Proteomics
Mapping proteolytic events in apoptosis
Current platforms for studying proteolysis have not generally allowed researchers to obtain a complete picture of the cleaved fragments of protease substrates on a large scale. Dix et al. now present an algorithm that integrates data from electrophoresis and quantitative liquid chromatography–tandem mass spectrometry analyses of fragment peptides into a 'peptograph', which plots a complete sequence map. They used this method to map caspase-mediated proteolytic events in apoptosis.
Dix, M.M. et al. Cell 134, 679–691 (2008).
Bioinformatics
An atlas of mouse embryo morphology
Petiet et al. describe a high-resolution, magnetic resonance microscopy (MRM)-based atlas of normal, transgenic and mutant mouse model morphology at the embryonic and neonatal stages. The database of three-dimensional MRM images with more than 200 annotated structures is freely available at http://www.civm.duhs.duke.edu/devatlas/index.html and should be a useful resource for developmental studies.
Petiet, A.E. et al. Proc. Natl. Acad. Sci. USA 105, 12331–12336 (2008).
Genomics
Quality control in next-generation sequencing
It is a challenge to assemble the millions of short sequence reads generated by next-generation sequencers such as the Applied Biosystems SOLiD and the Illumina Genetic Analyzer. Li et al. now present 'mapping and assembling with quality' (MAQ), a freely available software tool that uses a mapping quality score to improve alignment accuracy. The tool should be especially useful for detecting single-nucleotide polymorphisms and insertion-deletions.
Li, H. et al. Genome Res., published online 19 August 2008.
Immunochemistry
Polyubiquitin linkage–specific antibodies
The fate of a polyubiquitinated protein is thought to depend on the lysine residue of ubiquitin through which the chains are linked. To investigate this question more thoroughly, Newton et al. developed polyubiquitin linkage–specific antibodies, which recognize two of the best-characterized linkages, via Lys48 or Lys63. These antibodies can be used in different applications, including immunoprecipitation, immunofluorescence, immunohistochemistry and western blotting.
Newton, K. et al. Cell 134, 668–678 (2008).
Bioinformatics
A NetPhorest of phosphorylation motifs
Miller et al. present NetPhorest, a valuable database of protein phosphorylation consensus sequence motifs that are recognized by protein kinases and phosphorylation-dependent binding domains. This publicly available atlas (http://netphorest.info/) is fed by an automated data pipeline: these data are mapped to phylogenetic trees to derive linear motif models.
Miller, M.L. et al. Sci. Signal. 1, ra2 (2008).
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News in brief. Nat Methods 5, 859 (2008). https://doi.org/10.1038/nmeth1008-859
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DOI: https://doi.org/10.1038/nmeth1008-859