Advancing Next-Generation Proteomics through Computational Research

Published: May 31, 2011

r 2011 American Chemical Society 2895 dx.doi.org/10.1021/pr200484b | J. Proteome Res. 2011, 10, 2895–2895

EDITORIAL

pubs.acs.org/jpr

Advancing Next-Generation Proteomics through ComputationalResearch

Computation has become a major factor in high-throughputproteomics, and computational aspects frequently represent

the core intellectual contributions of many scientificmanuscripts.Yet compared to the opportunities, only a relatively small number ofresearch groups are capable of undertaking such computationallycentric research agendas in part due to the combination oftechnical skills and substantive mass spectrometry knowledgerequired. There has been an unprecedented improvement in thequality and quantity of commercial proteomics data generationtechnologies, making data generation more accessible to manyresearchers. However, more and more discoveries will be led byresearchers in command of the skills necessary to mine andextensively interpret the volumes of data. Already the ability togenerate data vastly outpaces our ability to interpret it, and thelack of expertise in interpreting data is the current gating factor inthe advancement of proteomics sciences. Proteomics scientistswith training solely in data generation techniques will be shut outof more and more research opportunities. Likewise, computa-tional scientists lacking any training in analytic or biochemistrytechniques will be largely relegated to a support role. Initiativesare needed to bridge the gap between research opportunities andrelated algorithmic and statistical expertise and to usher in a newgeneration of computational mass spectrometry researchers.Achieving the full potential of innovative cutting-edge techniqueswill only be possible if these sibling communities come togetherat regular open forums designed to promote close interactionsand cross-disciplinary training, including training laboratoryscientists in computation, but also to encourage more computa-tional researchers to take their rightful role in leading substantiveresearch programs in proteomics.The RECOMB Satellite Conference on Computational Pro-

teomics (RECOMB-CP) is a yearly conference that aims tobridge this communication gap by directly connecting leaders inthe development of new mass spectrometry approaches withscientists with the skills to develop algorithmic and statisticalapproaches aimed at high-throughput interpretation of massspectrometry data. The parent RECOMB (Research in COm-putational Molecular Biology) conference is the leading genericbioinformatics conference covering all aspects of computationalbiology; RECOMB Satellite conferences are usually smaller andmore focused conferences aimed at specific areas of bioinfor-matics with well-defined research communities. The healthygrowth of the computational proteomics community and thepartnership with the Journal of Proteome Research since RE-COMB-CP 2010 further underscore the success of RECOMB-CP in directly connecting our community to leaders in the develop-ment of new mass spectrometry instruments (e.g., ion mobilityand electron dissociation methods), protocols (e.g., post-transla-tional modifications and alternative enzymatic digestions), andapplications (e.g., systems biology and protein�protein inter-actions). Not to be outdone, the computational communityresponded with novel contributions ranging from traditional (e.g.,peptide and protein identification) to emerging (e.g., cross-linking

and peptide/domain interactions) areas of computational re-search. These were further complemented by a series of tutorialsintroducing novel computational strategies and lively postersessions sparking enthusiastic discussions around connectingpressing needs in one field with their potential solutions fromthe other. Establishing such communication channels betweeninnovative computational advances and deep hands-on knowledgeof the critical needs and cutting-edge developments in proteomicsmass spectrometry are key to ushering in an era of computation-ally enabled mass spectrometry discoveries and researchers.We are committed to continuing the RECOMB-CP forum by

inviting your contributions of original manuscripts, poster ab-stracts, and active participation at its fearless discussions andlively interactions.

Nuno Bandeira,† Alexey Nesvizhskii,‡ andMartin McIntosh*,§

†Department of Computer Science and Engineering, Skaggs School ofPharmacy and Pharmaceutical Sciences, University of California,San Diego, California, United States‡Department of Pathology, University of Michigan, Ann Arbor, Michigan,United States§Computational Biology, Fred Hutchinson Cancer Research Center,Seattle, Washington, United States

’AUTHOR INFORMATION

Corresponding Author*E-mail: mmcintos@fhcrc.org.