Archive by category | Spotlights

SWATH-MS at Nature Protocols and Scientific Data

SWATH-MS at Nature Protocols and Scientific Data

The lab of Ruedi Aebersold recently published a Nature Protocol for generating peptide libraries for targeted analysis of SWATH MS data-independent acquisition mass spectrometry. This protocol complements a data descriptor (published in Scientific Data by the same authors) for a large-scale human assay library that can be used to support protein quantification by SWATH-MS.  Read more

Top 100 papers of all time

Top 100 papers of all time

I recently gave a talk in Singapore about publishing in Nature Protocols. When I give these talks, one of the things I explain is why Nature Publishing Group is interested in publishing methodological information. For that specific talk I had great new supporting document – an article in the previous weeks Nature about the “top 100 papers”. Of course, my top 100 papers is going to be very different from yours, but the top 100 for the purposes of this article was defined as the most cited papers of all time in the Science Citation Index, owned by Thomson Reuters.  Read more

CAUTION: Don’t mix concentrated nitric acid with organic solvents!

Radiolabelling with copper-64 (or any other metal cation radioisotope) is done by attaching a metal chelating group to the probe of interest. In 2006, we worked with Thaddeus J Wadas & Carolyn J Anderson to publish a protocol for radiolabelling peptides with copper-64 which included a procedure for making sure that the reaction tubes and pippette tips used for the labelling were free from any other metals that might compete with copper-64 for the space in the chelator (Box 1 in the protocol). This procedure involved washing the equipment with nitric acid, followed by rinses with ethanol followed by diethyl ether.  Read more

Preventing overfitting during the reconstruction of macromolecule images from CryoEM data

Preventing overfitting during the reconstruction of macromolecule images from CryoEM data

Using cryo-electron microscopy (cryoEM) it is possible to get information about the three-dimensional structure of macromolecules. Samples can be prepared using, for example, a protocol by Grassucci et al., and EM images obtained.  Read more

Radiochemistry at Nature Protocols

Radiochemistry at Nature Protocols

In March 2000 I came to England to start a PhD, and pet went from meaning a small animal you kept at home to meaning Positron Emission Tomography. There were months where my timetable was set by the half-life of iodine-124 (4.16 h), and my mind was occupied by the relative merits and problems with direct and indirect labelling of annexin V.  Read more

Protocols relating to the Structure and Composition of Plant Cell Walls

People have already exploited the physical properties of plant cell walls in, for example, the production of paper, textiles and building materials. In the future it may be possible to engineer plants to produce other environmentally friendly / biocompatible materials with different performance characteristics.  Read more