Volume 10 Issue 1, January 2013

Digging deep into proteomes

Tools to study hematopoietic stem cell development, engraftment and interaction with the niche.

Self-assembling DNA nanopores could offer a powerful, customizable tool for a host of biological applications.

Single-molecule sequencing allows simultaneous reading of DNA bases and their methylation state in bacterial genomes.

A bounty of short peptides found in cells points to a larger, more mysterious proteome.

A popular sequencing platform can add long-range information to short sequence reads.

Scientists reverse engineer fluorescent proteins for light-mediated control.

Analysis of a preselected group of proteins delivers more precise, quantitative, sensitive data to more biologists. Vivien Marx reports.

A brief overview of mass spectrometry technology for targeted proteomics applications is presented.

By delivering precise, reproducible quantification of proteins of interest in biological samples, targeted proteomics approaches are allowing researchers to apply the scientific method using mass spectrometry.

The role of targeted mass spectrometry technology in the field of clinical proteomics is discussed in this Perspective.

2013 will see the first commercial nanopore sequencers.

In studies of microbiome function, marker sequencing will be balanced by alternative profiling approaches.

Development of genetically encoded tools with absorption and emission spectra in the near infrared is worth the trouble.

Nitrogen vacancy center defects in diamonds confer remarkably useful properties.

Attempts to replicate the stem cell microenvironment in the culture dish continue.

Microscopes that render tissue-volume images from single snapshots are making their way into biology.

Mass spectrometry technology to detect and characterize large, intact protein complexes is becoming more accessible.

Automated classifiers speed up biological phenotyping.

Researchers are injecting ever more conscious design into their bioengineering workflow.

A fully automated pipeline that systematically models three-dimensional (3D) structural details of protein interactions will allow researchers to interpret perturbation effects within protein pathways and networks.

Two groups derived neural and mesodermal cells from human fibroblasts by going through a partially reprogrammed intermediate.

Interactome3D is an interactive resource allowing biologists to use available structural information to model protein-protein interactions and structurally annotate protein interaction networks.

Improved mass spectrometry–based detection of low-abundance proteins in complex proteomes is made possible with a method to selectively digest and deplete high-abundance proteins.

A systematic evaluation of parameters that affect short amplicons sequenced on Illumina platforms provides guidelines for how to eliminate erroneous reads and improve data interpretation.

An epifluorescence microscope is turned into a multifocus microscope for fast three-dimensional imaging of live biological samples.

Open-source software that allows biologists to create a variety of behavior classifiers for automatically annotating video of behaving animals is presented. The program, called JAABA, uses state-of-the-art machine-learning methods and is applicable to tracking data from different organisms, including mice and adult and larval Drosophila.

A method is reported for optical trap calibration on lipid droplets in cell extract. It should permit quantitative studies of motor proteins in a more natural context than on beads.

The eXpress software uses an online algorithm to accurately assign ambiguously mapping sequence reads for real-time read abundance estimation, thereby dramatically enhancing the efficiency of any analysis that uses large-scale sequencing.

A Rosetta algorithm improves RNA structure by scoring each nucleotide's possible conformations based on an energy function and electron-density data.

Human fibroblasts undergo conversion to angioblast-like progenitors and then to endothelial cells by brief exposure to pluripotency factors, which is then followed by differentiation.

A brief exposure to episomally delivered pluripotency factors permits the reprogramming of cells in human urine to neural progenitor cells.

Nature Methods' choice for Method of the Year 2012 is targeted proteomics. A collection of articles showcases how mass spectrometry technology is being developed and applied for targeted protein analysis in both basic and translational research.