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brianb's proteomics [104 articles]

Recent papers added to brianb's library classified by the tag proteomics. You can also see everyone's proteomics.
  • PatternLab for proteomics: a tool for differential shotgun proteomics
    BMC Bioinformatics, Vol. 9 (21 July 2008), 316.
    by Paulo C Carvalho, Juliana SG Fischer, Emily I Chen, John R Yates, Valmir C Barbosa
    posted to statistics proteomics bioinformatics by brianb on 2008-07-23 22:12:35 as **
  • Cleaning of raw peptide MS/MS spectra: improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise.
    Proteomics, Vol. 6, No. 19. (October 2006), pp. 5117-5131.
    by N Mujezinovic, G Raidl, JR Hutchins, JM Peters, K Mechtler, F Eisenhaber
    posted to proteomics fdr bioinformatics by brianb on 2008-07-23 21:21:42 as **
  • Surface Area of Reversed-Phase HPLC Columns
    Anal. Chem. (23 July 2008)
    by A Giaquinto, Zhaoxia Liu, Andrew Bach, Yuri Kazakevich
    posted to proteomics chromatography by brianb on 2008-07-23 16:17:16 as **
  • DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring
    J. Proteome Res. (17 July 2008)
    by David L Tabb, Ze-Qiang Ma, Daniel B Martin, Amy-Joan L Ham, Matthew C Chambers
    posted to proteomics bioinformatics by brianb on 2008-07-22 15:38:33 as **
  • Enhanced detection of low abundant human plasma proteins using a tandem IgY12-supermix immunoaffinity separation strategy
    Mol Cell Proteomics (15 July 2008), M800008-MCP200.
    by Wei-Jun Qian, David T Kaleta, Brianne O Petritis, Hongliang Jiang, Tao Liu, Xu Zhang, Heather M Mottaz, Susan M Varnum, David G Camp, Lei Huang, Xiangming Fang, Wei-Wei Zhang, Richard D Smith
    posted to proteomics plasma chromatography antibody by brianb on 2008-07-22 15:38:07 as **
  • Reductive Glutaraldehydation of Amine Groups for Identification of Protein N-termini
    J. Proteome Res. (18 July 2008)
    by Allison Russo, Nagarajan Chandramouli, Linqi Zhang, Haiteng Deng
    posted to proteomics fragmentation formaldehyde by brianb on 2008-07-22 15:36:17 as **
  • Application of Proteomic Tools To Detect the Nonspecificity of a Polyclonal Antibody against Lipoprotein Lipase
    J. Proteome Res. (17 July 2008)
    by Albert Casanovas, Montserrat Carrascal, Joaquín Abián, Dolores M López-Tejero, Miquel Llobera
    posted to proteomics antibody by brianb on 2008-07-22 15:35:15 as **
  • Multiple Reaction Monitoring of mTRAQ-Labeled Peptides Enables Absolute Quantification of Endogenous Levels of a Potential Cancer Marker in Cancerous and Normal Endometrial Tissues
    J. Proteome Res. (17 July 2008)
    by Leroi V Desouza, Adrian M Taylor, Wei Li, Marjorie S Minkoff, Alexander D Romaschin, Terence J Colgan, Michael KW Siu
    posted to quantitation proteomics by brianb on 2008-07-22 15:34:36 as **
  • Protein Interaction Data Set Highlighted with Human Ras-MAPK/PI3K Signaling Pathways
    J. Proteome Res. (15 July 2008)
    by Jian Wang, Yanzhi Yuan, Ying Zhou, Longhua Guo, Lingqiang Zhang, Xuezhang Kuai, Binwei Deng, Zhi Pan, Dong Li, Fuchu He
    posted to y2h proteomics modeling interaction by brianb on 2008-07-16 02:04:59 as **
  • Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects.
    Electrophoresis, Vol. 29, No. 13. (10 July 2008), pp. 2768-2778.
    by Benjamin J J Cargile, Joel R R Sevinsky, Amal S S Essader, Jerry P P Eu, James L L Stephenson
    posted to proteomics modeling electrophoresis bioinformatics by brianb on 2008-07-13 01:07:20 as **
  • Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites
    Nature Biotechnology, Vol. 26, No. 6. (25 May 2008), pp. 685-694.
    by Oliver Schilling, Christopher M Overall
    posted to ptm proteomics by brianb on 2008-07-07 05:22:54 as ** along with 1 person nedwards
  • Protease-catalysed protein splicing: a new post-translational modification?
    Trends in Biochemical Sciences, Vol. In Press, Corrected Proof
    by Ivana Saska, David J Craik
    posted to ptm proteomics by brianb on 2008-07-07 05:08:13 as **
  • Non-functional phosphorylations?
