TY - JOUR AU - Hoffert, J. D. AU - Pisitkun, T. AU - Wang, G. AU - Shen, R. F. AU - Knepper, M. A. PY - 2006 DA - 2006// TI - Quantitative phosphoproteomics of vasopressin-sensitive renal cells: Regulation of aquaporin-2 phosphorylation at two sites JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0600895103 DO - 10.1073/pnas.0600895103 ID - Hoffert2006 ER - TY - JOUR AU - Li, X. AU - Gerber, S. A. AU - Rudner, A. D. AU - Beausoleil, S. A. AU - Haas, W. AU - Elias, J. E. AU - Gygi, S. P. PY - 2007 DA - 2007// TI - Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae JO - J Proteome Res VL - 6 UR - https://doi.org/10.1021/pr060559j DO - 10.1021/pr060559j ID - Li2007 ER - TY - JOUR AU - Gruhler, A. AU - Olsen, J. V. AU - Mohammed, S. AU - Mortensen, P. AU - Fargeman, N. J. AU - Mann, M. AU - Jensen, O. N. PY - 2005 DA - 2005// TI - Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway JO - Molecular & Cellular Proteomics VL - 4 UR - https://doi.org/10.1074/mcp.M400219-MCP200 DO - 10.1074/mcp.M400219-MCP200 ID - Gruhler2005 ER - TY - CHAP AU - Whitelegge, J. P. ED - Aguilar, M. I. PY - 2004 DA - 2004// TI - HPLC and Mass Spectrometry of Intrinsic Membrane Proteins BT - HPLC of Peptides and Proteins, Volume 251 of Methods in Molecular Biology ID - Whitelegge2004 ER - TY - JOUR AU - Tanner, S. AU - Shu, H. AU - Frank, A. AU - Wang, L. C. AU - Zandi, E. AU - Mumby, M. AU - Pevzner, P. A. AU - Bafna, V. PY - 2005 DA - 2005// TI - InsPecT: identification of post translationally modified peptides from tandem mass spectra JO - Analytical Chemistry VL - 77 UR - https://doi.org/10.1021/ac050102d DO - 10.1021/ac050102d ID - Tanner2005 ER - TY - JOUR AU - Eng, J. K. AU - Fischer, B. AU - Grossmann, J. AU - MacCoss, M. J. PY - 2008 DA - 2008// TI - A Fast SEQUEST Cross Correlation Algorithm JO - Journal of Proteome Research VL - 7 UR - https://doi.org/10.1021/pr800420s DO - 10.1021/pr800420s ID - Eng2008 ER - TY - JOUR AU - M susbacher, N. AU - Schreiber, T. B. AU - Daub, H. PY - 2010 DA - 2010// TI - Glycoprotein Capture and Quantitative Phosphoproteomics Indicate Coordinated Regulation of Cell Migration upon Lysophosphatidic Acid Stimulation JO - Molecular & Cellular Proteomics VL - 9 UR - https://doi.org/10.1074/mcp.M110.000737 DO - 10.1074/mcp.M110.000737 ID - M susbacher2010 ER - TY - JOUR AU - Solit, D. B. AU - Mellinghoff, I. K. PY - 2010 DA - 2010// TI - Tracing cancer networks with phosphoproteomics JO - Nat Biotech VL - 28 UR - https://doi.org/10.1038/nbt1010-1028 DO - 10.1038/nbt1010-1028 ID - Solit2010 ER - TY - JOUR AU - Gruhler, A. AU - Olsen, J. V. AU - Mohammed, S. AU - Mortensen, P. AU - Frgeman, N. J. AU - Mann, M. AU - Jensen, O. N. PY - 2005 DA - 2005// TI - Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway JO - Mol Cell Proteomics VL - 4 UR - https://doi.org/10.1074/mcp.M400219-MCP200 DO - 10.1074/mcp.M400219-MCP200 ID - Gruhler2005 ER - TY - JOUR AU - Wolf-Yadlin, A. AU - Hautaniemi, S. AU - Lauffenburger, D. A. AU - White, F. M. PY - 2007 DA - 2007// TI - Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks JO - Proc Natl Acad Sci USA VL - 104 UR - https://doi.org/10.1073/pnas.0608638104 DO - 10.1073/pnas.0608638104 ID - Wolf-Yadlin2007 ER - TY - JOUR AU - Cantin, G. T. AU - Venable, J. D. AU - Cociorva, D. AU - Yates, J. R. PY - 2006 DA - 2006// TI - Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway JO - J Proteome Res VL - 5 UR - https://doi.org/10.1021/pr050270m DO - 10.1021/pr050270m ID - Cantin2006 ER - TY - JOUR AU - Beausoleil, S. A. AU - Jedrychowski, M. AU - Schwartz, D. AU - Elias, J. E. AU - Vill, J. AU - Li, J. AU - Cohn, M. A. AU - Cantley, L. C. AU - Gygi, S. P. PY - 2004 DA - 2004// TI - Large-scale characterization of HeLa cell nuclear phosphoproteins JO - Proc. Natl. Acad. Sci. USA VL - 101 UR - https://doi.org/10.1073/pnas.0404720101 DO - 10.1073/pnas.0404720101 ID - Beausoleil2004 ER - TY - JOUR AU - Olsen, J. V. AU - Blagoev, B. AU - Gnad, F. AU - Macek, B. AU - Kumar, C. AU - Mortensen, P. AU - Mann, M. PY - 2006 DA - 2006// TI - Global, in vivo, and site-specific phosphorylation dynamics in signaling networks JO - Cell VL - 127 UR - https://doi.org/10.1016/j.cell.2006.09.026 DO - 10.1016/j.cell.2006.09.026 ID - Olsen2006 ER - TY - JOUR AU - Du, X. AU - Yang, F. AU - Manes, N. P. AU - Stenoien, D. L. AU - Monroe, M. E. AU - Adkins, J. N. AU - States, D. J. AU - Purvine, S. O. AU - Camp, D. G. AU - Smith, R. D. PY - 2008 DA - 2008// TI - Linear Discriminant Analysis-Based Estimation of the False Discovery Rate for Phosphopeptide Identifications JO - Journal of Proteome Research VL - 7 UR - https://doi.org/10.1021/pr070510t DO - 10.1021/pr070510t ID - Du2008 ER - TY - JOUR AU - Ruttenberg, B. E. AU - Pisitkun, T. AU - Knepper, M. A. AU - Hoffert, J. D. PY - 2008 DA - 2008// TI - PhosphoScore: an open-source phosphorylation site assignment tool for MSn data JO - Journal of Proteome Research VL - 7 UR - https://doi.org/10.1021/pr800169k DO - 10.1021/pr800169k ID - Ruttenberg2008 ER - TY - JOUR AU - Ritz, A. AU - Shakhnarovich, G. AU - Salomon, A. R. AU - Raphael, B. J. PY - 2009 DA - 2009// TI - Discovery of phosphorylation motif mixtures in phosphoproteomics data JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btn569 DO - 10.1093/bioinformatics/btn569 ID - Ritz2009 ER - TY - JOUR AU - Beausoleil, S. A. AU - Villen, J. AU - Gerber, S. A. AU - Rush, J. AU - Gygi, S. P. PY - 2006 DA - 2006// TI - A probability-based approach for high-throughput protein phosphorylation analysis and site localization JO - Nature Biotechnology VL - 24 UR - https://doi.org/10.1038/nbt1240 DO - 10.1038/nbt1240 ID - Beausoleil2006 ER - TY - JOUR AU - Cox, J. AU - Mann, M. PY - 2008 DA - 2008// TI - MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification JO - Nat Biotech VL - 26 UR - https://doi.org/10.1038/nbt.1511 DO - 10.1038/nbt.1511 ID - Cox2008 ER - TY - JOUR AU - Li, D. AU - Fu, Y. AU - Sun, R. AU - Ling, C. X. AU - Wei, Y. AU - Zhou, H. AU - Zeng, R. AU - Yang, Q. AU - He, S. AU - Gao, W. PY - 2005 DA - 2005// TI - pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti439 DO - 10.1093/bioinformatics/bti439 ID - Li2005 ER - TY - JOUR AU - Swaney, D. L. AU - Wenger, C. D. AU - Thomson, J. A. AU - Coon, J. J. PY - 2009 DA - 2009// TI - Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry JO - Proceedings of the National Academy of Sciences VL - 106 UR - https://doi.org/10.1073/pnas.0811964106 DO - 10.1073/pnas.0811964106 ID - Swaney2009 ER - TY - JOUR AU - Payne, S. H. AU - Yau, M. AU - Smolka, M. B. AU - Tanner, S. AU - Zhou, H. AU - Bafna, V. PY - 2008 DA - 2008// TI - Phosphorylation-Specific MS/MS Scoring for Rapid and Accurate Phosphoproteome Analysis JO - Journal of Proteome Research VL - 7 UR - https://doi.org/10.1021/pr800129m DO - 10.1021/pr800129m ID - Payne2008 ER - TY - JOUR AU - Taus, T. AU - Kocher, T. AU - Pichler, P. AU - Paschke, C. AU - Schmidt, A. AU - Henrich, C. AU - Mechtler, K. PY - 2011 DA - 2011// TI - Universal and Confident Phosphorylation Site Localization Using phosphoRS JO - Journal of Proteome Research VL - 10 UR - https://doi.org/10.1021/pr200611n DO - 10.1021/pr200611n ID - Taus2011 ER - TY - STD TI - Baker