Fixing Proteomics Campaign

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Papers

This section highlights the papers which have been published around issues raised by the Fixing Proteomics Campaign. If you know of any other papers which support the messages of the Fixing Proteomics Campaign, and would like them to be added to this list, please contact us.

Assessing the use of thermal treatment to preserve the intact proteomes of post-mortem heart and brain tissue. Proteomics, Jan 8 2009, (2):974-981 Robinson et al more ╗

A CPTAC inter-laboratory study characterizing a yeast performance standard for benchmarking LC-MS Platform performance. Mol Cell Proteomics Epub ahead of print, Oct 2009   Paulovich AG, Billheimer D, Ham AJ, Vega-Montoto LJ, Rudnick PA, Tabb DL, Wang P, Blackman RK, Bunk DM, Cardasis HL, Clauser KR, Kinsinger CR, Schilling B, Tegeler TJ, Variyath AM, Wang M, Whiteaker JR, Zimmerman LJ, Fenyo D, Carr SA, Fisher SJ, Gibson BW, Mesri M, Neubert TA, Reginier FE, Rodriguez H, Spiegelman C, Stein SE, Tempst P, Liebler DC. more ╗

Comparative analysis to guide quality improvements in proteomics. Nature Methods 6 (Oct 2009), pages 717 - 719   Matthias Mann more ╗

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma. Nature Biotechnology 27 (28 June 2009), pages 633 - 641   Terri Addona, Susan Abbatiello, Birgit Schilling, Steven Skates, D Mani, David Bunk,Clifford Spiegelman, Lisa Zimmerman, Amy-Joan Ham, Hasmik Keshishian, Steven Hall, Simon Allen, Ronald Blackman, Christoph Borchers,Charles Buck, Helene Cardasis, Michael Cusack, Nathan Dodder, Bradford Gibson, Jason Held, Tara Hiltke, Angela Jackson, Eric Johansen, Christopher Kinsinger, Jing Li, Mehdi Mesri, Thomas Neubert, Richard Niles, Trenton Pulsipher, David Ransohoff, Henry Rodriguez, Paul Rudnick, Derek Smith, David Tabb, Tony Tegeler, Asokan Variyath, Lorenzo Vega-Montoto, ┼sa Wahlander, Sofia Waldemarson, Mu Wang, Jeffrey Whiteaker, Lei Zhao, Leigh Anderson, Susan Fisher, Daniel Liebler, Amanda Paulovich, Fred Regnier, Paul Temps, Steven Carr more ╗

A HUPO test sample study reveals common problems in mass spectrometry–based proteomics. Nature Methods 6 (2009), pages 423 - 430 Alexander Bell, Eric Deutsch, Catherine Au, Robert Kearney, Ron Beavis, Salvatore Sechi, Tommy Nilsson, John J M Bergeron & HUPO Test Sample Working Group. more ╗

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: The Amsterdam Principles. J. Proteome Res. April 2009, 8 (7), pages 3689–3692   Henry Rodriguez, Mike Snyder, Mathias Uhln, Phil Andrews, Ronald Beavis,Christoph Borchers, Robert Chalkley, Sang Yun Cho, Katie Cottingham, Michael Dunn, Tomasz Dylag, Ron Edgar, Peter Hare,Albert Heck, Roland Hirsch, Karen Kennedy, Patrik Kolar, Hans-Joachim Kraus, Parag Mallick, Alexey Nesvizhskii, Peipei Ping, Fredrik Pontn, Liming Yang, John Yates, Stephen Stein, Henning Hermjakob, Christopher Kinsinger and Rolf Apweiler more ╗

Considerations for powering a clinical proteomics study: Normal variability in the human plasma proteome. Proteomics - Clinical Applications, Feb 2009, 3, issue 3, pages 394 - 407 David Jackson, Athula Herath, Jonathan Swinton, David Bramwell, Rajesh Chopra, Andrew Hughes, Kevin Cheeseman, Robert Tonge. more ╗

Heat Stabilization of the Tissue Proteome: A New Technology for Improved Proteomics. J. Proteome Res., Jan 8 2009, (2):974-981 Marcus Svensson, Mats Boren, Karl;Skold, Maria Falth, Benita Sjogren, Malin Andersson, Per Svenningsson and Per E.Andren more ╗

Technical strategies to reduce the amount of “false significant” results in quantitative proteomics. Proteomics, 2008, 8, Issue 9, Pages 1780 – 1784. Sandra Fuxius, Murat Eravci, Oliver Broedel, Stephanie Weist, Ulrich Mansman, Selda Eravci, Andreas Baumgartner. more »

