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	The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. [My Copy] Journal of proteome research, Vol. 7, No. 1. (January 2008), pp. 96-103. by J. Klimek, J. S. Eddes, L. Hohmann, et al.J. Jackson, A. Peterson, S. Letarte, P. R. Gafken, J. E. Katz, P. Mallick, H. Lee, A. Schmidt, R. Ossola, J. K. Eng, R. Aebersold, D. B. Martin posted by 3 people nedwards brianb guhjy
	Accurate annotation of peptide modifications through unrestrictive database search. [My Copy] Journal of proteome research, Vol. 7, No. 1. (January 2008), pp. 170-181. by S. Tanner, S. H. Payne, S. Dasari, et al.Z. Shen, P. A. Wilmarth, L. L. David, W. F. Loomis, S. P. Briggs, V. Bafna posted by 4 people brianb nedwards fishtank guhjy
	Dynamic modularity in protein interaction networks predicts breast cancer outcome. [My Copy] Nature biotechnology, Vol. 27, No. 2. (1 February 2009), pp. 199-204. by Ian W. Taylor, Rune Linding, David Warde-Farley, et al.Yongmei Liu, Catia Pesquita, Daniel Faria, Shelley Bull, Tony Pawson, Quaid Morris, Jeffrey L. Wrana posted by 16 people ukhan zufar guhjy jfr frohike fenghezi ptrobajo jaimie nedwards dakelley absterga cube_and_beyond phoenixzxl grahamc provero brianb
	Comparative LC-MS: A landscape of peaks and valleys [My Copy] PROTEOMICS, Vol. 8, No. 4. (February 2008), pp. 731-749. by Antoine H. P. America, Jan H. G. Cordewener posted by 5 people nedwards brianb talponer guhjy olberd
	Protein networks in disease. [My Copy] Genome research, Vol. 18, No. 4. (1 April 2008), pp. 644-652. by Trey Ideker, Roded Sharan posted by 28 people shikin carlk isimpson chica saket zufar kaarsinogen giovenko guhjy balicea tmmurali Borelli jwdietrich frohike bootsy nedwards roys mclarenv phoenixzxl brianb schuylrp jfr paolomarcatili gracio thomaskelder ptrobajo raiyar zwang
	Pathway-based biomarker search by high-throughput proteomics profiling of secretomes. [My Copy] Journal of proteome research, Vol. 8, No. 3. (March 2009), pp. 1489-1503. by Kevin Lawlor, Arpi Nazarian, Lynne Lacomis, Paul Tempst, Josep Villanueva posted by 5 people guhjy xingxu nedwards neils brianb
	Development and validation of a novel protein extraction methodology for quantitation of protein expression in formalin-fixed paraffin-embedded tissues using western blotting. [My Copy] The Journal of pathology, Vol. 217, No. 4. (1 March 2009), pp. 497-506. by Niroshini J. Nirmalan, Patricia Harnden, Peter J. Selby, Rosamonde E. Banks posted by 2 people guhjy brianb
	Estimating the size of the human interactome [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 19. (13 May 2008), pp. 6959-6964. by Michael P. H. Stumpf, Thomas Thorne, Eric de Silva, et al.Ronald Stewart, Hyeong J. An, Michael Lappe, Carsten Wiuf posted by 25 people aelef thegoose2 bicko C. elegans / WormBase tharris zwang chrissp100 sanchezbuelna guhjy phoenixzxl tmmurali neils paolomarcatili mjoach xingxu Ema cabbagesofdoom balicea marck friendpine brianb roys Evangelia dragonrez bpcusack
	Protein sequence tags: A novel solution for comparative proteomics [My Copy] PROTEOMICS, Vol. 5, No. 9. (2005), pp. 2364-2368. by Karsten Kuhn, Thorsten Prinz, Jürgen Schäfer, et al.Christian Baumann, Marco Schärfke, Stefan Kienle, Josef Schwarz, Sandra Steiner, Christian Hamon posted by 2 people brianb nedwards
	A Framework for the Automated Analysis of Subcellular Patterns in Human Protein Atlas Images [My Copy] J. Proteome Res. (25 April 2008) by Justin Newberg, Robert F. Murphy posted by 2 people brianb guhjy
	False Discovery Rates and Related Statistical Concepts in Mass Spectrometry-Based Proteomics [My Copy] Journal of Proteome Research, Vol. 7, No. 1. (1 January 2008), pp. 47-50. by Hyungwon Choi, Alexey I. Nesvizhskii posted by 5 people shikin brianb nedwards guhjy robert
