In 2008, Nature Methods Editors asked our readers for their input in helping us select the Method of the Year. They responded by recommending methods and voting for their choice for Method of the Year. We are very grateful for their input and here are the final top ten picks. Come back in mid 2009 and help us pick a new Method of the Year!

• 65 votes

  Proteomics

  • • 49+ votes

      16- votes

    • Voting complete

  • Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase

    • Nadia Taouatas, Madalina M Drugan, Albert J R Heck, Shabaz Mohammed
      Original article citation: Nat Meth 5, 405-407, (2008).

    • Categories: Proteomics
    • Recommended by : Silvia Surinova on 09/15/2008 12:43PM GMT
      
      A novel method for de novo sequencing of peptides and the analysis of post-translational modifications using a metalloendopeptidase that cleaves proteins at the amino side of lysine (Lys-N). Lys-N-digested peptides can be easily sequenced by following the c-type fragment ions produced during electron transfer dissociation (ETD)-based mass spectrometric analysis.

• 59 votes

  Imaging

  • • 41+ votes

      18- votes

    • Voting complete

  • Seeing fluorescence at super-resolution

    • Daniel Evanko
      Original article citation: Nat Meth 5, 22-22, (2008).

    • Categories: Imaging, Biotechnology, and Cell biology
    • Recommended by the Editor: Daniel Evanko on 08/25/2008 08:56PM GMT
      
      Last year, Nature Methods singled out some impressive developments that had taken place in 2007 in super-resolution fluorescence imaging. Has the technology evolved enough in 2008 that it could be a serious contender for Method of the Year this year? Has it started to show the novel biology it promised?

• 69 votes

  Proteomics

  • • 46+ votes

      23- votes

    • Voting complete

  • Direct observation of individual endogenous protein complexes in situ by proximity ligation

    • Ola Söderberg, Mats Gullberg, Malin Jarvius, Karin Ridderstråle, Karl-Johan Leuchowius, Jonas Jarvius, Kenneth Wester, Per Hydbring, Fuad Bahram, Lars-Gunnar Larsson, Ulf Landegren
      Original article citation: Nat Meth 3, 995-1000, (2006).

    • Categories: Proteomics, Biotechnology, Cell biology, and Imaging
    • Recommended by : Olle Ericsson on 09/15/2008 02:56PM GMT
      
      In situ PLA for the first time enables researchers to analyze protein protein interaction in untampered samples like for example clinical material.Furthermore the technique identifies the exact subcellular localization where the interaction occurs. The utilization of the method is spreading rapidly in the research community and provide scientists with unique important functional information of cellular functions which so far has been unavailable.

• 61 votes

  Genetics and genomics

  • • 39+ votes

      22- votes

    • Voting complete

  • Short Quantitative Random RNA Libraries

    • N Cloonan
      Original article citation: Nature Methods 5, 613-619, (2008).

    • Categories: Genetics and genomics, Stem cells, Systems biology, and Cell biology
    • Recommended by : Anna Berdine on 09/04/2008 12:32AM GMT
      
      This paper is the first description of whole transciptome profiling of stem cells with a method that preserves the strand orientation of the original molecule. doi: 10.1038/nmeth.1223 link: http://www.nature.com/nmeth/journal/v5/n7/abs/nmeth.1223.html

• 20 votes

  Cell biology

  • • 14+ votes

      6- votes

    • Voting complete

  • Controlling cells with light

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

    • Categories: Cell biology, Biotechnology, Neuroscience, and Imaging
    • Recommended by the Editor: Daniel Evanko on 08/25/2008 09:00PM GMT
      
      Last year, in the wake of publications demonstrating the possibility to control neuronal signaling using photoactivable channels, we at Nature Methods hoped for development of new photo-stimulation methods and we predicted that broader applications of ChR2-based methods would bring a flood of new biological findings. Were we right? Wrong?

• 16 votes

  Genetics and genomics

  • • 11+ votes

      5- votes

    • Voting complete

  • Tools for neuroanatomy and neurogenetics in Drosophila

    • 
      Original article citation: Proceedings of the National Academy of Sciences 105, 9715-9720,

    • Categories: Genetics and genomics and Neuroscience
    • Recommended by : Terry Vale on 11/08/2008 11:25PM GMT
      
      The authors developed new vectors and methodologies to generate a large collection of GAL4 drivers in a cost effective, reproducible, and efficient manner. The modularity and precision of the system will not only allow researchers to probe various aspects of Drosophila biology but also help dissect the cis-regulatory grammar involved in gene regulation.

• 37 votes

  Stem cells

  • • 21+ votes

      16- votes

    • Voting complete

  • Induced pluripotency in human cells

    • Natalie de Souza
      Original article citation: Nat Meth 5, 24-24, (2008).

    • Categories: Stem cells
    • Recommended by the Editor: Natalie de Souza on 08/26/2008 01:44PM 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 noise about iPS cells in 2008. Enough so that methods to generate them be named Method of the Year?

• 17 votes

  Systems biology

  • • 11+ votes

      6- votes

    • Voting complete

  • The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition

    • 
      Original article citation: Genome Biol 9, R127, (2008).

    • Categories: Systems biology and Genetics and genomics
    • Recommended by : Amanda Zhou on 10/31/2008 09:01AM GMT
      
      In this paper the authors describe a systems biology method for detecting the biological function of microRNAs that does not require a priori knowledge of biologically validated gene targets - previously a bottleneck to studying the function of miRNAs. Nature Methods has previously highlighted the need for high-throughput target validation in part because of this bottleneck, demonstrating the importance of this approach.

• 11 votes

  Protein biochemistry

  • • 6+ votes

      5- votes

    • Voting complete

  • Structural analysis of macromolecular assemblies

    • Allison Doerr
      Original article citation: Nature Methods 5, 23-23, (2008).

    • Categories: Protein biochemistry, Cell biology, and Proteomics
    • Recommended by the Editor: Allison Doerr on 08/25/2008 08:19PM GMT
      
      Last year, 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 in 2008?

• 11 votes

  Cell biology

  • • 6+ votes

      5- votes

    • Voting complete

  • Watching single molecules in cells

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

    • Categories: Cell biology, Others, and Imaging
    • Recommended by the Editor: Daniel Evanko on 08/25/2008 09:03PM GMT
      
      In vivo measurement of single molecules is a very challenging area technically. But the enormity of the rewards at stake made us highlight, last year, this area of research as one to watch. We are not persuaded that there has been enough development in 2008 to make in vivo single molecule measurements a Method of the Year, yet. But we would be happy to hear some dissent among you...