PR, Trinidad JC, Chalkley RJ: Modification Site Localization Scoring Integrated into a Search Engine.Molecular & Cellular Proteomics 2011.,10(7): [http://www.mcponline.org/content/10/7/M111.008078.abstract] UR - http://www.mcponline.org/content/10/7/M111.008078.abstract ID - ref23 ER - TY - JOUR AU - Bailey, C. M. AU - Sweet, S. M. M. AU - Cunningham, D. L. AU - Zeller, M. AU - Heath, J. K. AU - Cooper, H. J. PY - 2009 DA - 2009// TI - SLoMo: Automated Site Localization of Modifications from ETD/ECD Mass Spectra JO - Journal of Proteome Research VL - 8 UR - https://doi.org/10.1021/pr800917p DO - 10.1021/pr800917p ID - Bailey2009 ER - TY - STD TI - Savitski MM, Lemeer S, Boesche M, Lang M, Mathieson T, Bantscheff M, Kuster B: Confident Phosphorylation Site Localization Using the Mascot Delta Score.Molecular and Cellular Proteomics 2011.,10(2): ID - ref25 ER - TY - CHAP AU - Saeed, F. AU - Pisitkun, T. AU - Hoffert, J. D. AU - Wang, G. AU - Gucek, M. AU - Knepper, M. A. PY - 2012 DA - 2012// TI - An efficient dynamic programming algorithm for phosphorylation site assignment of large-scale mass spectrometry data BT - Bioinformatics and Biomedicine Workshops (BIBMW), 2012 IEEE International Conference on UR - https://doi.org/10.1109/BIBMW.2012.6470210 DO - 10.1109/BIBMW.2012.6470210 ID - Saeed2012 ER - TY - JOUR AU - Barsnes, H. AU - Huber, S. AU - Sickmann, A. AU - Eidhammer, I. AU - Martens, L. PY - 2009 DA - 2009// TI - OMSSA Parser: an open-source library to parse and extract data from MS/MS search results JO - Proteomics VL - 9 UR - https://doi.org/10.1002/pmic.200900037 DO - 10.1002/pmic.200900037 ID - Barsnes2009 ER - TY - BOOK AU - Kleinberg, J. AU - Tardos, E. PY - 2005 DA - 2005// TI - Algorithm Design PB - Addison-Wesley Longman Publishing Co., Inc CY - Boston, MA. USA ID - Kleinberg2005 ER - TY - JOUR AU - Eng, J. K. AU - McCormack, A. L. AU - JRY PY - 1994 DA - 1994// TI - An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database JO - Journal of the American Society for Mass Spectrometry VL - 5 UR - https://doi.org/10.1016/1044-0305(94)80016-2 DO - 10.1016/1044-0305(94)80016-2 ID - Eng1994 ER - TY - JOUR AU - Tanner, S. AU - Pevzner, P. A. AU - Bafna, V. PY - 2006 DA - 2006// TI - Unrestrictive identification of post-translational modifications through peptide mass spectrometry JO - Nat Protocols VL - 1 UR - https://doi.org/10.1038/nprot.2006.10 DO - 10.1038/nprot.2006.10 ID - Tanner2006 ER - TY - JOUR AU - Tabb, D. L. AU - MacCoss, M. J. AU - Wu, C. C. AU - Anderson, S. D. AU - Yates, J. R. PY - 2003 DA - 2003// TI - Similarity among Tandem Mass Spectra from Proteomic Experiments:Detection, Significance, and Utility JO - Analytical Chemistry VL - 75 UR - https://doi.org/10.1021/ac026424o DO - 10.1021/ac026424o ID - Tabb2003 ER - TY - JOUR AU - Frank, A. M. AU - Bandeira, N. AU - Shen, Z. AU - Tanner, S. AU - Briggs, S. P. AU - Smith, R. D. AU - Pevzner, P. A. PY - 2008 DA - 2008// TI - Clustering Millions of Tandem Mass Spectra JO - Journal of Proteome Research VL - 7 UR - https://doi.org/10.1021/pr070361e DO - 10.1021/pr070361e ID - Frank2008 ER - TY - JOUR AU - Bandeira, N. AU - Tsur, D. AU - Frank, A. AU - Pevzner, P. A. PY - 2007 DA - 2007// TI - Protein identification by spectral networks analysis JO - Proceedings of the National Academy of Sciences VL - 104 UR - https://doi.org/10.1073/pnas.0701130104 DO - 10.1073/pnas.0701130104 ID - Bandeira2007 ER - TY - STD TI - Jedrychowski MP, Huttlin EL, Haas W, Sowa ME, Rad R, Gygi SP: Evaluation of HCD- and CID-type Fragmentation Within Their Respective Detection Platforms For Murine