TY - JOUR AU - Pounds, S. B. PY - 2006 DA - 2006// TI - Estimation and control of multiple testing error rates for microarray studies JO - Brief Bioinform VL - 7 UR - https://doi.org/10.1093/bib/bbk002 DO - 10.1093/bib/bbk002 ID - Pounds2006 ER - TY - JOUR AU - Gusnanto, A. AU - Calza, S. AU - Pawitan, Y. PY - 2007 DA - 2007// TI - Identification of differentially expressed genes and false discovery rate in microarray studies JO - Curr Opin Lipidol VL - 18 UR - https://doi.org/10.1097/MOL.0b013e3280895d6f DO - 10.1097/MOL.0b013e3280895d6f ID - Gusnanto2007 ER - TY - JOUR AU - Fan, J. AU - Ren, Y. PY - 2006 DA - 2006// TI - Statistical analysis of DNA microarray data in cancer research JO - Clin Cancer Res VL - 12 UR - https://doi.org/10.1158/1078-0432.CCR-06-1033 DO - 10.1158/1078-0432.CCR-06-1033 ID - Fan2006 ER - TY - JOUR AU - Listgarten, J. AU - Emili, A. PY - 2005 DA - 2005// TI - Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry JO - Mol Cell Proteomics VL - 4 UR - https://doi.org/10.1074/mcp.R500005-MCP200 DO - 10.1074/mcp.R500005-MCP200 ID - Listgarten2005 ER - TY - JOUR AU - Mueller, L. N. AU - Brusniak, M. Y. AU - Mani, D. R. AU - Aebersold, R. PY - 2008 DA - 2008// TI - An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data JO - J Proteome Res VL - 7 UR - https://doi.org/10.1021/pr700758r DO - 10.1021/pr700758r ID - Mueller2008 ER - TY - JOUR AU - Roxas, B. A. AU - Li, Q. PY - 2008 DA - 2008// TI - Significance analysis of microarray for relative quantitation of LC/MS data in proteomics JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-187 DO - 10.1186/1471-2105-9-187 ID - Roxas2008 ER - TY - JOUR AU - Maurer, M. H. AU - Feldmann, R. E. AU - Bromme, J. O. AU - Kalenka, A. PY - 2005 DA - 2005// TI - Comparison of statistical approaches for the analysis of proteome expression data of differentiating neural stem cells JO - J Proteome Res VL - 4 UR - https://doi.org/10.1021/pr049841l DO - 10.1021/pr049841l ID - Maurer2005 ER - TY - JOUR AU - Choi, H. AU - Fermin, D. AU - Nesvizhskii, A. I. PY - 2008 DA - 2008// TI - Significance analysis of spectral count data in label-free shotgun proteomics JO - Mol Cell Proteomics VL - 7 UR - https://doi.org/10.1074/mcp.M800203-MCP200 DO - 10.1074/mcp.M800203-MCP200 ID - Choi2008 ER - TY - JOUR AU - Pavelka, N. AU - Fournier, M. L. AU - Swanson, S. K. AU - Pelizzola, M. AU - Ricciardi-Castagnoli, P. AU - Florens, L. AU - Washburn, M. P. PY - 2008 DA - 2008// TI - Statistical similarities between transcriptomics and quantitative shotgun proteomics data JO - Mol Cell Proteomics VL - 7 UR - https://doi.org/10.1074/mcp.M700240-MCP200 DO - 10.1074/mcp.M700240-MCP200 ID - Pavelka2008 ER - TY - JOUR AU - Corzett, T. H. AU - Fodor, I. K. AU - Choi, M. W. AU - Walsworth, V. L. AU - Chromy, B. A. AU - Turteltaub, K. W. AU - McCutchen-Maloney, S. L. PY - 2006 DA - 2006// TI - Statistical analysis of the experimental variation in the proteomic characterization of human plasma by two-dimensional difference gel electrophoresis JO - J Proteome Res VL - 5 UR - https://doi.org/10.1021/pr060100p DO - 10.1021/pr060100p ID - Corzett2006 ER - TY - JOUR AU - Pavelka, N. AU - Pelizzola, M. AU - Vizzardelli, C. AU - Capozzoli, M. AU - Splendiani, A. AU - Granucci, F. AU - Ricciardi-Castagnoli, P. PY - 2004 DA - 2004// TI - A power law global error model for the identification of differentially expressed genes in microarray data JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-203 DO - 10.1186/1471-2105-5-203 ID - Pavelka2004 ER - TY - JOUR AU - Liu, H. AU - Sadygov, R. G. AU - Yates, J. R. PY - 2004 DA - 2004// TI - A model for random sampling and estimation of relative protein abundance in shotgun proteomics JO - Anal Chem VL - 76 UR - https://doi.org/10.1021/ac0498563 DO - 10.1021/ac0498563 ID - Liu2004 ER - TY - JOUR AU - Old, W. M. AU - Meyer-Arendt, K. AU - Aveline-Wolf, L. AU - Pierce, K. G. AU - Mendoza, A. AU - Sevinsky, J. R. AU - Resing, K. A. AU - Ahn, N. G. PY - 2005 DA - 2005// TI - Comparison of label-free methods for quantifying human proteins by shotgun proteomics JO - Mol Cell Proteomics VL - 4 UR - https://doi.org/10.1074/mcp.M500084-MCP200 DO - 10.1074/mcp.M500084-MCP200 ID - Old2005 ER - TY - JOUR AU - Strittmatter, E. F. AU - Ferguson, P. L. AU - Tang, K. AU - Smith, R. D. PY - 2003 DA - 2003// TI - Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry JO - J Am Soc Mass Spectrom VL - 14 UR - https://doi.org/10.1016/S1044-0305(03)00146-6 DO - 10.1016/S1044-0305(03)00146-6 ID - Strittmatter2003 ER - TY - JOUR AU - Lipton, M. S. AU - Pasa-Tolic, L. AU - Anderson, G. A. AU - Anderson, D. J. AU - Auberry, D. L. AU - Battista, J. R. AU - Daly, M. J. AU - Fredrickson, J. AU - Hixson, K. K. AU - Kostandarithes, H. PY - 2002 DA - 2002// TI - Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.172170199 DO - 10.1073/pnas.172170199 ID - Lipton2002 ER - TY - JOUR AU - Andreev, V. P. AU - Li, L. AU - Cao, L. AU - Gu, Y. AU - Rejtar, T. AU - Wu, S. L. AU - Karger, B. L. PY - 2007 DA - 2007// TI - A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS JO - J Proteome Res VL - 6 UR - https://doi.org/10.1021/pr0606880 DO - 10.1021/pr0606880 ID - Andreev2007 ER - TY - JOUR AU - Fang, R. AU - Elias, D. A. AU - Monroe, M. E. AU - Shen, Y. AU - McIntosh, M. AU - Wang, P. AU - Goddard, C. D. AU - Callister, S. J. AU - Moore, R. J. AU - Gorby, Y. A. PY - 2006 DA - 2006// TI - Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach JO - Mol Cell Proteomics VL - 5 UR - https://doi.org/10.1074/mcp.M500301-MCP200 DO - 10.1074/mcp.M500301-MCP200 ID - Fang2006 ER - TY - JOUR AU - Hochleitner, E. O. AU - Kastner, B. AU - Frohlich, T. AU - Schmidt, A. AU - Luhrmann, R. AU - Arnold, G. AU - Lottspeich, F. PY - 2005 DA - 2005// TI - Protein stoichiometry of a multiprotein complex, the human spliceosomal U1 small nuclear ribonucleoprotein: absolute quantification using isotope-coded tags and mass spectrometry JO - J Biol Chem VL - 280 UR - https://doi.org/10.1074/jbc.M409587200 DO - 10.1074/jbc.M409587200 ID - Hochleitner2005 ER - TY - JOUR AU - Wang, G. AU - Wu, W. W. AU - Zeng, W. AU - Chou, C. L. AU - Shen, R. F. PY - 2006 DA - 2006// TI - Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes JO - J Proteome Res VL - 5 UR - https://doi.org/10.1021/pr050406g DO - 10.1021/pr050406g ID - Wang2006 ER - TY - JOUR AU - Zhu, Z. AU - Boobis, A. R. AU - Edwards, R. J. PY - 2008 DA - 2008// TI - Identification of estrogen-responsive proteins in MCF-7 human breast cancer cells using label-free quantitative proteomics JO - Proteomics VL - 8 UR - https://doi.org/10.1002/pmic.200700901 DO - 10.1002/pmic.200700901 ID - Zhu2008 ER - TY - JOUR AU - Rao, P. K. AU - Rodriguez, G. M. AU - Smith, I. AU - Li, Q. PY - 2008 DA - 2008// TI - Protein Dynamics in Iron-Starved Mycobacterium tuberculosis Revealed by Turnover and Abundance Measurement Using Hybrid-Linear Ion Trap-Fourier Transform Mass Spectrometry JO - Anal Chem VL - 80 UR - https://doi.org/10.1021/ac800288t DO - 10.1021/ac800288t ID - Rao2008 ER - TY - JOUR AU - Benjamini, Y. AU - Hochberg, Y. PY - 1995 DA - 1995// TI - Controlling the false discovery rate: a practical and powerful approach to multiple testing JO - J R Stat Soc B VL - 57 ID - Benjamini1995 ER - TY - JOUR AU - Qian, H. R. AU - Huang, S. PY - 2005 DA - 2005// TI - Comparison of false discovery rate methods in identifying genes with differential expression JO - Genomics VL - 86 UR - https://doi.org/10.1016/j.ygeno.2005.06.007 DO - 10.1016/j.ygeno.2005.06.007 ID - Qian2005 ER - TY - JOUR AU - Tusher, V. G. AU - Tibshirani, R. AU - Chu, G. PY - 2001 DA - 2001// TI - Significance analysis of microarrays applied to the ionizing radiation response JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.091062498 DO - 10.1073/pnas.091062498 ID - Tusher2001 ER - TY - JOUR AU - Reidegeld, K. A. AU - Eisenacher, M. AU - Kohl, M. AU - Chamrad, D. AU - Korting, G. AU - Bluggel, M. AU - Meyer, H. E. AU - Stephan, C. PY - 2008 DA - 2008// TI - An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications JO - Proteomics VL - 8 UR - https://doi.org/10.1002/pmic.200701073 DO - 10.1002/pmic.200701073 ID - Reidegeld2008 ER - TY - JOUR AU - Hughes, M. A. AU - Silva, J. C. AU - Geromanos, S. J. AU - Townsend, C. A. PY - 2006 DA - 2006// TI - Quantitative proteomic analysis of drug-induced changes in mycobacteria JO - J Proteome Res VL - 5 UR - https://doi.org/10.1021/pr050248t DO - 10.1021/pr050248t ID - Hughes2006 ER - TY - JOUR AU - Andreev, V. P. AU - Li, L. AU - Rejtar, T. AU - Li, Q. AU - Ferry, J. G. AU - Karger, B. L. PY - 2006 DA - 2006// TI - New algorithm for 15N/14N quantitation with LC-ESI-MS using an LTQ-FT mass spectrometer JO - J Proteome Res VL - 5 UR - https://doi.org/10.1021/pr060105m DO - 10.1021/pr060105m ID - Andreev2006 ER - TY - JOUR AU - Vogt, J. A. AU - Schroer, K. AU - Holzer, K. AU - Hunzinger, C. AU - Klemm, M. AU - Biefang-Arndt, K. AU - Schillo, S. AU - Cahill, M. A. AU - Schrattenholz, A. AU - Matthies, H. PY - 2003 DA - 2003// TI - Protein abundance quantification in embryonic stem cells using incomplete metabolic labelling with 15N amino acids, matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry, and analysis of relative isotopologue abundances of peptides JO - Rapid Commun Mass Spectrom VL - 17 UR - https://doi.org/10.1002/rcm.1045 DO - 10.1002/rcm.1045 ID - Vogt2003 ER - TY - JOUR AU - Zimmer, J. S. AU - Monroe, M. E. AU - Qian, W. J. AU - Smith, R. D. PY - 2006 DA - 2006// TI - Advances in proteomics data analysis and display using an accurate mass and time tag approach JO - Mass Spectrom Rev VL - 25 UR - https://doi.org/10.1002/mas.20071 DO - 10.1002/mas.20071 ID - Zimmer2006 ER - TY - JOUR AU - Choi, H. AU - Nesvizhskii, A. I. PY - 2008 DA - 2008// TI - False discovery rates and related statistical concepts in mass spectrometry-based proteomics JO - J Proteome Res VL - 7 UR - https://doi.org/10.1021/pr700747q DO - 10.1021/pr700747q ID - Choi2008 ER - TY - JOUR AU - Wiener, M. C. AU - Sachs, J. R. AU - Deyanova, E. G. AU - Yates, N. A. PY - 2004 DA - 2004// TI - Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures JO - Anal Chem VL - 76 UR - https://doi.org/10.1021/ac0493875 DO - 10.1021/ac0493875 ID - Wiener2004 ER - TY - JOUR AU - Alves, G. AU - Wu, W. W. AU - Wang, G. AU - Shen, R. F. AU - Yu, Y. K. PY - 2008 DA - 2008// TI - Enhancing peptide identification confidence by combining search methods JO - J Proteome Res VL - 7 UR - https://doi.org/10.1021/pr700798h DO - 10.1021/pr700798h ID - Alves2008 ER - TY - JOUR AU - Kapp, E. A. AU - Schutz, F. AU - Connolly, L. M. AU - Chakel, J. A. AU - Meza, J. E. AU - Miller, C. A. AU - Fenyo, D. AU - Eng, J. K. AU - Adkins, J. N. AU - Omenn, G. S. PY - 2005 DA - 2005// TI - An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis JO - Proteomics VL - 5 UR - https://doi.org/10.1002/pmic.200500126 DO - 10.1002/pmic.200500126 ID - Kapp2005 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 - J Proteome Res VL - 7 UR - https://doi.org/10.1021/pr070510t DO - 10.1021/pr070510t ID - Du2008 ER - TY - JOUR AU - Levine, D. M. AU - Haynor, D. R. AU - Castle, J. C. AU - Stepaniants, S. B. AU - Pellegrini, M. AU - Mao, M. AU - Johnson, J. M. PY - 2006 DA - 2006// TI - Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways JO - Genome Biol VL - 7 UR - https://doi.org/10.1186/gb-2006-7-10-r93 DO - 10.1186/gb-2006-7-10-r93 ID - Levine2006 ER -