	Evaluation of confidence and reproducibility in quantitative proteomics performed by a capillary isoelectric focusing-based proteomic platform coupled with a spectral counting approach [My Copy] ELECTROPHORESIS, Vol. 29, No. 14. (2008), pp. 3047-3054. by Brian M. Balgley, Weijie Wang, Tao Song, Xueping Fang, Li Yang, Cheng S. Lee posted by 3 people alyssaporter brianb nedwards
	Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses [My Copy] PROTEOMICS, Vol. 8, No. 14. (2008), pp. 2791-2797. by Alexander Scherl, Yihsuan S. Tsai, Scott A. Shaffer, David R. Goodlett posted by 3 people guhjy nedwards brianb
	Variations in DNA elucidate molecular networks that cause disease. [My Copy] Nature, Vol. 452, No. 7186. (27 March 2008), pp. 429-435. by Yanqing Chen, Jun Zhu, Pek Yee Y. Lum, et al.Xia Yang, Shirly Pinto, Douglas J. MacNeil, Chunsheng Zhang, John Lamb, Stephen Edwards, Solveig K. Sieberts, Amy Leonardson, Lawrence W. Castellini, Susanna Wang, Marie-France F. Champy, Bin Zhang, Valur Emilsson, Sudheer Doss, Anatole Ghazalpour, Steve Horvath, Thomas A. Drake, Aldons J. Lusis, Eric E. Schadt posted by 25 people mnishimu Zephyrus biomcgary daforerog roys druvus 4th_floor_JC nicklynch semrich brianb jbsaltz djkt raiyar lp2 jo_davies shikin caseybrown GeneGo ptrobajo guhjy echinotrix natstreet sanchezbuelna jfr chrisamiller
	A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 52. (30 December 2008), pp. 20870-20875. by Kasper Lage, Niclas T. Hansen, Olof E. Karlberg, et al.Aron C. Eklund, Francisco S. Roque, Patricia K. Donahoe, Zoltan Szallasi, Thomas S. Jensen, Søren Brunak posted by 5 people grahamc bertelsen brianb nedwards jfr
	An in vivo map of the yeast protein interactome. [My Copy] Science (New York, N.Y.), Vol. 320, No. 5882. (13 June 2008), pp. 1465-1470. by Kirill Tarassov, Vincent Messier, Christian R. Landry, et al.Stevo Radinovic, Mercedes M. Serna Molina, Igor Shames, Yelena Malitskaya, Jackie Vogel, Howard Bussey, Stephen W. Michnick posted by 9 people phoenixzxl lawraga cabbagesofdoom guhjy neils aubinhon brianb tmmurali grahamc
	Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions. [My Copy] Journal of mass spectrometry : JMS (28 April 2008) by Brent W W. Sutherland, Judy Toews, Juergen Kast posted by 2 people guhjy brianb
	Evaluation of archival time on shotgun proteomics of formalin-fixed and paraffin-embedded tissues. [My Copy] Journal of proteome research, Vol. 8, No. 2. (February 2009), pp. 917-925. by Brian M. Balgley, Tong Guo, Kejia Zhao, Xueping Fang, Fattaneh A. Tavassoli, Cheng S. Lee posted by 2 people guhjy brianb
	Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS Instruments [My Copy] Anal. Chem. (15 October 2008) by Aleksey V. Tolmachev, Matthew E. Monroe, Samuel O. Purvine, et al.Ronald J. Moore, Navdeep Jaitly, Joshua N. Adkins, Gordon A. Anderson, Richard D. Smith posted by 3 people guhjy nedwards brianb
	A systems biology approach to drug discovery. [My Copy] Advances in genetics, Vol. 60 (2008), pp. 603-635. by J. Zhu, B. Zhang, E. E. Schadt posted by 4 people flbarroso ocs brianb guhjy
	Tissue-Specific Expression and Post-Translational Modification of Histone H3 Variants [My Copy] J. Proteome Res., Vol. 7, No. 10. (3 October 2008), pp. 4225-4236. by Benjamin A. Garcia, Eric C. Thomas, Neil L. Kelleher, Craig A. Mizzen posted by 2 people brianb nedwards
	Elevated hydrostatic pressure promotes protein recovery from formalin-fixed, paraffin-embedded tissue surrogates [My Copy] Laboratory Investigation, Vol. aop, No. current. by Carol B. Fowler, Robert E. Cunningham, Timothy J. Waybright, et al.Josip Blonder, Timothy D. Veenstra, Timothy J. O'Leary, Jeffrey T. Mason posted by 2 people brianb guhjy
	The properties of high-dimensional data spaces: implications for exploring gene and protein expression data [My Copy] Nat Rev Cancer, Vol. 8, No. 1. (01 January 2008), pp. 37-49. by Robert Clarke, Habtom W. Ressom, Antai Wang, et al.Jianhua Xuan, Minetta C. Liu, Edmund A. Gehan, Yue Wang posted by 19 people Zephyrus aviad_work ipark-kaist isimpson Scis0000002 baizhang bertelsen ptrobajo jfr guhjy tmmurali dwf frohike cjeans nedwards Bioinformatics shikin blackm0k brianb
