by quantitative mass spectrometry. Molecular & Cellular Proteomics : MCP. 2008. 7, 46-57. [PubMed]
434.Waanders, L. F., Hanke, S. and Mann, M.  Top-down quantitation and characterization of SILAC-labeled proteins. Journal of the American Society For Mass Spectrometry. 2007. 18, 2058-2064. [PubMed]
435.Vermeulen, M., Mulder, K. W., Denissov, S., Pijnappel, W. W., van, S., Varier, R. A., Baltissen, M. P., Stunnenberg, H. G., Mann, M. and Timmers, H. T.  Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell. 2007. 131, 58-69. [PubMed]
436.Soufi, B., Jers, C., Hansen, M. E., Petranovic, D. and Mijakovic, I.  Insights from site-specific phosphoproteomics in bacteria. Biochimica et Biophysica Acta. 2008. 1784, 186-192. [PubMed]
437.Liang, X., Fonnum, G., Hajivandi, M., Stene, T., Kjus, N. H., Ragnhildstveit, E., Amshey, J. W., Predki, P. and Pope, R. M.  Quantitative comparison of IMAC and TiO2 surfaces used in the study of regulated, dynamic protein phosphorylation. Journal of the American Society For Mass Spectrometry. 2007. 18, 1932-1944. [PubMed]
438.Van, H., Pinkse, M. W., Oostwaard, D. W., Mummery, C. L., Heck, A. J. and Krijgsveld, J.  An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomics. Nature Methods. 2007. 4, 677-678. [PubMed]
439.Jin, J., Davis, J., Zhu, D., Kashima, D. T., Leroueil, M., Pan, C., Montine, K. S. and Zhang, J.  Identification of novel proteins affected by rotenone in mitochondria of dopaminergic cells. BMC Neuroscience. 2007. 8, 67. [PubMed]
440.Liu, J., Zhou, Y., Wang, Y., Fong, H., Murray, T. M. and Zhang, J.  Identification of proteins involved in microglial endocytosis of alpha-synuclein. Journal of Proteome Research. 2007. 6, 3614-3627. [PubMed]
441.Bonenfant, D., Towbin, H., Coulot, M., Schindler, P., Mueller, D. R. and van, O.  Analysis of dynamic changes in post-translational modifications of human histones during cell cycle by mass spectrometry. Molecular & Cellular Proteomics : MCP. 2007. 6, 1917-1932. [PubMed]
442.Pinto, A. F., Ma, L., Dragulev, B., Guimaraes, J. A. and Fox, J. W.  Use of SILAC for exploring sheddase and matrix degradation of fibroblasts in culture by the PIII SVMP atrolysin A: identification of two novel substrates with functional relevance. Archives of Biochemistry and Biophysics. 2007. 465, 11-15. [PubMed]
443.Bouyssie, D., Gonzalez, d. e., Mouton, E., Albigot, R., Roussel, L., Ortega, N., Cayrol, C., Burlet-Schiltz, O., Girard, J. P. and Monsarrat, B.  Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endothelial cells. Molecular & Cellular Proteomics : MCP. 2007. 6, 1621-1637. [PubMed]
444.Wang, Z., Pandey, A. and Hart, G. W.  Dynamic interplay between O-linked N-acetylglucosaminylation and glycogen synthase kinase-3-dependent phosphorylation. Molecular & Cellular Proteomics : MCP. 2007. 6, 1365-1379. [PubMed]
445.Guerrera, I. C., Keep, N. H. and Godovac-Zimmermann, J.  Proteomics study reveals cross-talk between Rho guanidine nucleotide dissociation inhibitor 1 post-translational modifications in epidermal growth factor stimulated fibroblasts. Journal of Proteome Research. 2007. 6, 2623-2630. [PubMed]
446.Uitto, P. M., Lance, B. K., Wood, G. R., Sherman, J., Baker, M. S. and Molloy, M. P.  Comparing SILAC and two-dimensional gel electrophoresis image analysis for profiling urokinase plasminogen activator signaling in ovarian cancer cells. Journal of Proteome Research. 2007. 6, 2105-2112. [PubMed]