    Trends in Biochemical Sciences, Vol. In Press, Corrected Proof
    by Gustav E Lienhard
    posted to proteomics phosphorylation by brianb on 2008-07-07 05:04:15 as read along with 1 person neils
  • Deducing topology of protein-protein interaction networks from experimentally measured sub-networks
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Ling Yang, Thomas Vondriska, Zhangang Han, Robb Maclellan, James Weiss, Zhilin Qu
    posted to proteomics network modeling interaction by brianb on 2008-07-04 21:01:16 as ** along with 2 people renatomilani neils
  • A General System for Studying Protein−Protein Interactions in Gram-Negative Bacteria
    J. Proteome Res. (1 July 2008)
    by Dale A Pelletier, Gregory B Hurst, Linda J Foote, Patricia K Lankford, Catherine K Mckeown, Tse-Yuan Lu, Denise D Schmoyer, Manesh B Shah, Judson W Hervey, Hayes W Mcdonald, Brian S Hooker, William R Cannon, Don S Daly, Jason M Gilmore, Steven H Wiley, Deanna L Auberry, Yisong Wang, Frank W Larimer, Stephen J Kennel, Mitchel J Doktycz, Jennifer L Morrell-Falvey, Elizabeth T Owens, Michelle V Buchanan
    posted to proteomics interaction by brianb on 2008-07-03 22:37:36 as ** along with 1 person neils
  • Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases
    J. Proteome Res. (3 July 2008)
    by Sangtae Kim, Nitin Gupta, Pavel A Pevzner
    posted to proteomics fdr bioinformatics by brianb on 2008-07-03 16:08:04 as **
  • Quantitative Measurements of Protein Interactions in a Crowded Cellular Environment
    Anal. Chem. (3 July 2008)
    by Edwin Li, Jesse Placone, Mikhail Merzlyakov, Kalina Hristova
    posted to proteomics interaction fret by brianb on 2008-07-03 16:07:32 as ** along with 1 person marck
  • High confidence determination of specific protein-protein interactions using quantitative mass spectrometry.
    Current opinion in biotechnology (27 June 2008)
    by Michiel Vermeulen, Nina C C Hubner, Matthias Mann
    posted to quantitation proteomics interaction by brianb on 2008-07-03 16:06:53 as **
  • Protein microarrays for multiplex analysis of signal transduction pathways.
    Nat Med, Vol. 10, No. 12. (December 2004), pp. 1390-1396.
    by SM Chan, J Ermann, L Su, CG Fathman, PJ Utz
    posted to signaling proteomics modeling arrays by brianb on 2008-07-03 16:05:26 as ** along with 2 people and 2 groups kentsis breden FAB-lab SFUAntibodyResearch
  • Mass Spectrometry Analysis of Proteome-Wide Proteolytic Post-Translational Degradation of Proteins
    Anal. Chem. (26 June 2008)
    by Yufeng Shen, Kim K Hixson, Nikola Tolić, David G Camp, Samuel O Purvine, Ronald J Moore, Richard D Smith
    posted to ptm proteomics by brianb on 2008-07-03 16:04:53 as **
  • Phosphorylation-Specific MS/MS Scoring for Rapid and Accurate Phosphoproteome Analysis
    J. Proteome Res. (19 June 2008)
    by Samuel H Payne, Margaret Yau, Marcus B Smolka, Stephen Tanner, Huilin Zhou, Vineet Bafna
    posted to ptm proteomics phosphorylation fdr bioinformatics by brianb on 2008-07-03 16:04:33 as ** along with 1 person neils
  • Separating the Wheat from the Chaff: Unbiased Filtering of Background Tandem Mass Spectra Improves Protein Identification
    J. Proteome Res. (18 June 2008)
    by Magno Junqueira, Victor Spirin, Santana, Patrice Waridel, Vineeth Surendranath, Grigoriy Kryukov, Ivan Adzhubei, Henrik Thomas, Shamil Sunyaev, Andrej Shevchenko
    posted to proteomics fdr bioinformatics by brianb on 2008-07-03 16:03:43 as **
  • Digestion of Native Proteins for Proteomics Using a Thermocycler
    Anal. Chem. (26 June 2008)
    by Obolbek A Turapov, Galina V Mukamolova, Andrew R Bottrill, Michael K Pangburn
    posted to proteomics by brianb on 2008-07-03 15:59:19 as **
  • Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions.