Treatment of missing values for multivariate statistical analysis of gel-based proteomics data. Proteomics, 2008, 8, Issue 7, Pages 1371 – 1383. Romina Pedreschi, Maarten Hertog, Sebastien Carpentier, Jeroen Lammertyn, Johan Robben, Jean-Paul Noben, Bart Panis, Rony Swennen, Bart M. Nicola´ more »

Information quality in proteomics. Briefings in Bioinformatics Feb 2008 9,No. 2 pages 174-188.  David Stead, Norman Paton, Paolo Missier, Suzanne Embury, Cornelia Hedeler, Binling Jin, Alistair Brown and Alun Preece. more »

Mass spectrometry is only one piece of the puzzle in clinical proteomics. Briefings in Functional Genomics and Proteomics. Feb 2008 7 (1), pages 74-83   James McGuire, Julie Overgaard and Flemming Pociot more ╗

Analyzing Large-Scale Proteomics Projects with Latent Semantic Indexing. J Proteome Res. 2007 Nov 30; [Epub ahead of print] Klie S, Martens L, VizcaÝno JA, C˘tÚ R, Jones P, Apweiler R, Hinneburg A, Hermjakob H. more »

Assessing Bias in Experiment Design for Large Scale Mass Spectrometry-based Quantitative Proteomics. Mol. Cell. Proteomics. Oct 2007; 6: 1741 — 1748 Amol Prakash, Brian Piening, Jeff Whiteaker, Heidi Zhang, Scott A. Shaffer, Daniel Martin, Laura Hohmann, Kelly Cooke, James M. Olson, Stacey Hansen, Mark R. Flory, Hookeun Lee, Julian Watts, David R. Goodlett, Ruedi Aebersold, Amanda Paulovich, and Benno Schwikowski. more »

Design and analysis issues in quantitative proteomics studies. Proteomics. 2007 Sep; 7 Suppl 1:42-50 Karp NA, Lilley KS. more »

How shall we use the proteomics toolbox for biomarker discovery? J Proteome Res. 2007 Sep; 6(9):3371-6 Lescuyer P, Hochstrasser D, Rabilloud T. more »

The implications of proteolytic background for shotgun proteomics. Mol Cell Proteomics. 2007 Sep; 6(9):1589-98 Picotti P, Aebersold R, Domon B. more »

The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 2007 Aug; 25(8):887-93 Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H. more »

Proteomics data validation: why all must provide data. Mol Biosyst. 2007 Aug; 3(8):518-22 Martens L, Hermjakob H. more »

Experimental and statistical considerations to avoid false conclusions in proteomics studies using differential in-gel electrophoresis. Mol Cell Proteomics. 2007 Aug; 6(8):1354-64 Karp NA, McCormick PS, Russell MR, Lilley KS. more »

Sample size and replication in 2D gel electrophoresis studies. J Proteome Res. 2007 Jul; 6(7):2884-7. Horgan GW. more »

Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics - Clinical Applications. 2007 Jan; 1(2):148-156 Harald Mischak, Rolf Apweiler , Rosamonde E. Banks , Mark Conaway, Joshua Coon, Anna Dominiczak, Jochen H. H. Ehrich, Danilo Fliser, Mark Girolami, Henning Hermjakob, Denis Hochstrasser, Joachim Jankowski, Bruce A. Julian, Walter Kolch, Ziad A. Massy, Christian Neusuess, Jan Novak, Karlheinz Peter, Kasper Rossing, Joost Schanstra, O. John Semmes, Dan Theodorescu, Visith Thongboonkerd, Eva M. Weissinger, Jennifer E. Van Eyk, Tadashi Yamamoto. more »

Guidelines for the next 10 years of proteomics. Proteomics. 2006 Jan; 6(1):4-8 Wilkins MR, Appel RD, Van Eyk JE, Chung MC, G÷rg A, Hecker M, Huber LA, Langen H, Link AJ, Paik YK, Patterson SD, Pennington SR, Rabilloud T, Simpson RJ, Weiss W, Dunn MJ. more »

Rules of evidence for cancer molecular-marker discovery and validation. Nature Reviews Cancer 4, April 2004, 309-314 David F. Ransohoff more »

Reproducible research: a bioinformatics case study. Stat. Appl. Genet. Mol. Biol., 2004, 4 Robert Gentleman more »

Overcoming technical variation and biological variation in quantitative proteomics. Proteomics, 2003, 3, 1912-1919 Molloy MP, Brzezinski EE, Hang J, McDowell MT, VanBogelen RA more »

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