Publications Regarding SILAC

  1. 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.(2008) The Journal of Cell Biology. 183, 223-239 [PubMed]

  2. Cockman, M. E., Webb, J. D., Kramer, H. B., Kessler, B. M. and Ratcliffe, P. J. Proteomic-based identification of novel factor inhibiting HIF (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins.(2008) Molecular and Cellular Proteomics. electronic publication ahead of print. [PubMed]

  3. Pan, C., Gnad, F., Olsen, J. V. and Mann, M. Quantitative phosphoproteome analysis of a mouse liver cell line reveals specificity of phosphatase inhibitors.(2008) Proteomics. electronic publication ahead of print. [PubMed]

  4. 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.(2008) Journal of Proteome Research. electronic publication ahead of print. [PubMed]

  5. Harsha, H. C., Jimeno, A., Molina, H., Mihalas, A., Goggins, M., 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.(2008) Journal of Proteome Research. electronic publication ahead of print. [PubMed]

  6. de Godoy, L. M., 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. (2008) Nature. electronic publication ahead of print. [PubMed]

  7. 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.(2008) Cancer genomics & proteomics. 5, 161-168. [PubMed]

  8. Meierhofer, D., Wang, X., Huang, L. and Kaiser, P. Quantitative Analysis of global Ubiquitination in HeLa Cells by Mass Spectrometry.(2008) Journal of Proteome Research. electronic publication ahead of print. [PubMed]

  9. 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.(2008) Genes to Cells. electronic publication ahead of print. [PubMed]

  10. 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.(2008) Molecular Cell. 31, 762-772. [PubMed]

  11. 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.(2008) Proceedings of the National Academy of Sciences of the United States of America. electronic publication ahead of print. [PubMed]

  12. Dengjel, J., Kristensen, A. R. and Andersen, J. S. Ordered bulk degradation via autophagy.(2008) Autophagy. electronic publication ahead of print. [PubMed]

  13. 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.(2008) Journal of Proteomic Research. electronic publication ahead of print. [PubMed]

  14. 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.(2008) Biological Chemistry. electronic publication ahead of print. [PubMed]

  15. Song, H., Kong, W., Weatherspoon, N., Qin, G., Tyler, W., Turk, J., Curtiss, R 3rd. and Shi, Y. Modulation of the regulatory activity of bacterial two-component systems by slyA.(2008) The Journal of Biological Chemistry. electronic publication ahead of print. [PubMed]

  16. Dephoure, N., Zhou, C., Villén, J., Beausoleil, S. A., Bakalarski, C. E., Elledge, S. J. and Gygi, S. P. A quantitative atlas of mitotic phosphorylation.(2008) Proceedings of the National Academy of Sciences of the United States of America. electronic publication ahead of print. [PubMed]

  17. Baek, D., Villén, J., Shin, C., Camargo, F. D., Gygi, S. P. and Bartel, D. P. The impact of microRNAs on protein output.(2008) Nature. electronic publication ahead of print. [PubMed]

  18. Selbach, M., Schwanhäusser, B., Thierfelder, N., Fang, Z., Khanin, R. and Rajewsky, N. Widespread changes in protein synthesis induced by microRNAs.(2008) Nature. electronic publication ahead of print. [PubMed]

  19. 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.(2008) Proteomics. 8, 3061-3070. [PubMed]

  20. Skiba, M., Mettenleiter, T. C. and Karger, A. Quantitative whole-cell proteome analysis of pseudorabies virus infected cells.(2008) Journal of Virology. electronic publication ahead of print. [PubMed]

  21. Krüger, M., Moser, M., Ussar, S., Thievessen, I., Luber, C. A., Forner, F., Schmidt, S., Zanivan, S., Fässler, R. and Mann. M. SILAC Mouse for Quantitative Proteomics Uncovers Kindlin-3 as an Essential Factor for Red Blood Cell Function.(2008) Cell. 134, 353-364. [PubMed]

  22. 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.(2008) Journal of Proteome Research. electronic publication ahead of print. [PubMed]

  23. 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.(2008) Journal of Proteome Research. electronic publication ahead of print. [PubMed]