    Analytica chimica acta, Vol. 618, No. 2. (23 June 2008), pp. 168-183.
    by J Toews, JC Rogalski, TJ Clark, J Kast
    posted to xlink ptm proteomics formaldehyde by brianb on 2008-07-03 15:58:40 as ** along with 1 person jyuh
  • An Immuno-Chemo-Proteomics Method for Drug Target Deconvolution
    J. Proteome Res. (1 July 2008)
    by Chaitanya Saxena, Eugene Zhen, Richard E Higgs, John E Hale
    posted to proteomics modeling by brianb on 2008-07-03 15:57:32 as **
  • Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences
    Nucl. Acids Res. (27 June 2008), gkn390.
    by S Pitre, C North, M Alamgir, M Jessulat, A Chan, X Luo, JR Green, M Dumontier, F Dehne, A Golshani
    posted to proteomics interaction bioinformatics by brianb on 2008-07-03 15:56:47 as ** along with 3 people renatomilani pansapiens neils
  • A multidimensional chromatography technology for in-depth phosphoproteome analysis.
    Molecular & cellular proteomics : MCP (11 April 2008)
    by Claudio P P Albuquerque, Marcus B B Smolka, Samuel H H Payne, Vineet Bafna, Jimmy Eng, Huilin Zhou
    posted to proteomics phosphorylation chromatography by brianb on 2008-06-22 22:23:07 as **
  • Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection.
    Molecular & cellular proteomics : MCP, Vol. 7, No. 5. (May 2008), pp. 971-980.
    by DE McNulty, RS Annan
    posted to proteomics phosphorylation chromatography by brianb on 2008-06-22 22:22:29 as **
  • Evaluation and Optimization of ZIC-HILIC-RP as an Alternative MudPIT Strategy
    J. Proteome Res., Vol. 6, No. 3. (2 March 2007), pp. 937-946.
    by PJ Boersema, N Divecha, AJR Heck, S Mohammed
    posted to proteomics chromatography by brianb on 2008-06-22 22:18:02 as **
  • Enhancing Peptide Identification Confidence by Combining Search Methods
    J. Proteome Res. (18 June 2008)
    by Gelio Alves, Wells W Wu, Guanghui Wang, Rong-Fong Shen, Yi-Kuo Yu
    posted to proteomics fdr bioinformatics by brianb on 2008-06-21 01:21:47 as **
  • Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions.
    Journal of mass spectrometry : JMS (28 April 2008)
    by Brent W W Sutherland, Judy Toews, Juergen Kast
    posted to proteomics interaction formaldehyde by brianb on 2008-06-20 03:55:39 as ** along with 1 person jyuh
  • Proteomic studies in animal models of diabetes
    PROTEOMICS - CLINICAL APPLICATIONS, Vol. 2, No. 5. (2008), pp. 654-669.
    by Svante Resjö, Karin Berger, Malin Fex, Ola Hansson
    posted to review proteomics diabetes by brianb on 2008-06-19 14:42:03 as **
  • Comparison of the Electron Capture Dissociation Fragmentation Behavior of Doubly and Triply Protonated Peptides from Trypsin, Glu-C, and Chymotrypsin Digestion
    J. Proteome Res. (13 June 2008)
    by Anastasia Kalli, Kristina Håkansson
    posted to proteomics fragmentation by brianb on 2008-06-14 00:30:07 as **
  • Validation of Endogenous Peptide Identifications Using a Database of Tandem Mass Spectra
    J. Proteome Res. (13 June 2008)
    by Maria Fälth, Marcus Svensson, Anna Nilsson, Karl Sköld, David Fenyö, Per E Andren
    posted to proteomics bioinformatics by brianb on 2008-06-14 00:29:34 as **
  • PhosphoScore: An Open-Source Phosphorylation Site Assignment Tool for MSn Data
    J. Proteome Res. (11 June 2008)
    by Brian E Ruttenberg, Trairak Pisitkun, Mark A Knepper, Jason D Hoffert
    posted to proteomics fdr bioinformatics by brianb on 2008-06-12 14:41:00 as ** along with 2 people woaizuqiu neils
  • Comprehensive Comparison of Collision Induced Dissociation and Electron Transfer Dissociation
    Anal. Chem. (10 June 2008)
    by Henrik Molina, Rune Matthiesen, Kumaran Kandasamy, Akhilesh Pandey
    posted to proteomics fragmentation by brianb on 2008-06-12 14:34:03 as **
  • Mass spectrometric quantification of asparagine synthetase in circulating leukemia cells from acute lymphoblastic leukemia patients.