447.Thorsell, A., Portelius, E., Blennow, K. and Westman-Brinkmalm, A.  Evaluation of sample fractionation using micro-scale liquid-phase isoelectric focusing on mass spectrometric identification and quantitation of proteins in a SILAC experiment. Rapid Communications in Mass Spectrometry : RCM. 2007. 21, 771-778. [PubMed]
448.Saito, A., Nagasaki, M., Oyama, M., Kozuka-Hata, H., Semba, K., Sugano, S., Yamamoto, T. and Miyano, S.  AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. BMC Bioinformatics. 2007. 8, 15. [PubMed]
449.Comuzzi, B. and Sadar, M. D.  Proteomic analyses to identify novel therapeutic targets for the treatment of advanced prostate cancer. Cellscience. 2006. 3, 61-81. [PubMed]
450.Schilling, O. and Overall, C. M.  Proteomic discovery of protease substrates. Current Opinion in Chemical Biology. 2007. 11, 36-45. [PubMed]
451.Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P. and Mann, M.  Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell. 2006. 127, 635-648. [PubMed]
452.Yocum, A. K., Busch, C. M., Felix, C. A. and Blair, I. A.  Proteomics-based strategy to identify biomarkers and pharmacological targets in leukemias with t(4;11) translocations. Journal of Proteome Research. 2006. 5, 2743-2753. [PubMed]
453.Liang, X., Zhao, J., Hajivandi, M., Wu, R., Tao, J., Amshey, J. W. and Pope, R. M.  Quantification of membrane and membrane-bound proteins in normal and malignant breast cancer cells isolated from the same patient with primary breast carcinoma. Journal of Proteome Research. 2006. 5, 2632-2641. [PubMed]
454.An, E., Lu, X., Flippin, J., Devaney, J. M., Halligan, B., Hoffman, E. P., Strunnikova, N., Csaky, K. and Hathout, Y.  Secreted proteome profiling in human RPE cell cultures derived from donors with age related macular degeneration and age matched healthy donors. Journal of Proteome Research. 2006. 5, 2599-2610. [PubMed]
455.Vinther, J., Hedegaard, M. M., Gardner, P. P., Andersen, J. S. and Arctander, P.  Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Research. 2006. 34, e107. [PubMed]
456.Mannova, P., Fang, R., Wang, H., Deng, B., McIntosh, M. W., Hanash, S. M. and Beretta, L.  Modification of host lipid raft proteome upon hepatitis C virus replication. Molecular & Cellular Proteomics : MCP. 2006. 5, 2319-2325. [PubMed]
457.Park, K. S., Mohapatra, D. P., Misonou, H. and Trimmer, J. S.  Graded regulation of the Kv2.1 potassium channel by variable phosphorylation. Science. 2006. 313, 976-979. [PubMed]
458.Liang, X., Hajivandi, M., Veach, D., Wisniewski, D., Clarkson, B., Resh, M. D. and Pope, R. M.  Quantification of change in phosphorylation of BCR-ABL kinase and its substrates in response to Imatinib treatment in human chronic myelogenous leukemia cells. Proteomics. 2006. 6, 4554-4564. [PubMed]
459.Jin, J., Li, G. J., Davis, J., Zhu, D., Wang, Y., Pan, C. and Zhang, J.  Identification of novel proteins associated with both alpha-synuclein and DJ-1. Molecular & Cellular Proteomics : MCP. 2007. 6, 845-859. [PubMed]
460.Bose, R., Molina, H., Patterson, A. S., Bitok, J. K., Periaswamy, B., Bader, J. S., Pandey, A. and Cole, P. A.  Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proceedings of the National Academy of Sciences of the United States of America. 2006. 103, 9773-9778. [PubMed]
461.de, G., Olsen, J. V., de, S., Li, G., Mortensen, P. and Mann, M.  Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biology. 2006. 7, R50. [PubMed]