	N-Glycoproteomics - An automated workflow approach [My Copy] Glycobiology, Vol. 18, No. 4. (1 April 2008), pp. 339-349. by Sakari Joenvaara, Ilja Ritamo, Hannu Peltoniemi, Risto Renkonen posted by 3 people nedwards Terkko guhjy
	The Deuterator: Software for the determination of backbone amide deuterium levels from H/D exchange MS data [My Copy] BMC Bioinformatics, Vol. 8 (16 May 2007), 156. by Bruce D. Pascal, Michael J. Chalmers, Scott A. Busby, et al.Christopher C. Mader, Mark R. Southern, Nicholas F. Tsinoremas, Patrick R. Griffin posted by 2 people nedwards brianb
	Improved Sequence Tag Generation Method for Peptide Identification in Tandem Mass Spectrometry [My Copy] J. Proteome Res. (12 September 2008) by Xia Cao, Alexey I. Nesvizhskii posted by 2 people nedwards brianb
	Label-Free Protein Quantification Using LC-Coupled Ion Trap or FT Mass Spectrometry: Reproducibility, Linearity, and Application with Complex Proteomes [My Copy] Journal of Proteome Research, Vol. 5, No. 5. (1 May 2006), pp. 1214-1223. by Guanghui Wang, Wells W. Wu, Weihua Zeng, Chung-Lin Chou, Rong-Fong Shen posted by 3 people brianb nedwards nuin
	Peptide Sequence Confidence in Accurate Mass and Time Analysis and Its Use in Complex Proteomics Experiments [My Copy] J. Proteome Res. (28 October 2008) by Damon May, Yan Liu, Wendy Law, et al.Matt Fitzgibbon, Hong Wang, Samir Hanash, Martin Mcintosh posted by 3 people nedwards brianb neils
	Top-Down Identification of Protein Biomarkers in Bacteria with Unsequenced Genomes. [My Copy] Analytical chemistry, Vol. 0, No. 0. (2 November 2009) by Colin Wynne, Catherine Fenselau, Plamen A. Demirev, Nathan Edwards posted by 3 people gjuggler brianb nedwards
	DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring [My Copy] J. Proteome Res. (17 July 2008) by David L. Tabb, Ze-Qiang Ma, Daniel B. Martin, Amy-Joan L. Ham, Matthew C. Chambers posted by 2 people nedwards brianb
	Reduction of dynamic protein concentration range of biological extracts for the discovery of low-abundance proteins by means of hexapeptide ligand library [My Copy] Nat. Protocols, Vol. 3, No. 5. (April 2008), pp. 883-890. by Luc Guerrier, Pier G. Righetti, Egisto Boschetti posted by 2 people brianb guhjy
	PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. [My Copy] EMBO reports, Vol. 9, No. 5. (May 2008), pp. 429-434. by E. W. Deutsch, H. Lam, R. Aebersold posted by 3 people druvus brianb guhjy
	TandTRAQ: an open-source tool for integrated protein identification and quantitation. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 24. (15 December 2007), pp. 3394-3396. by T. Laderas, C. Bystrom, D. McMillen, G. Fan, S. McWeeney posted by 2 people guhjy brianb
	Proteomics FASTA archive and reference resource. [My Copy] Proteomics, Vol. 8, No. 9. (May 2008), pp. 1756-1757. by J. A. Falkner, J. A. Hill, P. C. Andrews posted by 2 people brianb guhjy
	Interpreting Top-Down Mass Spectra Using Spectral Alignment [My Copy] Analytical Chemistry, Vol. 80, No. 7. (1 April 2008), pp. 2499-2505. by Ari M. Frank, James J. Pesavento, Craig A. Mizzen, Neil L. Kelleher, Pavel A. Pevzner posted by 4 people nedwards alexgeorgiou guhjy brianb
	Tools for analyzing and predicting N-terminal protein modifications [My Copy] PROTEOMICS, Vol. 8, No. 4. (February 2008), pp. 626-649. by Thierry Meinnel, Carmela Giglione posted by 2 people nedwards guhjy
	Multiple Reaction Monitoring-based, Multiplexed, Absolute Quantitation of 45 Proteins in Human Plasma [My Copy] Mol Cell Proteomics, Vol. 8, No. 8. (1 August 2009), pp. 1860-1877. by Michael A. Kuzyk, Derek Smith, Juncong Yang, et al.Tyra J. Cross, Angela M. Jackson, Darryl B. Hardie, N. Leigh Anderson, Christoph H. Borchers posted by 4 people guhjy fishtank williamgunn brianb
	Mass Spectrometry Analysis of Proteome-Wide Proteolytic Post-Translational Degradation of Proteins [My Copy] Anal. Chem. (26 June 2008) by Yufeng Shen, Kim K. Hixson, Nikola Tolić, et al.David G. Camp, Samuel O. Purvine, Ronald J. Moore, Richard D. Smith posted by 3 people guhjy nedwards brianb
	Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases [My Copy] Journal of Proteome Research, Vol. 7, No. 8. (1 August 2008), pp. 3354-3363. by Sangtae Kim, Nitin Gupta, Pavel A. Pevzner posted by 5 people stefanorb nedwards simonhubbard guhjy brianb
	Dissection of the insulin signaling pathway via quantitative phosphoproteomics [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 7. (19 February 2008), pp. 2451-2456. by Marcus KrÃ¼ger, Irina Kratchmarova, Blagoy Blagoev, Yu-Hua Tseng, C. Ronald Kahn, Matthias Mann posted by 4 people guhjy renatomilani Evangelia brianb
	OpenMS - an open-source software framework for mass spectrometry. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008) by M. Sturm, A. Bertsch, C. Gröpl, et al.A. Hildebrandt, R. Hussong, E. Lange, N. Pfeifer, O. Schulz-Trieglaff, A. Zerck, K. Reinert, O. Kohlbacher posted by 8 people alyssaporter robert nedwards guhjy neils brianb olberd groepl
	Error bars in experimental biology [My Copy] J. Cell Biol., Vol. 177, No. 1. (9 April 2007), pp. 7-11. by Geoff Cumming, Fiona Fidler, David L. Vaux posted by 62 people Jporci pjmaybank inbetweener tt srmblack abhishek_tiwari druvus bangyuzhou schoeband brianb cambray dbikard rec3141 ajaymalik Gorzomagnificent daforerog sen_cheng yangjustinc maximilianh qwermish bayesian ntakano flips inesdesantiago brian ana batallah manduca kuhn Borelli dayjm kristina chad_davis tny dullhunk rabu lechristophe nelmor jdelcampo fishtank emmahe lisa1 Daria_G devender bmaust cabbagezs natstreet winterschlaefer krokicki loopback007 structural_bioinformatics Bioinformatics VisionLab FlowCytometry Microbial-Ecology wilbur tdmckee renatomilani delenca arindrartow guhjy mjoach
	Nonlinear Fitting Method for Determining Local False Discovery Rates from Decoy Database Searches [My Copy] J. Proteome Res. (14 August 2008) by Wilfred H. Tang, Ignat V. Shilov, Sean L. Seymour posted by 2 people nedwards brianb
	Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. [My Copy] Molecular & cellular proteomics : MCP (25 November 2008) by Ralph Schiess, Lukas N N. Mueller, Alexander Schmidt, Markus Mueller, Bernd Wollscheid, Ruedi Aebersold posted by 3 people nedwards guhjy brianb
	Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics [My Copy] BMC Bioinformatics, Vol. 8 (30 November 2007), 468. by Nico Pfeifer, Andreas Leinenbach, Christian G. Huber, Oliver Kohlbacher posted by 2 people brianb guhjy
	Real-Time DNA Sequencing from Single Polymerase Molecules [My Copy] Science, Vol. 323, No. 5910. (2 January 2009), pp. 133-138. by John Eid, Adrian Fehr, Jeremy Gray, et al.Khai Luong, John Lyle, Geoff Otto, Paul Peluso, David Rank, Primo Baybayan, Brad Bettman, Arkadiusz Bibillo, Keith Bjornson, Bidhan Chaudhuri, Frederick Christians, Ronald Cicero, Sonya Clark, Ravindra Dalal, Alex deWinter, John Dixon, Mathieu Foquet, Alfred Gaertner, Paul Hardenbol, Cheryl Heiner, Kevin Hester, David Holden, Gregory Kearns, Xiangxu Kong, Ronald Kuse, Yves Lacroix, Steven Lin, Paul Lundquist, Congcong Ma, Patrick Marks, Mark Maxham, Devon Murphy, Insil Park, Thang Pham, Michael Phillips, Joy Roy, Robert Sebra, Gene Shen, Jon Sorenson, Austin Tomaney, Kevin Travers, Mark Trulson, John Vieceli, Jeffrey Wegener, Dawn Wu, Alicia Yang, Denis Zaccarin, Peter Zhao, Frank Zhong, Jonas Korlach, Stephen Turner posted by 42 people hzoltan operon n00c kinestetika mtagaya iSEEM jlgreen dna idoerg absterga lukzky ImranRaoufMalik Archaeogenetics inesdesantiago 7ac5 wimufi cactus jasontsai mlangill melting polivares pkonings natstreet fhalbrit druvus felsani moernerlab samjlord Bioinformatics - CRUK Stew ghattem nedwards myzhang pengchy jbhiatt GeeSharpMinor GustavoLacerda azazello sconlan alexknight emptyhb caseybrown
