Nature Methods A multidisciplinary journal that publishes significant novel methods for life scientists and chemists. http://www.nature.com/nmeth/current_issue/ Nature Publishing Group en © 2008 Nature Publishing Group Nature Methods 1548-7091 1548-7105 © 2008 Nature Publishing Group permissions@nature.com Nature Methods http://www.nature.com/includes/rj_globnavimages/nmeth_logo.gif http://www.nature.com/nmeth/ Erratum: Mass spectrometry and proteomics: hitting the mark http://dx.doi.org/10.1038/nmeth1008-910 Erratum: Mass spectrometry and proteomics: hitting the mark

Nature Methods 5, 910 (2008). doi:10.1038/nmeth1008-910

Author: Nathan Blow

]]> Erratum: Mass spectrometry and proteomics: hitting the mark Nathan Blow doi:10.1038/nmeth1008-910 Nature Methods 5, 910 (2008) Nature Methods 5 10 Erratum 910 910 Scientific software: seeing the SNPs between us http://dx.doi.org/10.1038/nmeth1008-903 The results of large genome-wide association studies (GWASs) are being deposited in public databases with increasing frequency. But the software to analyze and interpret GWAS datasets can be difficult to use. Could a new generation of user-friendly programs fill the gap? Scientific software: seeing the SNPs between us

Nature Methods 5, 903 (2008). doi:10.1038/nmeth1008-903

Author: Steven David Buckingham

The results of large genome-wide association studies (GWASs) are being deposited in public databases with increasing frequency. But the software to analyze and interpret GWAS datasets can be difficult to use. Could a new generation of user-friendly programs fill the gap?

]]> Scientific software: seeing the SNPs between us Steven David Buckingham doi:10.1038/nmeth1008-903 Nature Methods 5, 903 (2008) Nature Methods 5 10 Technology Feature 903 908 Phosphorylation and the cell cycle http://dx.doi.org/10.1038/nmeth1008-858b Two groups used quantitative mass spectrometry to look at changes in protein phosphorylation across the cell cycle. Phosphorylation and the cell cycle

Nature Methods 5, 858 (2008). doi:10.1038/nmeth1008-858b

Author: Allison Doerr

Two groups used quantitative mass spectrometry to look at changes in protein phosphorylation across the cell cycle.

]]> Phosphorylation and the cell cycle Allison Doerr doi:10.1038/nmeth1008-858b Nature Methods 5, 858 (2008) Nature Methods 5 10 Research Highlights 858 859 Classical genetics goes high-tech http://dx.doi.org/10.1038/nmeth1008-863 A combination of automated screening and next-generation sequencing makes it possible to identify Caenorhabditis elegans mutants at unprecedented speed and scale. Classical genetics goes high-tech

Nature Methods 5, 863 (2008). doi:10.1038/nmeth1008-863

Author: David S Fay

A combination of automated screening and next-generation sequencing makes it possible to identify Caenorhabditis elegans mutants at unprecedented speed and scale.

]]> Classical genetics goes high-tech David S Fay doi:10.1038/nmeth1008-863 Nature Methods 5, 863 (2008) Nature Methods 5 10 News and Views 863 864 A surrogate scaffold tested http://dx.doi.org/10.1038/nmeth1008-861 Researchers tested an alternate antibody scaffold, creating so-called Surrobodies. A surrogate scaffold tested

Nature Methods 5, 861 (2008). doi:10.1038/nmeth1008-861

Author: Irene Kaganman

Researchers tested an alternate antibody scaffold, creating so-called Surrobodies.

]]> A surrogate scaffold tested Irene Kaganman doi:10.1038/nmeth1008-861 Nature Methods 5, 861 (2008) Nature Methods 5 10 Research Highlights 861 861 Antibodypedia http://dx.doi.org/10.1038/nmeth1008-860 A web portal to share antibody validation data. Antibodypedia

Nature Methods 5, 860 (2008). doi:10.1038/nmeth1008-860

Author: Veronique Kiermer

A web portal to share antibody validation data.

