Method of the Year 2009

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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.

• 194 votes

  Proteomics

  • • 177+ 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

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      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: 4 comments made

• 40 votes

  Proteomics

  • • 38+ votes

      2- votes

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

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      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

• 58 votes

  Imaging

  • • 37+ votes

      21- votes

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  • Label-Free Biomedical Imaging with High Sensitivity by Stimulated Raman Scattering Microscopy

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      Original article citation: Science 322," 1857 - 1861, (2008).

    • Categories: Imaging and Biotechnology
    • Recommended by the Editor: Daniel Evanko on 08/10/2009 10:44PM GMT
      
      Label-free microscopy using various signal mechanisms not based on florescence has been around for years but has seen comparatively little uptake by users. Sunney Xie's report of Stimulated Raman Scattering (SRS) microscopy in Science last year looks like it has the potential to greatly increase the impact of this methodology.
    • Comment on this subject: 0 comments made

• 45 votes

  Stem cells

  • • 29+ votes

      16- votes

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  • Induced pluripotency

    • 
      Original article citation: Nat Meth 6," 33 - 33, (2009).

    • Categories: Stem cells and Biotechnology
    • Recommended by the Editor: Natalie de Souza on 07/27/2009 10:25AM GMT
      
      At the end of 2007, the generation of human induced pluripotent stem (iPS) cells brought much promise, but also many questions, to the field of stem cells. There certainly has been a lot of development in this area since then, and it has recently been accelerating rapidly. Enough so that methods to generate iPS cells be named Method of the Year 2009?
    • Comment on this subject: 0 comments made

• 63 votes

  Biotechnology

  • • 37+ votes

      26- votes

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  • Development of an Inhibitor Screening Platform via Mass Spectrometry

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      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

• 32 votes

  Cell biology

  • • 21+ votes

      11- votes

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  • Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

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      Original article citation: Science 326," 289 - 293, (2009).

    • Categories: Cell biology and Genetics and genomics
    • Recommended by : David Galas on 10/21/2009 03:43PM GMT
      
      The added power of this modified method to lay out the 3D arrangement of the chromosomes of the genome in the nucleus is a major advance. we had some information before this, but now we can look at the full arrangement, in any cells, underany conditions. Very clever technique coupled with beautiful computational analysis.
    • Comment on this subject: 0 comments made

• 35 votes

  Cell biology

  • • 22+ votes

      13- votes

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  • Watching single molecules in cells

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

    • Categories: Cell biology, Imaging, and Others
    • Recommended by the Editor: Daniel Evanko on 07/23/2009 09:10PM GMT
      
      In vivo measurement of single molecules is a very challenging area technically. But the enormity of the rewards at stake made us highlight, back in 2007, this area of research as one to watch. The level of progress in 2008 was incremental but developments seem to be gradually improving and there is no question that some landmark papers have been published. Has the progress been sufficient?
    • Comment on this subject: 1 comment made

• 16 votes

  Proteomics

  • • 11+ votes

      5- votes

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

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      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

• 20 votes

  Biotechnology

  • • 13+ votes

      7- votes

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  • A 3D digital atlas of C. elegans and its application to single-cell analyses

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      Original article citation: Nat Meth 6," 667 - 672, (2009).

    • Categories: Biotechnology, Genetics and genomics, Systems biology, and Cell biology
    • Recommended by : Hanchuan Peng on 09/09/2009 02:45AM GMT
      
      Isn't it a cool thing to be able to target individual cells uniquely and unambiguously?
    • Comment on this subject: 2 comments made

• 18 votes

  Proteomics

  • • 11+ votes

      7- votes

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  • Quantitative mass spectrometry

    • 
      Original article citation: Nat Meth 6," 34 - 34, (2009).

    • Categories: Proteomics, Biotechnology, Protein biochemistry, and Cell biology
    • Recommended by the Editor: Allison Doerr on 07/27/2009 01:46PM GMT
      
      Quantitative mass spectrometry-based proteomics has been increasingly applied on a large scale to address interesting biological questions; we thus selected it as a Method to Watch in 2008. Has the technology matured enough yet to be considered as Method of the Year in 2009, or are further methodological developments still needed?
    • Comment on this subject: 1 comment made

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