	Linear Discriminant Analysis-Based Estimation of the False Discovery Rate for Phosphopeptide Identifications [My Copy] J. Proteome Res. (19 April 2008) by Xiuxia Du, Feng Yang, Nathan P. Manes, et al.David L. Stenoien, Matthew E. Monroe, Joshua N. Adkins, David J. States, Samuel O. Purvine, Ii Camp, Richard D. Smith posted by 3 people neils brianb nedwards
	Automated de novo protein sequencing of monoclonal antibodies [My Copy] Nature Biotechnology, Vol. 26, No. 12., pp. 1336-1338. by Nuno Bandeira, Victoria Pham, Pavel Pevzner, David Arnott, Jennie R. Lill posted by 4 people pineapple brianb nedwards fgibson
	Genetics of gene expression and its effect on disease. [My Copy] Nature, Vol. 452, No. 7186. (27 March 2008), pp. 423-428. by Valur Emilsson, Gudmar Thorleifsson, Bin Zhang, et al.Amy S. Leonardson, Florian Zink, Jun Zhu, Sonia Carlson, Agnar Helgason, G. Bragi Walters, Steinunn Gunnarsdottir, Magali Mouy, Valgerdur Steinthorsdottir, Gudrun H. Eiriksdottir, Gyda Bjornsdottir, Inga Reynisdottir, Daniel Gudbjartsson, Anna Helgadottir, Aslaug Jonasdottir, Adalbjorg Jonasdottir, Unnur Styrkarsdottir, Solveig Gretarsdottir, Kristinn P. Magnusson, Hreinn Stefansson, Ragnheidur Fossdal, Kristleifur Kristjansson, Hjortur G. Gislason, Tryggvi Stefansson, Bjorn G. Leifsson, Unnur Thorsteinsdottir, John R. Lamb, Jeffrey R. Gulcher, Marc L. Reitman, Augustine Kong, Eric E. Schadt, Kari Stefansson posted by 23 people nicholso Zephyrus greg daforerog athma zufar druvus 4th_floor_JC brianb djkt lp2 jo_davies shikin caseybrown GeneGo ptrobajo vplagnol smbe2008 echinotrix natstreet sanchezbuelna guhjy Borelli
	Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol. [My Copy] Genome research, Vol. 19, No. 1. (January 2009), pp. 128-135. by Sébastien Gallien, Emmanuel Perrodou, Christine Carapito, et al.Caroline Deshayes, Jean-Marc M. Reyrat, Alain Van Dorsselaer, Olivier Poch, Christine Schaeffer, Odile Lecompte posted by 2 people nedwards guhjy
	Enhancing Peptide Identification Confidence by Combining Search Methods [My Copy] J. Proteome Res. (18 June 2008) by Gelio Alves, Wells W. Wu, Guanghui Wang, Rong-Fong Shen, Yi-Kuo Yu posted by 2 people nedwards brianb
	An Unsupervised, Model-Free, Machine-Learning Combiner for Peptide Identifications from Tandem Mass Spectra [My Copy] Clinical Proteomics by Nathan Edwards, Xue Wu, Chau-Wen Tseng posted by 2 people nedwards brianb
	The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results. [My Copy] BMC Bioinformatics, Vol. 9 (09 December 2008), 529. by John, Rembert Pieper posted by 7 people brianb nedwards robert nuin guhjy sjcockell braistedj
	Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. [My Copy] Molecular & cellular proteomics : MCP, Vol. 8, No. 8. (24 August 2009), pp. 1988-1998. by Robert W. Sprung, Jonathan W. Brock, Jarred P. Tanksley, et al.Ming Li, Mary Kay K. Washington, Robbert J. Slebos, Daniel C. Liebler posted by 3 people csimmons guhjy brianb
	A perfect genome annotation is within reach with the proteomics and genomics alliance [My Copy] Current Opinion in Microbiology, Vol. 12, No. 3. (4 June 2009), pp. 292-300. by Jean Armengaud posted by 3 people brianb nedwards guhjy
	Top-Down Protein Identification/Characterization of a Priori Unknown Proteins via Ion Trap Collision-Induced Dissociation and Ion/Ion Reactions in a Quadrupole/Time-of-Flight Tandem Mass Spectrometer [My Copy] Analytical Chemistry, Vol. 81, No. 4. (15 February 2009), pp. 1433-1441. by Jian Liu, Teng-Yi Huang, Scott A. Mcluckey posted by 2 people brianb nedwards
	Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments [My Copy] Brief Bioinform, Vol. 9, No. 2. (1 March 2008), pp. 156-165. by Jason W. H. Wong, Matthew J. Sullivan, Gerard Cagney posted by 5 people brianb nedwards guhjy neils olberd
	Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites [My Copy] Nature Biotechnology, Vol. 26, No. 6. (25 May 2008), pp. 685-694. by Oliver Schilling, Christopher M. Overall posted by 3 people guhjy brianb nedwards