    Journal of proteomics, Vol. 71, No. 1. (30 April 2008), pp. 61-70.
    by SE Abbatiello, YX Pan, M Zhou, AS Wayne, TD Veenstra, SP Hunger, MS Kilberg, JR Eyler, NG Richards, TP Conrads
    posted to quantitation proteomics by brianb on 2008-06-12 14:32:35 as **
  • Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics
    BMC Bioinformatics, Vol. 8 (30 November 2007), 468.
    by Nico Pfeifer, Andreas Leinenbach, Christian G Huber, Oliver Kohlbacher
    posted to proteomics chromatography bioinformatics by brianb on 2008-06-09 13:25:46 as ** along with 1 person jyuh
  • OpenMS - An open-source software framework for mass spectrometry
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Marc Sturm, Andreas Bertsch, Clemens Groepl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole S Trieglaff, Alexandra Zerck, Knut Reinert, Oliver Kohlbacher
    posted to quantitation proteomics bioinformatics by brianb on 2008-06-09 13:23:59 as ** along with 4 people groepl olberd jyuh neils
  • Protein abundance profiling of the Escherichia coli cytosol
    BMC Genomics, Vol. 9 (27 February 2008), 102.
    by Yasushi Ishihama, Thorsten Schmidt, Juri Rappsilber, Matthias Mann, Ulrich F Hartl, Michael J Kerner, Dmitrij Frishman
    posted to quantitation proteomics by brianb on 2008-06-08 04:08:16 as ** along with 2 people Retchless osilander
  • Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification
    Mol Cell Proteomics (4 June 2008), M800218-MCP200.
    by Jacob D Jaffe, Hasmik Keshishian, Betty Chang, Theresa A Addona, Michael A Gillette, Steven A Carr
    posted to proteomics bioinformatics by brianb on 2008-06-08 02:55:53 as **
  • Protein Quantification by Selective Isolation and Fragmentation of Isotopic Pairs Using FT-ICR MS.
    Journal of the American Society for Mass Spectrometry (8 April 2008)
    by Hannah Johnson, Stephen C C Wong, Deborah M M Simpson, Robert J Beynon, Simon J J Gaskell
    posted to quantitation proteomics by brianb on 2008-06-06 21:37:26 as **
  • Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes.
    Nature protocols, Vol. 1, No. 2. (2006), pp. 1029-1043.
    by JM Pratt, DM Simpson, MK Doherty, J Rivers, SJ Gaskell, RJ Beynon
    posted to quantitation proteomics by brianb on 2008-06-06 20:34:41 as **
  • Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT.
    Molecular & cellular proteomics : MCP, Vol. 6, No. 8. (August 2007), pp. 1416-1427.
    by J Rivers, DM Simpson, DH Robertson, SJ Gaskell, RJ Beynon
    posted to quantitation proteomics by brianb on 2008-06-06 20:32:17 as **
  • Targeted comparative proteomics by liquid chromatography/matrix-assisted laser desorption/ionization triple-quadrupole mass spectrometry.
    Rapid communications in mass spectrometry : RCM, Vol. 20, No. 5. (2006), pp. 904-910.
    by JE Melanson, KA Chisholm, DM Pinto
    posted to quantitation proteomics formaldehyde by brianb on 2008-06-06 05:06:54 as **
  • High-coverage quantitative proteomics using amine-specific isotopic labeling.
    Proteomics, Vol. 6, No. 16. (August 2006), pp. 4466-4474.
    by JE Melanson, SL Avery, DM Pinto
    posted to quantitation proteomics formaldehyde by brianb on 2008-06-06 04:58:05 as **
  • Protein networks in disease
    Genome Res., Vol. 18, No. 4. (1 April 2008), pp. 644-652.
    by Trey Ideker, Roded Sharan
    posted to proteomics network modeling bioinformatics by brianb on 2008-06-05 05:07:23 as ** along with 19 people zwang balicea raiyar ptrobajo jfr paolomarcatili thomaskelder gracio schuylrp jyuh tmmurali Borelli jwdietrich frohike bootsy nedwards roys mclarenv phoenixzxl
  • NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways
    Nucl. Acids Res. (4 June 2008), gkn336.
    by Sylvain Brohee, Karoline Faust, Gipsi Lima-Mendez, Olivier Sand, Rekin's Janky, Gilles Vanderstocken, Yves Deville, Jacques van Helden
    posted to proteomics network modeling bioinformatics by brianb on 2008-06-05 04:57:45 as ** along with 2 people balicea neils
  • A two-stage differential hydrogen deuterium exchange method for the rapid characterization of protein/ligand interactions.
    Journal of biomolecular techniques : JBT, Vol. 18, No. 4. (September 2007), pp. 194-204.
    by MJ Chalmers, SA Busby, BD Pascal, MR Southern, PR Griffin
    posted to hdx proteomics interaction by brianb on 2008-06-05 04:47:07 as **
  • The Deuterator: Software for the determination of backbone amide deuterium levels from H/D exchange MS data
    BMC Bioinformatics, Vol. 8 (16 May 2007), 156.
    by Bruce D Pascal, Michael J Chalmers, Scott A Busby, Christopher C Mader, Mark R Southern, Nicholas F Tsinoremas, Patrick R Griffin
    posted to hdx proteomics interaction by brianb on 2008-06-04 22:31:24 as **
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