Phosphoproteomics.Molecular & Cellular Proteomics 2011.,10(12): [http://www.mcponline.org/content/10/12/M111.009910.abstract] UR - http://www.mcponline.org/content/10/12/M111.009910.abstract ID - ref34 ER - TY - JOUR AU - Rinschen, M. M. AU - Yu, M. J. AU - Wang, G. AU - Boja, E. S. AU - Hoffert, J. D. AU - Pisitkun, T. AU - Knepper, M. A. PY - 2010 DA - 2010// TI - Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor Independent signaling pathways in renal collecting duct cells JO - Proceedings of the National Academy of Sciences VL - 107 UR - https://doi.org/10.1073/pnas.0910646107 DO - 10.1073/pnas.0910646107 ID - Rinschen2010 ER - TY - JOUR AU - Saeed, F. AU - Khokhar, A. PY - 2009 DA - 2009// TI - A domain decomposition strategy for alignment of multiple biological sequences on multiprocessor platforms JO - Journal of Parallel and Distributed Computing VL - 69 UR - https://doi.org/10.1016/j.jpdc.2009.03.006 DO - 10.1016/j.jpdc.2009.03.006 ID - Saeed2009 ER - TY - JOUR AU - Saeed, F. AU - Perez-Rathke, A. AU - Gwarnicki, J. AU - Berger-Wolf, T. AU - Khokhar, A. PY - 2012 DA - 2012// TI - A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomes JO - Journal of parallel and distributed computing VL - 72 UR - https://doi.org/10.1016/j.jpdc.2011.08.001 DO - 10.1016/j.jpdc.2011.08.001 ID - Saeed2012 ER - TY - CHAP AU - Saeed, F. AU - Hoffert, J. AU - Pisitkun, T. AU - Knepper, M. PY - 2012 DA - 2012// TI - High performance phosphorylation site assignment algorithm for mass spectrometry data using multicore systems BT - Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine UR - https://doi.org/10.1145/2382936.2383056 DO - 10.1145/2382936.2383056 ID - Saeed2012 ER - TY - JOUR AU - Zhao, B. AU - Pisitkun, T. AU - Hoffert, J. D. AU - Knepper, M. A. AU - Saeed, F. PY - 2012 DA - 2012// TI - CPhos: A program to calculate and visualize evolutionarily conserved functional phosphorylation sites JO - Proteomics VL - 12 UR - https://doi.org/10.1002/pmic.201200189 DO - 10.1002/pmic.201200189 ID - Zhao2012 ER - TY - JOUR AU - Nguyen Ba, A. N. AU - Moses, A. M. PY - 2010 DA - 2010// TI - Evolution of Characterized Phosphorylation Sites in Budding Yeast JO - Molecular Biology and Evolution VL - 27 UR - https://doi.org/10.1093/molbev/msq090 DO - 10.1093/molbev/msq090 ID - Nguyen Ba2010 ER - TY - JOUR AU - Pavicevic, Z. AU - Leslie, C. C. AU - Malik, K. U. PY - 2008 DA - 2008// TI - cPLA2 phosphorylation at serine-515 and serine-505 is required for arachidonic acid release in vascular smooth muscle cells JO - Journal of Lipid Research VL - 49 UR - https://doi.org/10.1194/jlr.M700419-JLR200 DO - 10.1194/jlr.M700419-JLR200 ID - Pavicevic2008 ER - TY - CHAP AU - Saeed, F. AU - Pisitkun, T. AU - Knepper, M. A. AU - Hoffert, J. D. PY - 2012 DA - 2012// TI - An efficient algorithm for clustering of large-scale mass spectrometry data BT - Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference on UR - https://doi.org/10.1109/BIBM.2012.6392738 DO - 10.1109/BIBM.2012.6392738 ID - Saeed2012 ER - TY - CHAP AU - Saeed, F. AU - Hoffert, J. D. AU - Knepper, M. A. PY - 2012 DA - 2012// TI - A High Performance Algorithm for Clustering of Large-Scale Protein Mass Spectrometry Data using Multi-Core Architectures BT - International Symposium on Network Enabled Health Informatics, Biomedicine and Bioinformatics ID - Saeed2012 ER - TY - STD TI - Hoffert J, Pisitkun T, Saeed F, Song J, Chou C, Knepper M: Dynamics of the G protein-coupled vasopressin V2 receptor signaling network revealed by quantitative phosphoproteomics.Molecular & Cellular Proteomics 2012.,11(2): ID - ref44 ER -