462.Everley, P. A., Bakalarski, C. E., Elias, J. E., Waghorne, C. G., Beausoleil, S. A., Gerber, S. A., Faherty, B. K., Zetter, B. R. and Gygi, S. P.  Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation. Journal of Proteome Research. 2006. 5, 1224-1231. [PubMed]
463.Neher, S. B., Villen, J., Oakes, E. C., Bakalarski, C. E., Sauer, R. T., Gygi, S. P. and Baker, T. A.  Proteomic profiling of ClpXP substrates after DNA damage reveals extensive instability within SOS regulon. Molecular Cell. 2006. 22, 193-204. [PubMed]
464.Hwang, S. I., Lundgren, D. H., Mayya, V., Rezaul, K., Cowan, A. E., Eng, J. K. and Han, D. K.  Systematic characterization of nuclear proteome during apoptosis: a quantitative proteomic study by differential extraction and stable isotope labeling. Molecular & Cellular Proteomics : MCP. 2006. 5, 1131-1145. [PubMed]
465.Qiao, Y., Molina, H., Pandey, A., Zhang, J. and Cole, P. A.  Chemical rescue of a mutant enzyme in living cells. Science. 2006. 311, 1293-1297. [PubMed]
466.Zhang, G., Spellman, D. S., Skolnik, E. Y. and Neubert, T. A.  Quantitative phosphotyrosine proteomics of EphB2 signaling by stable isotope labeling with amino acids in cell culture (SILAC). Journal of Proteome Research. 2006. 5, 581-588. [PubMed]
467.McLaughlin, P., Zhou, Y., Ma, T., Liu, J., Zhang, W., Hong, J. S., Kovacs, M. and Zhang, J.  Proteomic analysis of microglial contribution to mouse strain-dependent dopaminergic neurotoxicity. Glia. 2006. 53, 567-582. [PubMed]
468.Cantin, G. T., Venable, J. D., Cociorva, D. and Yates, J. R.  Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway. Journal of Proteome Research. 2006. 5, 127-134. [PubMed]
469.Foster, L. J., Rudich, A., Talior, I., Patel, N., Huang, X., Furtado, L. M., Bilan, P. J., Mann, M. and Klip, A.  Insulin-dependent interactions of proteins with GLUT4 revealed through stable isotope labeling by amino acids in cell culture (SILAC). Journal of Proteome Research. 2006. 5, 64-75. [PubMed]
470.Thiede, B., Kretschmer, A. and Rudel, T.  Quantitative proteome analysis of CD95 (Fas/Apo-1)-induced apoptosis by stable isotope labeling with amino acids in cell culture, 2-DE and MALDI-MS. Proteomics. 2006. 6, 614-622. [PubMed]
471.Yan, Y., Weaver, V. M. and Blair, I. A.  Analysis of protein expression during oxidative stress in breast epithelial cells using a stable isotope labeled proteome internal standard. Journal of Proteome Research. 2005. 4, 2007-2014. [PubMed]
472.Guerrero, C., Tagwerker, C., Kaiser, P. and Huang, L.  An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Molecular & Cellular Proteomics : MCP. 2006. 5, 366-378. [PubMed]
473.Gronborg, M., Kristiansen, T. Z., Iwahori, A., Chang, R., Reddy, R., Sato, N., Molina, H., Jensen, O. N., Hruban, R. H., Goggins, M. G., Maitra, A. and Pandey, A.  Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Molecular & Cellular Proteomics : MCP. 2006. 5, 157-171. [PubMed]
474.Amanchy, R., Kalume, D. E., Iwahori, A., Zhong, J. and Pandey, A.  Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC). Journal of Proteome Research. 2005. 4, 1661-1671. [PubMed]
475.Gruhler, A., Schulze, W. X., Matthiesen, R., Mann, M. and Jensen, O. N.  Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry. Molecular & Cellular Proteomics : MCP. 2005. 4, 1697-1709. [PubMed]
476.Zhou, Y., Wang, Y., Kovacs, M., Jin, J. and Zhang, J.  Microglial activation induced by neurodegeneration: a proteomic analysis. Molecular & Cellular Proteomics : MCP. 2005. 4, 1471-1479. [PubMed]
