TY - JOUR AU - Aebersold, R. AU - Mann, M. PY - 2003 DA - 2003// TI - Mass spectrometry-based proteomics JO - Nature VL - 422 UR - https://doi.org/10.1038/nature01511 DO - 10.1038/nature01511 ID - Aebersold2003 ER - TY - CHAP AU - Domon, B. AU - Aebersold, R. PY - 2006 DA - 2006// TI - Mass spectrometry and protein analysis BT - Science ID - Domon2006 ER - TY - JOUR AU - Wilm, M. AU - Mann, M. PY - 1996 DA - 1996// TI - Analytical properties of the nanoelectrospray ion source JO - Anal Chem VL - 68 UR - https://doi.org/10.1021/ac9509519 DO - 10.1021/ac9509519 ID - Wilm1996 ER - TY - JOUR AU - Steen, H. AU - Mann, M. PY - 2004 DA - 2004// TI - The ABC's (and XYZ's) of peptide sequencing JO - Nat Rev Mol Cell Biol VL - 5 UR - https://doi.org/10.1038/nrm1468 DO - 10.1038/nrm1468 ID - Steen2004 ER - TY - JOUR AU - Yates, J. R. AU - Eng, J. K. AU - McCormack, A. L. AU - Schieltz, D. PY - 1995 DA - 1995// TI - Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database JO - Anal Chem VL - 67 UR - https://doi.org/10.1021/ac00104a020 DO - 10.1021/ac00104a020 ID - Yates1995 ER - TY - JOUR AU - Perkins, D. N. AU - Pappin, D. J. AU - Creasy, D. M. AU - Cottrell, J. S. PY - 1999 DA - 1999// TI - Probability-based protein identification by searching sequence databases using mass spectrometry data JO - Electrophoresis VL - 20 UR - https://doi.org/3.0.CO;2-2 DO - 3.0.CO;2-2 ID - Perkins1999 ER - TY - JOUR AU - Mann, M. AU - Jensen, O. N. PY - 2003 DA - 2003// TI - Proteomic analysis of post-translational modifications JO - Nat Biotechnol VL - 21 UR - https://doi.org/10.1038/nbt0303-255 DO - 10.1038/nbt0303-255 ID - Mann2003 ER - TY - JOUR AU - Dancik, V. AU - Addona, T. A. AU - Clauser, K. R. AU - Vath, J. E. AU - Pevzner, P. A. PY - 1999 DA - 1999// TI - De novo peptide sequencing via tandem mass spectrometry JO - J Comput Biol VL - 6 UR - https://doi.org/10.1089/106652799318300 DO - 10.1089/106652799318300 ID - Dancik1999 ER - TY - JOUR AU - Taylor, J. A. AU - Johnson, R. S. PY - 1997 DA - 1997// TI - Sequence database searches via de novo peptide sequencing by tandem mass spectrometry JO - Rapid Commun Mass Spectrom VL - 11 UR - https://doi.org/3.0.CO;2-L DO - 3.0.CO;2-L ID - Taylor1997 ER - TY - JOUR AU - Taylor, J. A. AU - Johnson, R. S. PY - 2001 DA - 2001// TI - Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry JO - Anal Chem VL - 73 UR - https://doi.org/10.1021/ac001196o DO - 10.1021/ac001196o ID - Taylor2001 ER - TY - JOUR AU - Frank, A. AU - Pevzner, P. PY - 2005 DA - 2005// TI - PepNovo: de novo peptide sequencing via probabilistic network modeling JO - Anal Chem VL - 77 UR - https://doi.org/10.1021/ac048788h DO - 10.1021/ac048788h ID - Frank2005 ER - TY - JOUR AU - Ma, B. AU - Zhang, K. AU - Hendrie, C. AU - Liang, C. AU - Li, M. AU - Doherty-Kirby, A. PY - 2003 DA - 2003// TI - PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry JO - Rapid Commun Mass Spectrom VL - 17 UR - https://doi.org/10.1002/rcm.1196 DO - 10.1002/rcm.1196 ID - Ma2003 ER - TY - JOUR AU - Ma, B. AU - Zhang, K. AU - Liang, C. PY - 2005 DA - 2005// TI - An effective algorithm for peptide de novosequencing from MS/MS spectra JO - J Comput Syst Sci VL - 70 UR - https://doi.org/10.1016/j.jcss.2004.12.001 DO - 10.1016/j.jcss.2004.12.001 ID - Ma2005 ER - TY - JOUR AU - Fischer, B. AU - Roth, V. AU - Roos, F. AU - Grossmann, J. AU - Baginsky, S. AU - Widmayer, P. PY - 2005 DA - 2005// TI - NovoHMM: a hidden Markov model for de novo peptide sequencing JO - Anal Chem VL - 77 UR - https://doi.org/10.1021/ac0508853 DO - 10.1021/ac0508853 ID - Fischer2005 ER - TY - JOUR AU - DiMaggio, P. A. AU - Floudas, C. A. PY - 2007 DA - 2007// TI - De novo peptide identification via tandem mass spectrometry and integer linear optimization JO - Anal Chem VL - 79 UR - https://doi.org/10.1021/ac0618425 DO - 10.1021/ac0618425 ID - DiMaggio2007 ER - TY - JOUR AU - Bertsch, A. AU - Leinenbach, A. AU - Pervukhin, A. AU - Lubeck, M. AU - Hartmer, R. AU - Baessmann, C. PY - 2009 DA - 2009// TI - De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation JO - Electrophoresis VL - 30 UR - https://doi.org/10.1002/elps.200900332 DO - 10.1002/elps.200900332 ID - Bertsch2009 ER - TY - JOUR AU - Matthiesen, R. PY - 2007 DA - 2007// TI - Methods, algorithms and tools in computational proteomics: A practical point of view JO - Proteomics VL - 7 UR - https://doi.org/10.1002/pmic.200700116 DO - 10.1002/pmic.200700116 ID - Matthiesen2007 ER - TY - JOUR AU - Seidler, J. AU - Zinn, N. AU - Boehm, M. E. AU - Lehmann, W. D. PY - 2009 DA - 2009// TI - De novo Sequencing of Peptides by Tandem Mass Spectrometry JO - Proteomics VL - 10 UR - https://doi.org/10.1002/pmic.200900459 DO - 10.1002/pmic.200900459 ID - Seidler2009 ER - TY - JOUR AU - Pevtsov, S. AU - Fedulova, I. AU - Mirzaei, H. AU - Buck, C. AU - Zhang, X. PY - 2006 DA - 2006// TI - Performance evaluation of existing de novo sequencing algorithms JO - J Proteome Res VL - 5 UR - https://doi.org/10.1021/pr060222h DO - 10.1021/pr060222h ID - Pevtsov2006 ER - TY - JOUR AU - Pitzer, E. AU - Masselot, A. AU - Colinge, J. PY - 2007 DA - 2007// TI - Assessing peptide de novo sequencing algorithms performance on large and diverse data sets JO - Proteomics VL - 7 UR - https://doi.org/10.1002/pmic.200700224 DO - 10.1002/pmic.200700224 ID - Pitzer2007 ER - TY - JOUR AU - Kohlbacher, O. AU - Reinert, K. AU - Gropl, C. AU - Lange, E. AU - Pfeifer, N. AU - Schulz-Trieglaff, O. PY - 2007 DA - 2007// TI - TOPP--the OpenMS proteomics pipeline JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl299 DO - 10.1093/bioinformatics/btl299 ID - Kohlbacher2007 ER - TY - JOUR AU - Sturm, M. AU - Bertsch, A. AU - Gropl, C. AU - Hildebrandt, A. AU - Hussong, R. AU - Lange, E. PY - 2008 DA - 2008// TI - OpenMS - an open-source software framework for mass spectrometry JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-163 DO - 10.1186/1471-2105-9-163 ID - Sturm2008 ER - TY - JOUR AU - Zhang, N. AU - Aebersold, R. AU - Schwikowski, B. PY - 2002 DA - 2002// TI - ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data JO - Proteomics VL - 2 UR - https://doi.org/3.0.CO;2-9 DO - 3.0.CO;2-9 ID - Zhang2002 ER - TY - JOUR AU - Venable, J. D. AU - Yates, J. R. PY - 2004 DA - 2004// TI - Impact of ion trap tandem mass spectra variability on the identification of peptides JO - Anal Chem VL - 76 UR - https://doi.org/10.1021/ac0348219 DO - 10.1021/ac0348219 ID - Venable2004 ER - TY - JOUR AU - Frank, A. M. AU - Savitski, M. M. AU - Nielsen, M. L. AU - Zubarev, R. A. AU - Pevzner, P. A. PY - 2007 DA - 2007// TI - De novo peptide sequencing and identification with precision mass spectrometry JO - J Proteome Res VL - 6 UR - https://doi.org/10.1021/pr060271u DO - 10.1021/pr060271u ID - Frank2007 ER - TY - JOUR AU - Shevchenko, A. AU - Sunyaev, S. AU - Loboda, A. AU - Shevchenko, A. AU - Bork, P. AU - Ens, W. PY - 2001 DA - 2001// TI - Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching JO - Anal Chem VL - 73 UR - https://doi.org/10.1021/ac0013709 DO - 10.1021/ac0013709 ID - Shevchenko2001 ER - TY - JOUR AU - Mackey, A. J. AU - Haystead, T. A. AU - Pearson, W. R. PY - 2002 DA - 2002// TI - Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences JO - Mol Cell Proteomics VL - 1 UR - https://doi.org/10.1074/mcp.M100004-MCP200 DO - 10.1074/mcp.M100004-MCP200 ID - Mackey2002 ER - TY - JOUR AU - Searle, B. C. AU - Dasari, S. AU - Turner, M. AU - Reddy, A. P. AU - Choi, D. AU - Wilmarth, P. A. PY - 2004 DA - 2004// TI - High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results JO - Anal Chem VL - 76 UR - https://doi.org/10.1021/ac035258x DO - 10.1021/ac035258x ID - Searle2004 ER - TY - JOUR AU - Searle, B. C. AU - Dasari, S. AU - Wilmarth, P. A. AU - Turner, M. AU - Reddy, A. P. AU - David, L. L. PY - 2005 DA - 2005// TI - Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm JO - J Proteome Res VL - 4 UR - https://doi.org/10.1021/pr049781j DO - 10.1021/pr049781j ID - Searle2005 ER - TY - JOUR AU - Han, Y. AU - Ma, B. AU - Zhang, K. PY - 2005 DA - 2005// TI - SPIDER: software for protein identification from sequence tags with de novo sequencing error JO - J Bioinform Comput Biol VL - 3 UR - https://doi.org/10.1142/S0219720005001247 DO - 10.1142/S0219720005001247 ID - Han2005 ER - TY - JOUR AU - Waridel, P. AU - Frank, A. AU - Thomas, H. AU - Surendranath, V. AU - Sunyaev, S. AU - Pevzner, P. PY - 2007 DA - 2007// TI - Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing JO - Proteomics VL - 7 UR - https://doi.org/10.1002/pmic.200700003 DO - 10.1002/pmic.200700003 ID - Waridel2007 ER - TY - JOUR AU - Tannu, N. S. AU - Hemby, S. E. PY - 2007 DA - 2007// TI - De novo protein sequence analysis of Macaca mulatta JO - BMC Genomics VL - 8 UR - https://doi.org/10.1186/1471-2164-8-270 DO - 10.1186/1471-2164-8-270 ID - Tannu2007 ER - TY - CHAP AU - Ma, B. AU - Lajoie, G. PY - 2009 DA - 2009// TI - De novo interpretation of tandem mass spectra BT - Curr Protoc Bioinformatics ID - Ma2009 ER - TY - JOUR AU - Grossmann, J. AU - Fischer, B. AU - Baerenfaller, K. AU - Owiti, J. AU - Buhmann, J. M. AU - Gruissem, W. PY - 2007 DA - 2007// TI - A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments JO - Proteomics VL - 7 UR - https://doi.org/10.1002/pmic.200700474 DO - 10.1002/pmic.200700474 ID - Grossmann2007 ER - TY - JOUR AU - Liu, Y. AU - Lamkemeyer, T. AU - Jakob, A. AU - Mi, G. AU - Zhang, F. AU - Nordheim, A. PY - 2006 DA - 2006// TI - Comparative proteome analyses of maize (Zea mays L.) primary roots prior to lateral root initiation reveal differential protein expression in the lateral root initiation mutant rum1 JO - Proteomics VL - 6 UR - https://doi.org/10.1002/pmic.200600145 DO - 10.1002/pmic.200600145 ID - Liu2006 ER - TY - JOUR AU - Cohen, Y. AU - Sackston, W. E. PY - 1973 DA - 1973// TI - Factors affecting infection of sunflowers by Plasmopara halstedii JO - Can J Bot VL - 51 UR - https://doi.org/10.1139/b73-003 DO - 10.1139/b73-003 ID - Cohen1973 ER - TY - JOUR AU - Spring, O. AU - Rozynek, B. AU - Zipper, R. PY - 1997 DA - 1997// TI - Leaf disk inoculation - a useful tool for selecting infections of sunflower downy mildew at low inoculum concentration, but inappropriate to pathotype characterization JO - J Phytopathol (Berl) VL - 145 UR - https://doi.org/10.1111/j.1439-0434.1997.tb00384.x DO - 10.1111/j.1439-0434.1997.tb00384.x ID - Spring1997 ER - TY - JOUR AU - Shevchenko, A. AU - Tomas, H. AU - Havlis, J. AU - Olsen, J. V. AU - Mann, M. PY - 2006 DA - 2006// TI - In-gel digestion for mass spectrometric characterization of proteins and proteomes JO - Nat Protoc VL - 1 UR - https://doi.org/10.1038/nprot.2006.468 DO - 10.1038/nprot.2006.468 ID - Shevchenko2006 ER -