Method of the Year 2009

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• Subject categories

• • Biotechnology
  • Cell biology
  • Chemical biology
  • Genetics and genomics
  • Imaging
  • Immunology
  • Microbiology
  • Neuroscience
  • Others
  • Protein biochemistry
  • Proteomics
  • Stem cells
  • Synthetic biology
  • Systems biology

In 2007 we chose Next Generation Sequencing.
In 2008 we chose Super-resolution Imaging.

Now it is time for you, our readers, to help us choose the Method of the Year 2009. Just sign in using your free nature.com registration and vote on our Methods to Watch from previous years or a paper that a visitor has recommended.

Alternatively, you can recommend a paper that represents a method you believe came into its own in 2009 and will have a wide-ranging impact on biology. This paper can be any recently published paper from this year or past years published in any journal. Just provide a link to the paper or other online description of the method and vote away!

Want more information or want to comment? Read the editorial or go to our blog methagora and comment.

• Proteomics

  • • 36+ votes

      2- votes

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  • Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

    • 
      Original article citation: Cell 138," 795 - 806, (2009).

    • Categories: Proteomics, Genetics and genomics, and Systems biology
    • Recommended by : Herman Altenried on 11/05/2009 02:42AM GMT
      
      The publication shows that by using MRM based targeted proteomics an unsurpassed sensitivity, reproducibility and throughput in proteomics experiments is achieved. This is the first glimpse into the future of proteomics!!
    • Comment on this subject: 0 comments made

  • • 4+ votes

      1- votes

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  • Preparative gel electrophoresis of native metalloproteins

    • Bernd Kastenholz
      Original article citation: The American Electrophoresis Society Newsletter 14," 2 - 3, (2009).

    • Categories: Proteomics, Biotechnology, and Neuroscience
    • Recommended by : Bernd Kastenholz on 10/24/2009 10:59AM GMT
      
      Preparative gel electrophoresis of native metalloproteins is an essential method for elucidating the structures of misfolded metalloproteins in complex protein mixtures. Thus, this method may contribute to an early diagnosis and therapy of protein-misfolding diseases (e.g., Alzheimer's disease) and help to develop new medications from medicinal plants.
    • Comment on this subject: 0 comments made

  • • 174+ votes

      17- votes

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  • Extensive Analysis of the Cytoplasmic Proteome of Human Erythrocytes Using the Peptide Ligand Library Technology and Advanced Mass Spectrometry

    • 
      Original article citation: Molecular & Cellular Proteomics 7," 2254 - 2269, (2008).

    • Categories: Proteomics and Protein biochemistry
    • Recommended by : Roberto Sebastiano on 09/18/2009 10:47AM GMT
      
      This combinatorial peptide ligand library is an extraordinary methodology that will certainly make a big revolution in the field of proteomics! Who would have ever thought that RBCs would contain in the minority cytoplasmic proteome no less than 1578 unique gene product? Great piece of work.
    • Comment on this subject: 3 comments made

  • • 2+ votes

      9- votes

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  • Universal sample preparation method for proteome analysis

    • 
      Original article citation: Nat Meth 6," 359 - 362, (2009).

    • Categories: Proteomics, Biotechnology, Protein biochemistry, and Systems biology
    • Recommended by : Peter Nollert on 08/24/2009 11:54PM GMT
      
      1. the filter-aided sample preparation method impacts the 'forgotten half' of proteomics: membrane proteins & their complexes 2. the method described is *very* simple: SDS & urea reagent and a MWCO filter; no new tools required at all
    • Comment on this subject: 1 comment made

  • • 2+ votes

      4- votes

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  • Peptide Microarrays

    • Ramars Amanchy
      Original article citation: Journal of Proteome research 7," 3900 - 3910, (2008).

    • Categories: Proteomics, Biotechnology, Protein biochemistry, and Chemical biology
    • Recommended by : Ramars Amanchy on 08/24/2009 09:09PM GMT
      
      1. Peptide microarrays is a new technology with tremendous potential 2. Tremendous impact 3. Multitude of applications 4. Complements tradional kinase motif finding algorithms and techniques. 5. cancer/Kinase profiling
    • Comment on this subject: 1 comment made

  • • 36+ votes

      26- votes

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  • Development of an Inhibitor Screening Platform via Mass Spectrometry

    • 
      Original article citation: Journal of Biomolecular Screening 13," 1007 - 1013, (2008).