  24. 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.(2008) Journal of Proteome Research. electronic publication ahead of print. [PubMed]

  25. 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. (2008) Journal of Proteome Research. 71, 97-108. [PubMed]

  26. 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. (2008) Journal of Proteome Research. electronic publication ahead of print. [PubMed]

  27. 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. (2008) Analytical Chemistry. electronic publication ahead of print. [PubMed]

  28. 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. (2008) Proteins. electronic publication ahead of print. [PubMed]

  29. 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. (2008) Molecular and Cellular Proteomics. electronic publication ahead of print. [PubMed]

  30. 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. (2008) Journal of Proteome Research. electronic publication ahead of print. [PubMed]

  31. Dobreva, I., Fielding, A., Foster, L. J. and Dedhar, S. Mapping the Integrin-Linked Kinase Interactome Using SILAC.(2008) Journal of Proteome Research. 7, 1740-1749. [PubMed]

  32. Harsha, H. C., Molina, H. and Pandey, A. Quantitative proteomics using stable isotope labeling with amino acids in cell culture (SILAC). (2008) Nature Protocols. 3, 505-516 [PubMed]

  33. Asara, J. M., Christofk, H. R., Freimark, L. M. and Cantley, L. C. A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. (2008) Proteomics. 8, 994-999 [PubMed]

  34. 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. (2008) Glia. 56, 675-685. [PubMed]

  35. Hanke, S., Besir, H., Oesterhelt, D. and Mann, M. Absolute SILAC for Accurate Quantitation of Proteins in Complex Mixtures Down to the Attomole Level. (2008) Journal of Proteome Research. 7, 1118-1130. [PubMed]

  36. Krüger, M., Kratchmarova, I., Blagoev, B., Tseng, Y. H., Kahn, C. R. and Mann, M. Dissection of the insulin signaling pathway via quantitative phosphoproteomics. (2008) Proceedings of the National Academy of Sciences of the United States of America. 105, 2451-2456. [PubMed]

  37. Spellman, D.S., Deinhardt, K., Darie, C. C., Chao, M. V. and Neubert, T.A. Stable isotopic labeling of amino acids in cultured primary neurons: Application to BDNF-dependent phosphotyrosine-associated signaling. (2008) Molecular and Cellular Proteomics. electronic publication ahead of print. [PubMed]

  38. 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. (2008) Journal of Proteome Research. 7, 678-686. [PubMed]

  39. 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. (2008) Proceedings of the National Academy of Sciences of the United States of America. 105, 692-697. [PubMed]

  40. Zhong, J., Molina, H. and Pandey, A. Phosphoproteomics.(2007) Current protocols in protein science. Chapter 24:Unit24.4 [PubMed]

  41. 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.(2007) Channels (Austin, Tex.). 1, 59-61. [PubMed]

  42. Colzani, M., Schütz, F., Potts, A., Waridel, P. and Quadroni, M. Relative protein quantification by isobaric SILAC with immonium ion splitting (ISIS). (2007) Molecular and Cellular Proteomics. 7, 927-937. [PubMed]

  43. 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. (2007) Amino acids. electronic publication ahead of print. [PubMed]

  44. 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. (2007) Molecular and Cellular Proteomics. 7, 845-852. [PubMed]

  45. 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. (2007) Proceedings of the National Academy of Sciences of the United States of America. 104, 19855-19860. [PubMed]

  46. Graumann, J., Hubner, N. C., Kim, J. B., Ko, K., Moser, M., Kumar, C., Cox, J., Schoeler, H. and Mann, M. SILAC-labeling and proteome quantitation of mouse embryonic stem cells to a depth of 5111 proteins. (2007) Molecular and Cellular Proteomics. electronic publication ahead of print. [PubMed]

  47. 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. (2007) Electrophoresis. electronic publication ahead of print. [PubMed]

  48. 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). (2007) Rapid Communications in Mass Spectrometry. 21, 3919-3926. [PubMed]

  49. Wang, X. and Huang, L. Identifying dynamic interactors of protein complexes by quantitative mass spectrometry. (2007) Molecular and Cellular Proteomics. electronic publication ahead of print. [PubMed]

