Following the sequencing of the human genome and the revelation of smaller numbers of genes than had been anticipated, protein-based analyses and therefore proteomics have burst upon the scientific centre-stage. The core proteomics technology is mass spectrometry and advances in this field will be significant in increasing further the utility of protein-based analyses. Mass spectrometry, following digestion of the protein to peptides, has been the preferred strategy for protein identification for a number of years and no other method provides an unbiased approach to the characterisation of post-translational modifications. Advances continue to be made in all aspects of the field of mass spectrometry as applied in proteomics. In this collection of papers we have endeavoured to bring together practitioners from both the biochemistry and mass spectrometry fields providing the opportunity for these papers to be published jointly in two premier journals that service both of these fields: European Journal of Mass Spectrometry and Proteomics.

Topics covered include a novel top-down mass spectrometry based approach that starts by analysing the intact protein at high mass-resolution prior to digestion (Kelleher et al.). Griffiths and Jonsson address the influence of gas-phase conformation on peptide ion fragmentation in tandem mass spectrometry. Issues in the analysis of proteins using matrix-assisted laser desorption/ionisation (MALDI) discussed by Schmitter et al. include the selective-suppression effect. Improved approaches to and methods of sample preparation in MALDI are presented by Stensballe and Jensen and by Foti et al.

Advances in technology presented include use of acid hydrolysis in protein-chip array studies (Weinberger et al.) and systems integration for high throughput using a microfabricated device (Thibault et al.). A sequential digestion protocol for MALDI is described by Doucette and Li, and Smith et al. demonstrate the worth of multiple separations in gaining a complete understanding of protein modifications.

The papers concluding this issue describe various applications of mass spectrometry-based proteomics analyses. Identification of proteins co-purifying with lipid rafts is presented by Watts et al. Larsen et al. describes identification of proteins affected by the transcription regulating yeast genes. Giometti et al. report structural modifications of Methanococcus jannaschii flagellin proteins. The detection and location of disulfide bonds in synthetic peptides containing multiple cysteine residues is the subject of the final paper in the issue by Ceraulo et al.

The editors of this issue would like to thank the authors for their excellent contributions, the reviewers for timely critiques and Mike Dunn for his support of this unique project. It has been a pleasure to be part of this joint issue, and we hope that you will find it as informative as we have.

Peter J. Derrick
University of Warwick

Scott D. Patterson
Celera Genomics