10.1586/14789450.4.6.709 © 2007 Future Drugs Ltd ISSN 1478-9450 709

Meeting Report

Proteomics: from technology development to biomarker applicationsHUPO 6th Annual World Congress, 6–10 October, 2007, Seoul, Korea

Sandra OrchardEMBL – European Bioinformatics Institute, Wellcome Trust, Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; orchard@ebi.ac.uk

Expert Rev. Proteomics 4(6), 709–710 (2007)

The 6th Annual World Congress of theHuman Proteome Organization(HUPO) took place in Seoul, Koreafrom 6–10 October with co-chairsYoung-Ki Paik (Yonsei University,Korea), Richard Simpson (Ludwig Insti-tute for Cancer Research, Australia) andYoung Mok Park (Korea Basic ScienceInstitute, Korea) welcoming nearly2500 delegates. The aim of the meetingwas to reflect the state-of-the-art of pro-teomics, from current technologicaldevelopments through to its practicaluse in cell biology and biomarker dis-covery. As in previous years, the first2 days of the congress were dedicated toHUPO initiatives workshops, an educa-tional day during which students werelectured to by a series of domainexperts, and a clinical day session, atwhich clinicians and bench scientistscombined to review the advances madein progressing the results of this tech-nology into healthcare settings. Theinterest in this area was reflected by atotal of over 1200 posters, presentingnovel and innovative approaches toapplying this technology to the fields ofcell biology, disease monitoring anddrug discovery.

HUPO initiativesThere are now a number of HUPO ini-tiatives that coordinate the research ofgroups all over the world, which com-bine to work on a common area ofinterest, to agreed communal standardsand with the eventual aim of making

the results of all this world freely availa-ble to the scientific community at large.Several of these groups are concentrat-ing on identifying the entire proteomeof a particular tissue and observing howthis changes with particular disease con-ditions. The initial results of the plasmaand brain proteome projects havealready been published and made availa-ble in public domain databases, such asPRIDE [1]. Data from the liver pro-teome project is currently being collatedand deposited, and the newly formedcardiovascular initiative is expected tostart generating results in 2008.

Underpinning all these efforts is aneed to ensure that the participatinglaboratories are achieving:

• Maximum sensitivity from their proteinidentification technology of choice

• Reagents available to verify observations

• Results are produced in a common for-mat, to enable datasets to be directlycomparable

• Facilitate deposition into commondatabases

• Subsequent users to access anddownload the information

The Protein Standards Group haveworked with Invitrogen Corp. to pro-duce a protein standard mixture thatcan be distributed to all groups partici-pating in the tissue initiatives, in orderto assess the various methods being usedin each laboratory. High-specificityantibodies for which the quality controldata are readily available are required by

proteomics scientists to confirm thepresence of proteins on particular tis-sues, and are essential tools for data ver-ification. The Human Antibody Initia-tive is working with several groups thatare committed to making such reagentsavailable. Finally, the task of the Pro-teomics Standards Initiative is to unifythe efforts of all these groups, as well asworking with instrumentation and soft-ware manufacturers to produce inter-changeable formats enabling both rawdata and the protein identificationsderived from them to be taken frommass spectrometers to search engines todatabases in a single data format [2]. Toaccompany this, the initiative is cur-rently publishing a series of minimumreporting standards documents toensure that the papers accompanyingthese datasets contain the essentialinformation that will enable the end-user to both understand and, if appro-priate, reproduce the experiment fromwhich they were produced.

Main sessionThe main body of the conference fea-tured a series of keynote lectures,20 parallel sessions, several industry-sponsored technology workshops andtwo special function meetings, whichfeatured the HUPO Young ScientistAward lectures and disease biomarkers.The main sessions featured a number ofrenowned speakers discussing aspects oftheir work. Kurt Wuthrich (ETZZurich, Switzerland) described thedevelopment of NMR spectroscopy,both for producing de novo determina-tions of 3D protein structures and alsofor identifying appropriate candidatesfor crystallography in structuralgenomics projects. Aaron Ciechanova(Rappaport Faculty of Medicine andResearch Institute, Israel) traced thehistory of our understanding of theprocess of protein degradation and therole of ubiquitination in this proce-dure. He laid down three challenges tothe proteomics community:

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Orchard

710 Expert Rev. Proteomics 4(6), (2007)

• To identify the full range of proteinstargeted by each specific ubiquitinligase

• To identify the downstream elementsrecognized by these tagged proteins

• To understand the significance of thedifferent patterns of polyubiquitinchains that tag these proteins.