	Performance of Combinatorial Peptide Libraries in Capturing the Low-Abundance Proteome of Red Blood Cells. 1. Behavior of Mono- to Hexapeptides [My Copy] Anal. Chem. (10 April 2008) by Carolina Simó, Angela Bachi, Angela Cattaneo, et al.Luc Guerrier, Frederic Fortis, Egisto Boschetti, Alexander Podtelejnikov, Pier G. Righetti posted by 2 people guhjy brianb
	Improving Protein Identification Sensitivity by Combining MS and MS/MS Information for Shotgun Proteomics Using LTQ-Orbitrap High Mass Accuracy Data [My Copy] Anal. Chem., Vol. 80, No. 6. (15 March 2008), pp. 2018-2025. by B. Lu, A. Motoyama, C. Ruse, J. Venable, J. R. Yates posted by 4 people fishtank guhjy nedwards brianb
	A Fast SEQUEST Cross Correlation Algorithm [My Copy] J. Proteome Res. (6 September 2008) by Jimmy K. Eng, Bernd Fischer, Jonas Grossmann, Michael J. Maccoss posted by 4 people alexgeorgiou fishtank nedwards brianb
	Off-Line Two-Dimensional Liquid Chromatography with Maximized Sample Loading to Reversed-Phase Liquid Chromatography-Electrospray Ionization Tandem Mass Spectrometry for Shotgun Proteome Analysis [My Copy] Analytical Chemistry, Vol. 81, No. 3. (1 February 2009), pp. 1049-1060. by Nan Wang, Chuanhui Xie, J. Bryce Young, Liang Li posted by 2 people brianb nedwards
	mzML: A single, unifying data format for mass spectrometer output [My Copy] PROTEOMICS, Vol. 8, No. 14. (2008), pp. 2776-2777. by Eric Deutsch posted by 4 people moonhouse guhjy brianb nedwards
	Calibrating E-values for MS2 database search methods [My Copy] Biology Direct, Vol. 2 (05 November 2007), 26. by Gelio Alves, Aleksey Y. Ogurtsov, Wells W. Wu, Guanghui Wang, Rong-Fong Shen, Yi-Kuo Yu posted by 2 people nedwards brianb
	Modelling and analysis of gene regulatory networks [My Copy] Nat Rev Mol Cell Biol, Vol. 9, No. 10. (October 2008), pp. 770-780. by Guy Karlebach, Ron Shamir posted by 15 people antonkratz agonzale cannin tklee aviad_work kaarsinogen thomaskelder fgibson druvus balicea brianb nedwards dakelley guhjy tmmurali
	Crosstalk among Histone Modifications [My Copy] Vol. 135, No. 4. (14 November 2008), pp. 604-607. by Tamaki Suganuma, Jerry L. Workman posted by 2 people brianb nedwards
	A suite of Perl modules for handling microarray data. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 8. (15 April 2008), pp. 1102-1103. by J. A. Morris, S. A. Gayther, I. J. Jacobs, C. Jones posted by 8 people isimpson neils daforerog guhjy wisdom_love brianb jfr AlexanderPico
	DAnTE: a statistical tool for quantitative analysis of -omics data [My Copy] Bioinformatics (3 May 2008), btn217. by Ashoka D. Polpitiya, Wei-Jun Qian, Navdeep Jaitly, et al.Vladislav A. Petyuk, Joshua N. Adkins, David G. Camp, Gordon A. Anderson, Richard D. Smith posted by 5 people robert guhjy brianb renatomilani GeeSharpMinor
	False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule [My Copy] Journal of Proteome Research, Vol. 8, No. 9. (4 September 2009), pp. 4173-4181. by Nitin Gupta, Pavel A. Pevzner posted by 4 people gjuggler nedwards carlosjavierna brianb
	Alignment of LC-MS images, with applications to biomarker discovery and protein identification. [My Copy] Proteomics, Vol. 8, No. 4. (February 2008), pp. 650-672. by Mathias Vandenbogaert, Sébastien Li-Thiao-Té, Hans-Michael M. Kaltenbach, Runxuan Zhang, Tero Aittokallio, Benno Schwikowski posted by 3 people nedwards guhjy olberd
	Versatile Online−Offline Engine for Automated Acquisition of High-Resolution Tandem Mass Spectra [My Copy] Analytical Chemistry, Vol. 80, No. 21. (1 November 2008), pp. 8055-8063. by Craig D. Wenger, Michael T. Boyne, Jonathan T. Ferguson, Dana E. Robinson, Neil L. Kelleher posted by 2 people nedwards brianb
	Proteogenomics: needs and roles to be filled by proteomics in genome annotation [My Copy] Brief Funct Genomic Proteomic, Vol. 7, No. 1. (1 January 2008), pp. 50-62. by Charles Ansong, Samuel O. Purvine, Joshua N. Adkins, Mary S. Lipton, Richard D. Smith posted by 1 person nedwards
	Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs [My Copy] Nature Biotechnology, Vol. 25, No. 6., pp. 651-655. by Jan Eriksson, David Fenyö posted by 4 people guhjy grahamc nedwards brianb