]]> Antibodypedia Veronique Kiermer doi:10.1038/nmeth1008-860 Nature Methods 5, 860 (2008) Nature Methods 5 10 Research Highlights 860 860 Large-scale evaluation of protein reductive methylation for improving protein crystallization http://dx.doi.org/10.1038/nmeth1008-853 Large-scale evaluation of protein reductive methylation for improving protein crystallization

Nature Methods 5, 853 (2008). doi:10.1038/nmeth1008-853

Authors: Youngchang Kim, Pearl Quartey, Hui Li, Lour Volkart, Catherine Hatzos, Changsoo Chang, Boguslaw Nocek, Marianne Cuff, Jerzy Osipiuk, Kemin Tan, Yao Fan, Lance Bigelow, Natalia Maltseva, Ruiying Wu, Maria Borovilos, Erika Duggan, Min Zhou, T Andrew Binkowski, Rong-guang Zhang & Andrzej Joachimiak

]]> Large-scale evaluation of protein reductive methylation for improving protein crystallization Youngchang Kim Pearl Quartey Hui Li Lour Volkart Catherine Hatzos Changsoo Chang Boguslaw Nocek Marianne Cuff Jerzy Osipiuk Kemin Tan Yao Fan Lance Bigelow Natalia Maltseva Ruiying Wu Maria Borovilos Erika Duggan Min Zhou T Andrew Binkowski Rong-guang Zhang Andrzej Joachimiak doi:10.1038/nmeth1008-853 Nature Methods 5, 853 (2008) Nature Methods 5 10 Correspondence 853 854 Microbes right on target http://dx.doi.org/10.1038/nmeth1008-857 Researchers use a targeted metagenomic approach to functionally characterize complex microbial communities. Microbes right on target

Nature Methods 5, 857 (2008). doi:10.1038/nmeth1008-857

Author: Michelle Pflumm

Researchers use a targeted metagenomic approach to functionally characterize complex microbial communities.

]]> Microbes right on target Michelle Pflumm doi:10.1038/nmeth1008-857 Nature Methods 5, 857 (2008) Nature Methods 5 10 Research Highlights 857 857 A pilot project to generate affinity reagents to human proteins http://dx.doi.org/10.1038/nmeth1008-854 A pilot project to generate affinity reagents to human proteins

Nature Methods 5, 854 (2008). doi:10.1038/nmeth1008-854

Authors: Mathias Uhlen, Susanne Gräslund & Michael Sundström

]]> A pilot project to generate affinity reagents to human proteins Mathias Uhlen Susanne Gräslund Michael Sundström doi:10.1038/nmeth1008-854 Nature Methods 5, 854 (2008) Nature Methods 5 10 Correspondence 854 855 New twists on photoswitchable proteins http://dx.doi.org/10.1038/nmeth1008-858a Fluorescent proteins with new photoswitching properties allow multilabel imaging at a single detection wavelength and dual-color superresolution microscopy. New twists on photoswitchable proteins

Nature Methods 5, 858 (2008). doi:10.1038/nmeth1008-858a

Author: Natalie de Souza

Fluorescent proteins with new photoswitching properties allow multilabel imaging at a single detection wavelength and dual-color superresolution microscopy.

]]> New twists on photoswitchable proteins Natalie de Souza doi:10.1038/nmeth1008-858a Nature Methods 5, 858 (2008) Nature Methods 5 10 Research Highlights 858 859 News in brief http://dx.doi.org/10.1038/nmeth1008-859 News in brief

Nature Methods 5, 859 (2008). doi:10.1038/nmeth1008-859

]]> News in brief doi:10.1038/nmeth1008-859 Nature Methods 5, 859 (2008) Nature Methods 5 10 Research Highlights 859 859 Elective affinities http://dx.doi.org/10.1038/nmeth1008-851 A feasibility study for the systematic generation of affinity reagents to human proteins provides an opportunity to test the merits of recombinant affinity reagents. Elective affinities

Nature Methods 5, 851 (2008). doi:10.1038/nmeth1008-851

A feasibility study for the systematic generation of affinity reagents to human proteins provides an opportunity to test the merits of recombinant affinity reagents.

]]> Elective affinities doi:10.1038/nmeth1008-851 Nature Methods 5, 851 (2008) Nature Methods 5 10 Editorial 851 851 Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering http://dx.doi.org/10.1038/nmeth.1255 Time-resolved wide-angle X-ray scattering (TR-WAXS) using synchrotron radiation can be used to observe dynamic protein structural changes with nanosecond time resolution in solution, complementing time-resolved optical spectroscopy and Laue crystallography methods. Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering

Nature Methods 5, 881 (2008). doi:10.1038/nmeth.1255

Authors: Marco Cammarata, Matteo Levantino, Friedrich Schotte, Philip A Anfinrud, Friederike Ewald, Jungkweon Choi, Antonio Cupane, Michael Wulff & Hyotcherl Ihee