He also briefly touched on the recentlyidentified nonproteolytic functions ofprotein ubiquitination, which have yetto be fully explored. Matthias Uhlen(Royal Institute of Technology, Sweden)described further advances in theHuman Protein Atlas, which nowincludes confocal images showing thesubcellular locations of proteins targetedby the 3000 high-specificity antibodiesproduced by this initiative, whilst JohnBergeron (McGill University, Canada)described the use of organellar proteo-mics (the identification of the proteincontent of a specific subcellular locationusing tandem mass spectrometry) to pre-dict the function of molecules from theirposition in the cell.

One question asked in many sessionswas the value of the ‘one hit wonder’,the proteins identified by a single pep-tide, which are currently excluded frommany datasets. It is becoming increas-ingly apparent from large-scale dataresources, such as the Peptide Atlasdescribed by Rudi Aebersold (ETH,Zurich, Switzerland), that many pro-teins may only be identified by a single‘proto-typic’ peptide and that valuabledata may be discarded if it is notretained for subsequent re-analysis. RolfApweiler (European BioinformaticsInstitute, UK), the current President ofHUPO, spoke of the value of publicdomain databases to manage and collatethis information and make it available tousers. Such efforts require data to be

presented in a common format to enablecomparability and portability, andrequire proteomics scientists to be awareof and utilize the data interchangestandards being developed by theHUPO Proteomics Standards Initiative.

Chemical proteomics was a relativelynew topic for the congress, with anumber of speakers describing strategiesby which small molecules have beenused as baits to pull out classes of pro-teins that bind to them. Matthew Hoyo(Stamford University, CT, USA)described cell-permeable protease inhibi-tors, which labeled their target moleculesthrough an enzyme-catalyzed chemicalreaction. Henrik Daub (Max PlanckInstitute, Germany) used immobilizedsmall molecules to affinity capture pro-tein kinases involved in the cell cycle andidentified novel mitotic function forthree of these enzymes.

The host nation, Korea, was well repre-sented amongst the speakers. For exam-ple, Jong Bok Yoon (Yonsei University,Korea) spoke about the role of phosphor-ylation in regulating the 26S proteosomevia the proteins interacting with phos-phorylated amino acids. By using atrypsin-catalyzed O16 to O18 exchangereaction, novel phosphorylation siteswere identified and phosphorylation siteswere also shown to vary with externalstimuli. A number of proteins that bindto these modified residues were affinitypurified and subsequently identified.These data suggest that the proteosomemay be differentially regulated by achange in the proteins with which itassociates. This talk was complementedby a presentation by Peipei Ping (UCLA,CA, USA), which also looked at thephosphorylation sites of the murine 20Sproteosome, with this group agreeingthat this is a key regulatory process forthis organelle.

SummaryThis was a vibrant conference thatreflected this active and dynamic field inwhich we work. The local organizingcommittee assembled an exciting scientificprogram and complemented this withexcellent facilities and an entertainingsocial agenda. Before Richard Simpsonmade the closing remarks, Albert Heck(Utrecht University, Netherlands) inviteddelegates to attend the next congress inAmsterdam, The Netherlands, 16–20August 2008.

Financial & competing interests disclosureThe author has no relevant affiliations orfinancial involvement with any organiza-tion or entity with a financial interest in orfinancial conflict with the subject matter ormaterials discussed in the manuscript. Thisincludes employment, consultancies, hono-raria, stock ownership or options, experttestimony, grants or patents received orpending, or royalties.

No writing assistance was utilized in theproduction of this manuscript.

Website

1 PRoteomics IDEntifications database www.ebi.ac.uk/pride

2 The HUPO Proteomics Standards Initiative www.psidev.info

Affiliation

• Sandra OrchardEMBL – European Bioinformatics Institute, Wellcome Trust, Genome Campus,Hinxton, Cambridge, CB10 1SD, UKorchard@ebi.ac.uk