	Efficient High-Throughput Discovery of Large Peptidic Hormones and Biomarkers [My Copy] J. Proteome Res., Vol. 5, No. 7. (7 July 2006), pp. 1776-1784. by S. W. Taylor, N. L. Andon, J. M. Bilakovics, et al.C. Lowe, M. R. Hanley, R. Pittner, S. S. Ghosh posted by 2 people brianb nedwards
	Computational verification of protein-protein interactions by orthologous co-expression. [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005) by I. Tirosh, N. Barkai posted by 7 people brianb nedwards marcius conkymacro bluto BioinfoCIPF SGU-CIPF
	Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra [My Copy] Mol Cell Proteomics (14 August 2008), M800103-MCP200. by Sangtae Kim, Nitin Gupta, Nuno Bandeira, Pavel A. Pevzner posted by 3 people alexgeorgiou nedwards brianb
	High confidence determination of specific protein–protein interactions using quantitative mass spectrometry [My Copy] Current Opinion in Biotechnology, Vol. 19, No. 4. (27 August 2008), pp. 331-337. by Michiel Vermeulen, Nina C. Hubner, Matthias Mann posted by 3 people flbarroso guhjy brianb
	Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins [My Copy] Nat Biotech, Vol. 27, No. 4. (April 2009), pp. 378-386. by Bernd Wollscheid, Damaris Bausch-Fluck, Christine Henderson, et al.Robert O'Brien, Miriam Bibel, Ralph Schiess, Ruedi Aebersold, Julian D. Watts posted by 4 people GeeSharpMinor chemnerd1 brianb absterga
	Hierarchical structure and the prediction of missing links in networks [My Copy] Nature, Vol. 453, No. 7191. (01 May 2008), pp. 98-101. by Aaron Clauset, Cristopher Moore, M. E. J. Newman posted by 47 people ipark-kaist carlk gtgt15 saket wei_tang Kovanen diamantis cfelipesp orahcio rcrane kubyaddi pbull Ema jago cmor balicea kengg jjray soramame_0518 deanmalmgren briordan hryk tny AbnerCYH cactus tmmurali akshat bryanhughes gagliol margaritis guhjy craigwilson06 cmmorel eyliu markusd elsantosneto pinney i-stevenson fbaroni nedwards apwesolowski Borelli ptrobajo dpf rds lfriedl sen_cheng
	Low Cost, Scalable Proteomics Data Analysis Using Amazon’s Cloud Computing Services and Open Source Search Algorithms [My Copy] Journal of Proteome Research, Vol. 8, No. 6. (5 June 2009), pp. 3148-3153. by Brian D. Halligan, Joey F. Geiger, Andrew K. Vallejos, Andrew S. Greene, Simon N. Twigger posted by 6 people walshtp Scis0000002 nedwards sjcockell neils brianb
	Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. [My Copy] Nature, Vol. 460, No. 7256. (6 August 2009), pp. 762-765. by Johan Malmström, Martin Beck, Alexander Schmidt, Vinzenz Lange, Eric W. Deutsch, Ruedi Aebersold posted by 5 people brianb sjcockell roys jbhiatt absterga
	Universal sample preparation method for proteome analysis [My Copy] Nat Meth, Vol. 6, No. 5. (19 April 2009), pp. 359-362. by Jacek R. Wisniewski, Alexandre Zougman, Nagarjuna Nagaraj, Matthias Mann posted by 6 people ericsuh Yanno guhjy mhiromi absterga brianb
	Comparative Evaluation of Tandem MS Search Algorithms Using a Target-Decoy Search Strategy [My Copy] Mol Cell Proteomics, Vol. 6, No. 9. (1 September 2007), pp. 1599-1608. by Brian M. Balgley, Tom Laudeman, Li Yang, Tao Song, Cheng S. Lee posted by 3 people brianb robert nedwards
	Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling [My Copy] Genomics (04 August 2009) by Lisa Roberts, Jessica Bowers, Kelly Sensinger, Andrew Lisowski, Robert Getts, Mark G. Anderson posted by 2 people brianb guhjy
	Comprehensive yeast proteome analysis using a capillary isoelectric focusing-based multidimensional separation platform coupled with ESI-MS/MS [My Copy] PROTEOMICS, Vol. 7, No. 8. (2007), pp. 1178-1187. by Weijie Wang, Tong Guo, Tao Song, Cheng S. Lee, Brian M. Balgley posted by 2 people brianb nedwards
	Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues. [My Copy] Journal of proteome research, Vol. 7, No. 3. (March 2008), pp. 1098-1108. by H. Xu, L. Yang, W. Wang, et al.S. R. Shi, C. Liu, Y. Liu, X. Fang, C. R. Taylor, C. S. Lee, B. M. Balgley posted by 2 people brianb guhjy