  50. Waanders, L. F., Hanke, S. and Mann, M. Top-Down Quantitation and Characterization of SILAC-Labeled Proteins. (2007) Journal of the American Society for Mass Spectrometry 18, 2058-2064 [PubMed]

  51. Vermeulen, M., Mulder, K. W., Denissov, S., Pijnappel, W. W., van Schaik, F. M., 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. (2007) Cell 131, 58-69 [PubMed]

  52. 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 TiO(2) Surfaces Used in the Study of Regulated, Dynamic Protein Phosphorylation. (2007) Journal of the American Society for Mass Spectrometry 18, 1932-1944 [PubMed]

  53. Van Hoof D., 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. (2007) Nature Methods 4, 677-678 [PubMed]

  54. 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. (2007) BMC Neuroscience 8:67. [PubMed]

  55. Liu, J., Zhou, Y., Wang, Y., Fong, H., Murray, T. M. and Zhang, J. Identification of proteins involved in microglial endocytosis of alpha-synuclein. (2007) Journal of Proteome Research. 6, 3614-3627. [PubMed]

  56. Bonenfant, D., Towbin, H., Coulot, M., Schindler, P., Mueller, D. R. and van Oostrum, J. Analysis of Dynamic Changes in Post-translational Modifications of Human Histones during Cell Cycle by Mass Spectrometry. (2007) Molecular and Cellular Proteomics. 6, 1917-1932. [PubMed]

  57. Bouyssié, D., de Peredo, A. G., 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. (2007) Molecular and Cellular Proteomics. 6, 1621-1637. [PubMed]

  58. 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. (2007) Archives of Biochemistry and Biophysics. electronic publication ahead of print. [PubMed]

  59. Wang, Z., Pandey, A. and Hart, G. W. Dynamic interplay between O-GlcNAcylation and GSK-3-dependent phosphorylation. (2007) Molecular and Cellular Proteomics. electronic publication ahead of print. [PubMed]

  60. 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. (2007) Journal of Proteome Research. electronic publication ahead of print. [PubMed]

  61. Ong, S. E. and Mann, M. Stable isotope labeling by amino acids in cell culture for quantitative proteomic. (2007) Methods in Molecular Biology. 359, 37-52. [PubMed]

  62. 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. (2007) Journal of Proteome Research. electronic publication ahead of print. [PubMed]

  63. Ong, S. E. and Mann, M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). (2007) Nature Protocols. 1, 2650-2660. [PubMed]

  64. 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. (2007) Rapid Communications in Mass Spectrometry. 21, 771-778. [PubMed]

  65. Mann, M. Functional and quantitative proteomics using SILAC. (2006) Nature Reviews Molecular Cell Biology. 7, 952-958. [PubMed]

  66. Ong, S. E. and Mann, M. Identifying and Quantifying Sites of Protein Methylation by Heavy Methyl SILAC.(2006) Current protocols in protein science. Chapter 14:Unit14.9 [PubMed]

  67. 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. (2006) Cell. 127, 635-648. [PubMed]

  68. Selbach, M. and Mann, M. Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). (2006) Nature Methods. 3, 981-983. [PubMed]

  69. Schlosser, A., Amanchy, R. and Otto, H. Identification of tyrosine-phosphorylation sites in the nuclear membrane protein emerin. (2006) The FEBS Journal. 273,3204-3215 [PubMed]

  70. 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. (2006) Journal of Proteome Research. 5, 1224-1231 [PubMed]

  71. Cantin, G. T., Venable, J. D., Cociorva, D. and Yates, J.R. 3rd. Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway. (2006) Journal of Proteome Research. 5, 127-134 [PubMed]

  72. Blagoev, B. and Mann, M. Quantitative proteomics to study mitogen-activated protein kinases. (2006) Methods. 40, 243-250. [PubMed]

  73. Qiao, Y., Molina, H., Pandey, A., Zhang, J. and Cole, P. A. Chemical rescue of a mutant enzyme in living cells. (2006) Science. 311, 1293-1297. [PubMed]

  74. 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. (2006) Journal of Proteome Research. 5, 2743-2753. [PubMed]

