Proteomics: from technology development to biomarker applications

The 6th Annual World Congress of the Human Proteome Organization (HUPO) took place in Seoul, Korea from 6–10 October with co-chairs Young-Ki Paik (Yonsei University, Korea), Richard Simpson (Ludwig Institute for Cancer Research, Australia) and Young Mok Park (Korea Basic Science Institute, Korea) welcoming nearly 2500 delegates. The aim of the meeting was to reflect the state-of-the-art of proteomics, from current technological developments through to its practical use in cell biology and biomarker discovery. As in previous years, the first 2 days of the congress were dedicated to HUPO initiatives workshops, an educational day during which students were lectured to by a series of domain experts, and a clinical day session, at which clinicians and bench scientists combined to review the advances made in progressing the results of this technology into healthcare settings. The interest in this area was reflected by a total of over 1200 posters, presenting novel and innovative approaches to applying this technology to the fields of cell biology, disease monitoring and drug discovery.

HUPO initiatives

There are now a number of HUPO initiatives that coordinate the research of groups all over the world, which combine to work on a common area of interest, to agreed communal standards and with the eventual aim of making the results of all this world freely available to the scientific community at large. Several of these groups are concentrating on identifying the entire proteome of a particular tissue and observing how this changes with particular disease conditions. The initial results of the plasma and brain proteome projects have already been published and made available in public domain databases, such as PRIDE [1]. Data from the liver proteome project is currently being collated and deposited, and the newly formed cardiovascular initiative is expected to start generating results in 2008.

Underpinning all these efforts is a need to ensure that the participating laboratories are achieving:

•	Maximum sensitivity from their protein identification technology of choice
•	Reagents available to verify observations
•	Results are produced in a common format, to enable datasets to be directly comparable
•	Facilitate deposition into common databases
•	Subsequent users to access and download the information

The Protein Standards Group have worked with Invitrogen Corp. to produce a protein standard mixture that can be distributed to all groups participating in the tissue initiatives, in order to assess the various methods being used in each laboratory. High-specificity antibodies for which the quality control data are readily available are required by proteomics scientists to confirm the presence of proteins on particular tissues, and are essential tools for data verification. The Human Antibody Initiative is working with several groups that are committed to making such reagents available. Finally, the task of the Proteomics Standards Initiative is to unify the efforts of all these groups, as well as working with instrumentation and software manufacturers to produce interchangeable formats enabling both raw data and the protein identifications derived from them to be taken from mass spectrometers to search engines to databases in a single data format [2]. To accompany this, the initiative is currently publishing a series of minimum reporting standards documents to ensure that the papers accompanying these datasets contain the essential information that will enable the end-user to both understand and, if appropriate, reproduce the experiment from which they were produced.

Main session

The main body of the conference featured a series of keynote lectures, 20 parallel sessions, several industry-sponsored technology workshops and two special function meetings, which featured the HUPO Young Scientist Award lectures and disease biomarkers. The main sessions featured a number of renowned speakers discussing aspects of their work. Kurt Wuthrich (ETZ Zurich, Switzerland) described the development of NMR spectroscopy, both for producing de novo determinations of 3D protein structures and also for identifying appropriate candidates for crystallography in structural genomics projects. Aaron Ciechanova (Rappaport Faculty of Medicine and Research Institute, Israel) traced the history of our understanding of the process of protein degradation and the role of ubiquitination in this procedure. He laid down three challenges to the proteomics community:

•	To identify the full range of proteins targeted by each specific ubiquitin ligase
•	To identify the downstream elements recognized by these tagged proteins
•	To understand the significance of the different patterns of polyubiquitin chains that tag these proteins.

He also briefly touched on the recently identified nonproteolytic functions of protein ubiquitination, which have yet to be fully explored. Matthias Uhlen (Royal Institute of Technology, Sweden) described further advances in the Human Protein Atlas, which now includes confocal images showing the subcellular locations of proteins targeted by the 3000 high-specificity antibodies produced by this initiative, whilst John Bergeron (McGill University, Canada) described the use of organellar proteomics (the identification of the protein content of a specific subcellular location using tandem mass spectrometry) to predict the function of molecules from their position in the cell.

One question asked in many sessions was the value of the ‘one hit wonder’, the proteins identified by a single peptide, which are currently excluded from many datasets. It is becoming increasingly apparent from large-scale data resources, such as the Peptide Atlas described by Rudi Aebersold (ETH, Zurich, Switzerland), that many proteins may only be identified by a single ‘proto-typic’ peptide and that valuable data may be discarded if it is not retained for subsequent re-analysis. Rolf Apweiler (European Bioinformatics Institute, UK), the current President of HUPO, spoke of the value of public domain databases to manage and collate this information and make it available to users. Such efforts require data to be presented in a common format to enable comparability and portability, and require proteomics scientists to be aware of and utilize the data interchange standards being developed by the HUPO Proteomics Standards Initiative.

Chemical proteomics was a relatively new topic for the congress, with a number of speakers describing strategies by which small molecules have been used as baits to pull out classes of proteins that bind to them. Matthew Hoyo (Stamford University, CT, USA) described cell-permeable protease inhibitors, which labeled their target molecules through an enzyme-catalyzed chemical reaction. Henrik Daub (Max Planck Institute, Germany) used immobilized small molecules to affinity capture protein kinases involved in the cell cycle and identified novel mitotic function for three of these enzymes.

The host nation, Korea, was well represented amongst the speakers. For example, Jong Bok Yoon (Yonsei University, Korea) spoke about the role of phosphorylation in regulating the 26S proteosome via the proteins interacting with phosphorylated amino acids. By using a trypsin-catalyzed O¹⁶ to O¹⁸ exchange reaction, novel phosphorylation sites were identified and phosphorylation sites were also shown to vary with external stimuli. A number of proteins that bind to these modified residues were affinity purified and subsequently identified. These data suggest that the proteosome may be differentially regulated by a change in the proteins with which it associates. This talk was complemented by a presentation by Peipei Ping (UCLA, CA, USA), which also looked at the phosphorylation sites of the murine 20S proteosome, with this group agreeing that this is a key regulatory process for this organelle.

Summary

This was a vibrant conference that reflected this active and dynamic field in which we work. The local organizing committee assembled an exciting scientific program and complemented this with excellent facilities and an entertaining social agenda. Before Richard Simpson made the closing remarks, Albert Heck (Utrecht University, Netherlands) invited delegates to attend the next congress in Amsterdam, The Netherlands, 16–20 August 2008.

Financial & competing interests disclosure

The author has no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

No writing assistance was utilized in the production of this manuscript.