	How Much Peptide Sequence Information Is Contained in Ion Trap Tandem Mass Spectra? [My Copy] Journal of the American Society for Mass Spectrometry (7 August 2008) by Jürgen Cox, Nina C C. Hubner, Matthias Mann posted by 4 people yylin guhjy nedwards brianb
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	Toward a confocal subcellular atlas of the human proteome. [My Copy] Molecular & cellular proteomics : MCP, Vol. 7, No. 3. (March 2008), pp. 499-508. by L. Barbe, E. Lundberg, P. Oksvold, et al.A. Stenius, E. Lewin, E. Björling, A. Asplund, F. Pontén, H. Brismar, M. Uhlén, H. Andersson-Svahn posted by 2 people brianb guhjy
	A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. [My Copy] Genome research, Vol. 19, No. 2. (17 February 2009), pp. 284-293. by G. Mittler, F. Butter, M. Mann posted by 6 people xingxu absterga Koch_Lab skoch3 guhjy brianb
	Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions. [My Copy] Analytica chimica acta, Vol. 618, No. 2. (23 June 2008), pp. 168-183. by J. Toews, J. C. Rogalski, T. J. Clark, J. Kast posted by 2 people guhjy brianb
	Cleaning of raw peptide MS/MS spectra: improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise. [My Copy] Proteomics, Vol. 6, No. 19. (October 2006), pp. 5117-5131. by N. Mujezinovic, G. Raidl, J. R. Hutchins, J. M. Peters, K. Mechtler, F. Eisenhaber posted by 2 people nedwards brianb
	Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium Deinococcus deserti [My Copy] PLoS Genet, Vol. 5, No. 3. (27 March 2009), e1000434. by Arjan de Groot, Rémi Dulermo, Philippe Ortet, et al.Laurence Blanchard, Philippe Guérin, Bernard Fernandez, Benoit Vacherie, Carole Dossat, Edmond Jolivet, Patricia Siguier, Michael Chandler, Mohamed Barakat, Alain Dedieu, Valérie Barbe, Thierry Heulin, Suzanne Sommer, Wafa Achouak, Jean Armengaud posted by 1 person nedwards
	Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila [My Copy] Genome Research, Vol. 19, No. 5. (May 2009), pp. 886-896. by Geoffrey D. Findlay, Michael J. MacCoss, Willie J. Swanson posted by 1 person nedwards
	Protein quantification across hundreds of experimental conditions [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 37. (15 September 2009), pp. 15544-15548. by Zia Khan, Joshua S. Bloom, Benjamin A. Garcia, Mona Singh, Leonid Kruglyak posted by 6 people brianb nedwards bennos tmmurali roys GeeSharpMinor
	Phosphorylation-Specific MS/MS Scoring for Rapid and Accurate Phosphoproteome Analysis [My Copy] J. Proteome Res. (19 June 2008) by Samuel H. Payne, Margaret Yau, Marcus B. Smolka, Stephen Tanner, Huilin Zhou, Vineet Bafna posted by 3 people nedwards neils brianb
	Discovery and revision of Arabidopsis genes by proteogenomics [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 52. (30 December 2008), pp. 21034-21038. by Natalie E. Castellana, Samuel H. Payne, Zhouxin Shen, Mario Stanke, Vineet Bafna, Steven P. Briggs posted by 6 people natstreet dandaman brianb nedwards TRHvidsten jmartin49
	Assessing the limits of genomic data integration for predicting protein networks [My Copy] Genome Research, Vol. 15, No. 7. (July 2005), pp. 945-953. by Long J. Lu, Yu Xia, Alberto Paccanaro, Haiyuan Yu, Mark Gerstein posted by 21 people ashishanand Paccanaro Lab paccanarolab jaimie aelef okarsligil lfriedl balajis maryee opheliav wnpx mbeautru eukfn grahamc nedwards kdl Bioinformatics brianb iris_2001 carlk phoenixzxl
	Rapid and Accurate Peptide Identification from Tandem Mass Spectra [My Copy] J. Proteome Res. (28 May 2008) by Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael J. Maccoss, William S. Noble posted by 3 people guhjy nedwards brianb
	Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. [My Copy] Molecular & cellular proteomics : MCP (13 July 2009) by Hasmik Keshishian, Terri Addona, Michael Burgess, et al.D. R. Mani, Xu Shi, Eric Kuhn, Marc S. Sabatine, Robert E. Gerszten, Steven A. Carr posted by 2 people guhjy brianb