477.Romijn, E. P., Christis, C., Wieffer, M., Gouw, J. W., Fullaondo, A., van, d. e. r., Braakman, I. and Heck, A. J.  Expression clustering reveals detailed co-expression patterns of functionally related proteins during B cell differentiation: a proteomic study using a combination of one-dimensional gel electrophoresis, LC-MS/MS, and stable isotope labeling by amino acids in cell culture (SILAC). Molecular & Cellular Proteomics : MCP. 2005. 4, 1297-1310. [PubMed]
478.Molina, H., Parmigiani, G. and Pandey, A.  Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry. Analytical Chemistry. 2005. 77, 2739-2744. [PubMed]
479.Trester-Zedlitz, M., Burlingame, A., Kobilka, B. and von, Z.  Mass spectrometric analysis of agonist effects on posttranslational modifications of the beta-2 adrenoceptor in mammalian cells. Biochemistry. 2005. 44, 6133-6143. [PubMed]
480.Loyet, K. M., Ouyang, W., Eaton, D. L. and Stults, J. T.  Proteomic profiling of surface proteins on Th1 and Th2 cells. Journal of Proteome Research. 2005. 4, 400-409. [PubMed]
481.Gruhler, A., Olsen, J. V., Mohammed, S., Mortensen, P., Faergeman, N. J., Mann, M. and Jensen, O. N.  Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Molecular & Cellular Proteomics : MCP. 2005. 4, 310-327. [PubMed]
482.Andersen, J. S., Lam, Y. W., Leung, A. K., Ong, S. E., Lyon, C. E., Lamond, A. I. and Mann, M.  Nucleolar proteome dynamics. Nature. 2005. 433, 77-83. [PubMed]
483.Wu, C. C., MacCoss, M. J., Howell, K. E., Matthews, D. E. and Yates, J. R.  Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Analytical Chemistry. 2004. 76, 4951-4959. [PubMed]
484.Hinsby, A. M., Olsen, J. V. and Mann, M.  Tyrosine phosphoproteomics of fibroblast growth factor signaling: a role for insulin receptor substrate-4. The Journal of Biological Chemistry. 2004. 279, 46438-46447. [PubMed]
485.Blagoev, B., Ong, S. E., Kratchmarova, I. and Mann, M.  Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nature Biotechnology. 2004. 22, 1139-1145. [PubMed]
486.de, H., Foster, L. J. and Mann, M.  RNA and RNA binding proteins participate in early stages of cell spreading through spreading initiation centers. Cell. 2004. 117, 649-662. [PubMed]
487.Everley, P. A., Krijgsveld, J., Zetter, B. R. and Gygi, S. P.  Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Molecular & Cellular Proteomics : MCP. 2004. 3, 729-735. [PubMed]
488.Ibarrola, N., Molina, H., Iwahori, A. and Pandey, A.  A novel proteomic approach for specific identification of tyrosine kinase substrates using [13C]tyrosine. The Journal of Biological Chemistry. 2004. 279, 15805-15813. [PubMed]
489.Schulze, W. X. and Mann, M.  A novel proteomic screen for peptide-protein interactions. The Journal of Biological Chemistry. 2004. 279, 10756-10764. [PubMed]
490.Ong, S. E., Kratchmarova, I. and Mann, M.  Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). Journal of Proteome Research. 2003. 2, 173-181. [PubMed]
491.Jiang, H. and English, A. M.  Quantitative analysis of the yeast proteome by incorporation of isotopically labeled leucine. Journal of Proteome Research. 2002. 1, 345-350. [PubMed]
492.Blagoev, B., Kratchmarova, I., Ong, S. E., Nielsen, M., Foster, L. J. and Mann, M.  A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nature Biotechnology. 2003. 21, 315-318. [PubMed]
493.Zhu, H., Pan, S., Gu, S., Bradbury, E. M. and Chen, X.  Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Communications in Mass Spectrometry : RCM. 2002. 16, 2115-2123. [PubMed]
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