]]> Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering Marco Cammarata Matteo Levantino Friedrich Schotte Philip A Anfinrud Friederike Ewald Jungkweon Choi Antonio Cupane Michael Wulff Hyotcherl Ihee doi:10.1038/nmeth.1255 Nature Methods 5, 881 (2008) 2008-09-21 Nature Methods 2008-09-21 5 10 Article 881 886 Identification of genetic variants using bar-coded multiplexed sequencing http://dx.doi.org/10.1038/nmeth.1251 Targeted regions of the human genome are resequenced in multiplex with Illumina technology, and the pipeline is evaluated for polymorphism discovery and genotyping. Identification of genetic variants using bar-coded multiplexed sequencing

Nature Methods 5, 887 (2008). doi:10.1038/nmeth.1251

Authors: David W Craig, John V Pearson, Szabolcs Szelinger, Aswin Sekar, Margot Redman, Jason J Corneveaux, Traci L Pawlowski, Trisha Laub, Gary Nunn, Dietrich A Stephan, Nils Homer & Matthew J Huentelman

]]> Identification of genetic variants using bar-coded multiplexed sequencing David W Craig John V Pearson Szabolcs Szelinger Aswin Sekar Margot Redman Jason J Corneveaux Traci L Pawlowski Trisha Laub Gary Nunn Dietrich A Stephan Nils Homer Matthew J Huentelman doi:10.1038/nmeth.1251 Nature Methods 5, 887 (2008) 2008-09-14 Nature Methods 2008-09-14 5 10 Article 887 893 Optogenetic analysis of synaptic function http://dx.doi.org/10.1038/nmeth.1252 Using both behavioral and electrophysiological readouts, Channelrhodopsin-2, a light-gated cation channel, is applied to the study of synaptic function in Caenorhabditis elegans. Optogenetic analysis of synaptic function

Nature Methods 5, 895 (2008). doi:10.1038/nmeth.1252

Authors: Jana F Liewald, Martin Brauner, Greg J Stephens, Magali Bouhours, Christian Schultheis, Mei Zhen & Alexander Gottschalk

]]> Optogenetic analysis of synaptic function Jana F Liewald Martin Brauner Greg J Stephens Magali Bouhours Christian Schultheis Mei Zhen Alexander Gottschalk doi:10.1038/nmeth.1252 Nature Methods 5, 895 (2008) 2008-09-14 Nature Methods 2008-09-14 5 10 Article 895 902 Automated screening for mutants affecting dopaminergic-neuron specification in C. elegans http://dx.doi.org/10.1038/nmeth.1250 An automated sorting method using the COPAS Biosort machine allows the isolation of mutant C. elegans displaying differences in GFP expression in small numbers of cells. Compared to manual methods this increases the efficiency of the phenotypic selection step in cell-fate screens. Automated screening for mutants affecting dopaminergic-neuron specification in C. elegans

Nature Methods 5, 869 (2008). doi:10.1038/nmeth.1250

Authors: Maria Doitsidou, Nuria Flames, Albert C Lee, Alexander Boyanov & Oliver Hobert

We describe an automated method to isolate mutant Caenorhabditis elegans that do not appropriately execute cellular differentiation programs. We used a fluorescence-activated sorting mechanism implemented in the COPAS Biosort machine to isolate mutants with subtle alterations in the cellular specificity of GFP expression. This methodology is considerably more efficient than comparable manual screens and enabled us to isolate mutants in which dopamine neurons do not differentiate appropriately.

]]> Automated screening for mutants affecting dopaminergic-neuron specification in C. elegans Maria Doitsidou Nuria Flames Albert C Lee Alexander Boyanov Oliver Hobert doi:10.1038/nmeth.1250 Nature Methods 5, 869 (2008) 2008-08-31 Nature Methods 2008-08-31 5 10 Brief Communication 869 872 Building consensus spectral libraries for peptide identification in proteomics http://dx.doi.org/10.1038/nmeth.1254 Spectral searching, based on matching experimental peptide spectra to reference spectral libraries, is gaining interest as an alternative to traditional sequence-database searching in mass spectrometry–based proteomics. A software tool, SpectraST, now allows users to build their own high-quality spectral libraries from raw data. Building consensus spectral libraries for peptide identification in proteomics

Nature Methods 5, 873 (2008). doi:10.1038/nmeth.1254

Authors: Henry Lam, Eric W Deutsch, James S Eddes, Jimmy K Eng, Stephen E Stein & Ruedi Aebersold

Spectral searching has drawn increasing interest as an alternative to sequence-database searching in proteomics. We developed and validated an open-source software toolkit, SpectraST, to enable proteomics researchers to build spectral libraries and to integrate this promising approach in their data-analysis pipeline. It allows individual researchers to condense raw data into spectral libraries, summarizing information about observed proteomes into a concise and retrievable format for future data analyses.