  75. 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. (2006) Journal of Proteome Research. 5, 2632-2641. [PubMed]

  76. An, E., Lu, X., Flippin, J., Devaney, J. M., Halligan, B., Hoffman, E., 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. (2006) Journal of Proteome Research. 5, 2599-2610. [PubMed]

  77. 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. (2006) Nucleic Acids Research. 34, e107. [PubMed]

  78. 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. (2006) Molecular and Cellular Proteomics. 5, 2319-2325. [PubMed]

  79. Park, K. S., Mohapatra, D. P., Misonou, H. and Trimmer, J. S. Graded regulation of the Kv2.1 potassium channel by variable phosphorylation. (2006) Science. 313, 976-979. [PubMed]

  80. 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. (2006) Proteomics. 6, 4554-4564. [PubMed]

  81. Jin, J., Li, G. J., Davis, J., Zhu, D., Wang, Y., Pan, C. and Zhang, J. Identification of novel proteins interacting with both a-synuclein and DJ-1. (2007) Molecular and Cellular Proteomics. 6, 845-859. [PubMed]

  82. 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. (2006) Proceedings of the National Academy of Sciences of the United States of America. 103, 9773-9778. [PubMed]

  83. de Godoy, L. M., Olsen, J. V., de Souza, G. A., Li, G., Mortensen, P. and Mann, M. Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. (2006) Genome Biology. 7, R50. [PubMed]

  84. 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. (2006) Molecular Cell. 22, 193-204. [PubMed]

  85. 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. (2006) Molecular and Cellular Proteomics. 5, 1131-1145. [PubMed]

  86. 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). (2006) Journal of Proteome Research. 5, 581-588. [PubMed]

  87. 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. (2006) Glia. 53, 567-582. [PubMed]

  88. 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). (2006) Journal of Proteome Research. 5, 64-75. [PubMed]

  89. 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. (2006) Proteomics. 6, 614-622. [PubMed]

  90. 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. (2006) Molecular and Cellular Proteomics. 5, 366-378. [PubMed]

  91. 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. (2006) Molecular and Cellular Proteomics. 5, 157-171. [PubMed]

  92. 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. (2005) Journal of Proteome Research. 4, 2007-2014. [PubMed]

  93. 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). (2005) Journal of Proteome Research. 4, 1661-1671. [PubMed]

  94. 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. (2005) Molecular and Cellular Proteomics. 4, 1697-1709. [PubMed]

  95. Zhou, Y., Wang, Y., Kovacs, M., Jin, J. and Zhang, J. Microglial activation induced by neurodegeneration: a proteomic analysis. (2005) Molecular and Cellular Proteomics. 4, 1471-1479. [PubMed]

  96. Romijn, E. P., Christis, C., Wieffer, M., Gouw, J. W., Fullaondo, A., van der Sluijs, P., 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). (2005) Molecular and Cellular Proteomics. 4, 1297-1310 [PubMed]

  97. Molina, H., Parmigiani, G. and Pandey, A. Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry. (2005) Analytical chemistry. 77, 2739-2744. [PubMed]

  98. Trester-Zedlitz, M., Burlingame, A., Kobilka, B. and von Zastrow, M. Mass spectrometric analysis of agonist effects on posttranslational modifications of the beta-2 adrenoceptor in mammalian cells. (2005) Biochemistry. 44, 6133-6143. [PubMed]

  99. Loyet, K. M., Ouyang, W., Eaton, D. L. and Stults, J. T. Proteomic profiling of surface proteins on Th1 and Th2 cells. (2005) Journal of Proteome Research. 4, 400-409. [PubMed]

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  116. de Hoog, C. L., Foster, L. J. and Mann, M. RNA and RNA binding proteins participate in early stages of cell spreading through spreading initiation centers. (2004). Cell. 117, 649-62. [PubMed]

  117. Ibarrola, N., Molina, H., Iwahori, A. and Pandey, A. . A novel proteomic approach for specific identification of tyrosine kinase substrates using 13C tyrosine. (2004). Journal of Biological Chemistry. 279, 15805-15813. [PubMed]

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