PROTEOMICS – Clinical Applications

Clinical Proteomics Advances



Michael J. Dunn

With this double issue, Proteomics Clinical Applications enters its eighth year of publication. The term “proteome” was coined by Marc Wilkins and introduced to the scientific community at the 1st Siena Meeting in 1994. The term proteome was originally defined as the “PROTEin complement of a genOME” but soon became to be generally accepted to mean the set of proteins expressed by a particular organelle, cell type, or tissue under a particular set of conditions. The 10th Biannual Siena Meeting to be held from 31st August to 4th September 2014 will mark the 20th Anniversary of the science of “proteomics”. From the beginning it was clear that proteomics could have a profound impact in the area of biomedical and clinical research. Proteomic approaches can be used to examine global alterations in protein expression in human disease states and can provide valuable new insights into cellular mechanisms involved in dysfunction in disease. Moreover, the use of proteomics to investigate human diseases should result in the generation of new diagnostic and prognostic markers, and identify new potential targets for therapeutic intervention. Proteomics Clinical Applications was first published in 2007 to address the need for a specialist journal in this area, and since that time the number of papers published in this field according to data from PubMed/MEDLINE, has risen from around 1000 papers in 2007 to nearly 1600 in 2012. Our aim continues to be to ensure that Proteomics Clinical Applications remains the premier source of information in the field of the application of proteomics to the study of human disease and translation to the clinic. In 2012 the Impact Factor of the journal rose to 2.92 and we predict that we will see a further rise when the Impact Factor for 2013 is announced by ISI.

Over the last year, it has again been a pleasure to work with our two Associate Editors, Roz Banks (Leeds, UK) and Jennifer Van Eyk (Baltimore, MD, USA), together with Achim Kraus, Managing Editor of Proteomics Clinical Applications to help shape future development of the journal to ensure that it remains the leader in the field. I would also like to thank our group of Senior Editors who continue to make a major contribution to the journal by coordinating the peer review process for all of the papers submitted to their journal. Finally, I would like to express our sincere thanks to the panel of around 160 Reviewers who have taken part in the peer review process of papers submitted to Proteomics Clinical Applications over the last 12 months. Their names can be found in the list that appears at the end of this issue.

It is now two years since we made any extensive revisions to the Editorial Board of Proteomics Clinical Applications. We believe that now is an appropriate time to revitalise the Editorial Board by recruiting some new members to join as from January 2014 (Volume 8), so that I have had to ask a proportion of the current members to retire from the Board at this time. I would like to express my appreciation for the valuable input that these individuals have made as Board members to the development of the journal over the past years. I would now like to welcome the scientists who have accepted our invitation to join the Editorial Board of Proteomics Clinical Applications with effect from this issue. I am sure that their expertise and enthusiasm will enhance the journal in future. The names of the new members of the Editorial Board are: Graham Ball (UK), Michael Bereman (USA), Paul Cutler (Switzerland), Jeanette Eckel-Passow (USA), Peter Findeisen (Germany), Sebastien Gallien (Luxembourg), Hendrik Neubert (USA), and Jean-Daniel Tissot (Switzerland).

As of January 2013, we are publishing online a new set of Instructions to Authors for Proteomics Clinical Applications that includes some extensive additions and amendments. The new set of Instructions to Authors will be published in print in a future Issue of the journal. The requirements for full details of the experimental design and, where applicable, of patient groups and clinical samples have been expanded and made more rigorous. The need for data validation in comparative or shotgun-like discovery studies has been clarified. It is now mandatory that confirmatory data (e.g. from validated immunoassays, immunohistochemistry, alternative MS-based methods, Western blotting, etc.) using independent replication sets be provided for at least a subset of proteins. Deposition of supporting data in a public, and global open access database is strongly recommended for all types of manuscript and is mandatory for Dataset Briefs. Examples of such databases are the ProteomeXchange consortium ( [including the receiving repositories PRIDE and PASSEL] or World-2DPAGE ( For Dataset Briefs, placing of datasets only in private or institute websites is not acceptable, although the data can be deposited in both a global database and a private or institute website. Authors interested in submitting a manuscript to the journal are urged to consult carefully the current Instructions to Authors that can be found online. The current version of the Instructions to Authors is in HTML format with hyperlinks to different sections or other pages and can be seen at:

We will continue our policy of producing Special Issues devoted to collections of papers describing important and emerging areas of clinical proteomics. In Volume 8 we will publish Special Issues on Proteomics of the Eye (Editors: Richard Semba, Jan Enghild), Proteases and Disease (Editors: Peter Findeisen, Oliver Schilling), Animal Model Systems for Proteomics (Editor: Emoke Bendixen), Proteomics in Pediatrics (Editors: Alan Everett, Vera Ignjatovic), and Personalised Medicine for Cancer (Editor: Emmanuel Petricoin). In addition, we are continuing our tradition of having an annual issue devoted to reviews of hot topics in clinical proteomics, and these articles are published in this current issue of the journal. We are already planning the Reviews issue of Proteomics Clinical Applications for Volume 9 (2015) – see the Call for Reviews published in this issue.

Readers of Proteomics Clinical Applications should regularly visit the journal homepage on Wiley Online Library ( to access the latest issue of the journal and to find specific articles, especially those published as “Epubs” (Accepted Articles, Early View) well before their appearance in a specific issue of the journal. Furthermore you can explore the many additional features, such as Commentary Archive, Special Issue Archive, Meetings Diary, Personal Perspective Series and Viewpoint Forum that are updated regularly by our Web Editor, Christine Mayer. These features can be accessed by selecting items from the menu ‘‘Special Features’’.

Finally, I would like to thank the Associate Editors, Senior Editors, Editors of Special Issues, the Editorial Board, and in particular the Managing Editor, Achim Kraus, and his team in the Editorial Office for their efforts over the last year to maintain Proteomics Clinical Applications as the most comprehensive journal in the field. I hope that researchers will continue to choose Proteomics Clinical Applications as the journal in which to publish the results of their research. Finally, I would like to thank you, the readers, for your continued support of Proteomics Clinical Applications and hope that you will find much to stimulate and interest you in Proteomics Clinical Applications during 2014.


Michael J. Dunn