]]> Building consensus spectral libraries for peptide identification in proteomics Henry Lam Eric W Deutsch James S Eddes Jimmy K Eng Stephen E Stein Ruedi Aebersold doi:10.1038/nmeth.1254 Nature Methods 5, 873 (2008) 2008-09-21 Nature Methods 2008-09-21 5 10 Brief Communication 873 875 Imaging individual mRNA molecules using multiple singly labeled probes http://dx.doi.org/10.1038/nmeth.1253 A strategy using 48 or more singly labeled fluorescent oligonucleotide probes targeted to individual mRNA molecules allows the simultaneous localization and quantification of three mRNA species in fixed cells. mRNA visualization in whole animals and other organisms is also demonstrated. Imaging individual mRNA molecules using multiple singly labeled probes

Nature Methods 5, 877 (2008). doi:10.1038/nmeth.1253

Authors: Arjun Raj, Patrick van den Bogaard, Scott A Rifkin, Alexander van Oudenaarden & Sanjay Tyagi

We describe a method for imaging individual mRNA molecules in fixed cells by probing each mRNA species with 48 or more short, singly labeled oligonucleotide probes. This makes each mRNA molecule visible as a computationally identifiable fluorescent spot by fluorescence microscopy. We demonstrate simultaneous detection of three mRNA species in single cells and mRNA detection in yeast, nematodes, fruit fly wing discs, and mammalian cell lines and neurons.

]]> Imaging individual mRNA molecules using multiple singly labeled probes Arjun Raj Patrick van den Bogaard Scott A Rifkin Alexander van Oudenaarden Sanjay Tyagi doi:10.1038/nmeth.1253 Nature Methods 5, 877 (2008) 2008-09-21 Nature Methods 2008-09-21 5 10 Brief Communication 877 879 Caenorhabditis elegans mutant allele identification by whole-genome sequencing http://dx.doi.org/10.1038/nmeth.1249 Identifying the molecular lesions in mutants isolated in forward genetic screens can be a laborious process. A proof-of-principle study in Caenorhabditis elegans now shows that this can be achieved rapidly by whole-genome deep sequencing. Caenorhabditis elegans mutant allele identification by whole-genome sequencing

Nature Methods 5, 865 (2008). doi:10.1038/nmeth.1249

Authors: Sumeet Sarin, Snehit Prabhu, M Maggie O'Meara, Itsik Pe'er & Oliver Hobert

Identification of the molecular lesion in Caenorhabditis elegans mutants isolated through forward genetic screens usually involves time-consuming genetic mapping. We used Illumina deep sequencing technology to sequence a complete, mutant C. elegans genome and thus pinpointed a single-nucleotide mutation in the genome that affects a neuronal cell fate decision. This constitutes a proof-of-principle for using whole-genome sequencing to analyze C. elegans mutants.

]]> Caenorhabditis elegans mutant allele identification by whole-genome sequencing Sumeet Sarin Snehit Prabhu M Maggie O'Meara Itsik Pe'er Oliver Hobert doi:10.1038/nmeth.1249 Nature Methods 5, 865 (2008) 2008-08-01 Nature Methods 2008-08-01 5 10 Brief Communication 865 867 Rapid, on-demand protein stabilization and destabilization using the ProteoTuner™ systems http://dx.doi.org/10.1038/nmeth.f.223 Rapid, on-demand protein stabilization and destabilization using the ProteoTuner™ systems

Nature Methods 5, (2008). doi:10.1038/nmeth.f.223

Authors: Michael Haugwitz, Tatiana Garachtchenko, Omar Nourzaie, Suvarna Gandlur & Hiroaki Sagawa

]]> Rapid, on-demand protein stabilization and destabilization using the ProteoTuner™ systems Michael Haugwitz Tatiana Garachtchenko Omar Nourzaie Suvarna Gandlur Hiroaki Sagawa doi:10.1038/nmeth.f.223 Nature Methods 5, (2008) Nature Methods 5 10 Application Note Development of an Eg5 assay using the HTRF® Transcreener® ADP kit http://dx.doi.org/10.1038/nmeth.f.222 Development of an Eg5 assay using the HTRF® Transcreener® ADP kit

Nature Methods 5, (2008). doi:10.1038/nmeth.f.222

Authors: Laurence Jacquemart, Marion De Decker & Bastien Caumes

]]> Development of an Eg5 assay using the HTRF® Transcreener® ADP kit Laurence Jacquemart Marion De Decker Bastien Caumes doi:10.1038/nmeth.f.222 Nature Methods 5, (2008) Nature Methods 5 10 Application Note