The availability of whole genome sequences for many organisms has resulted in a rush to elucidate the function of the products of these genomes and their role in health and disease. But deciphering the complexity of the proteome is a daunting task, and the application of proteomics is still very much in its infancy. September 2004 saw the first Proteomics collection presented by Nature Publishing Group, which looked at the challenges that face this fledgling field and some of the technological advances that are required to overcome them. In this second collection, Applied Proteomics, we take a look at the wide range of applications that proteomics tools can be used for, from understanding the pathology of cancer to the development of diagnostics.

The collection includes forward-looking Perspectives, recent Research Highlights and an overarching Reviews article that gives an insight into the part proteomics is playing in industrial research, starting at the genome and ending with new therapeutic targets for disease. One of the most complex diseases to gain an insight into is cancer, and on page 9, Samir Hanash, discusses how integrating genomic and proteomic data to create a global profile of the disease might help us learn more about tumour behaviour. This global approach is also favoured by Ritsert Jansen, whose Perspective article argues that perturbing more than one gene, factor, or biological system at once could provide more realistic and relevant information from genomics and proteomics data.
One area that has received a lot of attention since the sequencing of the human genome is oligosaccharide research, and in particular the use of oligosaccharide arrays. In their 'Innovation' perspective article on page15, Ten Feizi and Wengang Chai describe how these arrays can be used both for understanding the functions of glycoproteins and for characterizing protein-protein interactions. The second Innovation article in the collection looks at how proteomic technologies have revolutionized the measurements of metabolites. Lothar Willmitzer and colleagues compare different technologies and discuss how these can be applied to the development of new and better diagnostics, as well as functional genomics and systems biology.

Additional content related to proteomics research, including the entire contents of the first Proteomics collection and the latest primary research in the field, is available at the recently updated Nature Reviews Proteomics web focus (http://www.nature.com/reviews/focus/proteomics). Thanks to the financial support of Sigma-Aldrich, which has made the production of this collection possible, access to the content was provided free until the end of August 2005.