    • Categories: Biotechnology, Protein biochemistry, and Proteomics
    • Recommended by : Rakesh Rathore on 08/20/2009 05:19PM GMT
      
      -MALDI-QqQMS readout is a direct measurement of the substrate and the product, this readout eliminates false positive and false negative inhibitor in HTS. -Provides comparable speeds, with superior signal-to-background, better reproducibility and a reagent cost of about 3 cents per well versus 60 cents per well for the fluorescent readout. -Have a real potential of opening an entirely new service application to the Drug Discovery research.
    • Comment on this subject: 3 comments made

  • • 11+ votes

      5- votes

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  • Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

    • 
      Original article citation: Nature 460," 762 - 765, (2009).

    • Categories: Proteomics, Systems biology, and Cell biology
    • Recommended by the Editor: Veronique Kiermer on 08/14/2009 03:33PM GMT
      
      Aebersold and colleagues achieve absolute quantification of protein concentration at the proteome level (83% of the mass spec-detectable proteome) for a microbe of moderate complexity (3,600+ predicted ORFs based on the genomic sequence). That's a feat! And it is very elegant as they use a clever combination of approaches. Proteotypic peptides-based absolute measurements for a subset of 'anchor' proteins provide calibration points to translate relative abundance measurements, obtained by spectral counting, into absolute quantitative values for the rest of the proteins. And they show it works by verifying with cryo-electron tomography. This technology allows the comparison of absolute abundance of different proteins across different samples (as opposed to typical mass spec approaches in which you compare relative abundance of proteins across samples, using one as reference to infer how the others compare). In my opinion, this is a big step forward and it opens up a lot of possibilities for using mass spec in systems biology.
    • Comment on this subject: 0 comments made

  • • 1+ votes

      12- votes

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  • A meta-network of -omics

    • 
      Original article citation: Nat Meth 5," 25 - 25, (2008).

    • Categories: Systems biology, Genetics and genomics, Cell biology, and Proteomics
    • Recommended by the Editor: Nicole Rusk on 07/28/2009 04:36PM GMT
      
      In 2007 we called for a network that would link databases in the biosciences in our Methods to Watch section. We envisaged a scenario in which a wealth of information on, for example, genome, epigenome, transcriptome, proteome, and glycome would be easily accessible to a researcher and aid in the scientific discovery process. Is there still a need for such a meta-network or are scientists satisfied with the current network of databases?
    • Comment on this subject: 0 comments made

  • • 9+ votes

      7- votes

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  • Top-down mass spectrometry

    • 
      Original article citation: Nat Meth 5," 24 - 24, (2008).

    • Categories: Proteomics, Biotechnology, Protein biochemistry, and Cell biology
    • Recommended by the Editor: Allison Doerr on 07/27/2009 01:57PM GMT
      
      Top-down mass spectrometry was selected as a Method to Watch at the end of 2007. This tool is particularly useful for analyzing protein post-translational modifications, but it is not yet a high-throughput method. Have we seen the developments needed to drive its limits?
    • Comment on this subject: 0 comments made

  • • 4+ votes

      5- votes

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  • Structural analysis of macromolecular assemblies

    • 
      Original article citation: Nat Meth 5," 23 - 23, (2008).

    • Categories: Protein biochemistry, Cell biology, Imaging, and Proteomics
    • Recommended by the Editor: Allison Doerr on 07/27/2009 01:56PM GMT
      
      In the 2007 Methods to Watch, Nature Methods highlighted how researchers have begun to integrate proteomics techniques, cryo-electron microscopy, X-ray crystallography, NMR spectroscopy and computational tools to tackle the structure of large macromolecular assemblies like the nuclear pore complex. What do you think of the progress in this area since?
    • Comment on this subject: 1 comment made

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