Feature Meeting Review: Progress in Establishing Common ...downloads.hindawi.com/journals/ijg/2003/[email protected] Received: 3 February 2003 Revised: 6 February

Comparative and Functional GenomicsComp Funct Genom 2003; 4: 203–206.Published online 1 April 2003 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.279

Feature

Meeting Review: Progress in EstablishingCommon Standards for ExchangingProteomics Data: the second meetingof the HUPO Proteomics StandardsInitiativeHinxton, Cambridge, UK, 22–24 January 2003

Sandra Orchard1, Paul Kersey1, Weimin Zhu1, Luisa Montecchi-Palazzi2, Henning Hermjakob1*and Rolf Apweiler1

1EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK2University of Rome ‘Tor Vergata’, Rome, Italy

*Correspondence to:Henning Hermjakob, EMBLOutstation, EuropeanBioinformatics Institute,Wellcome Trust GenomeCampus, Hinxton, Cambridge,UK.E-mail:[email protected]

Received: 3 February 2003Revised: 6 February 2003Accepted: 6 February 2003

AbstractThe Proteomics Standards Initiative (PSI) aims to define community standards fordata representation in proteomics and to facilitate data comparison, exchange andverification. Rapid progress has been made in the development of common standardsfor data exchange in the fields of both mass spectrometry and protein–protein inter-actions since the first PSI meeting [1]. Both hardware and software manufacturershave agreed to work to ensure that a proteomics-specific extension is created for theemerging ASTM mass spectrometry standard and the data model for a proteomicsexperiment has advanced significantly. The Protein–Protein Interactions (PPI) groupexpects to publish the Level 1 PSI data exchange format for protein–protein interac-tions by early summer this year, and discussion as to the additional content of Level2 has been initiated. Copyright 2003 John Wiley & Sons, Ltd.

Keywords: proteomics; spectrometry; protein–protein interactions; standards

Introduction

The inaugural meeting of the PSI in October 2002brought together representatives from the databaseproducer, user and software producer communi-ties who were seen as essential in establishing andmaintaining standards in the fields of mass spec-trometry and PPIs. The second PSI meeting focusedon consolidating and extending both the achieve-ments of the first meeting and work undertakenin the interim period. In addition to this, a widerdiscussion was initiated on the more global needsof the community. A requirement for standardsto allow the storage and exchange of the entirerange of proteomics data has been fed back to the

PSI over the past few months and there was somedebate as to how this could best be addressed.

Developing a global proteomics standard

One example of such a system is PEDRo, currentlyunder development at the University of Manchester[2]. PEDRo has been designed to encode labo-ratory produced data, producing an XML-basedPEML (proteomics experiment mark-up language)file for local storage or submission to a repositoryand allows the storage of sample origin and pro-cessing information, mass spectrometry data andthe results of in silico analysis. A related sys-tem, YPRC-PDC, was then described by Sangyun

Copyright 2003 John Wiley & Sons, Ltd.

204 Meeting Review

Cho (Yonsei University, Korea), which has beendesigned to systematically organize, store and anal-yse proteomic data. It can act as a repository ofdata in various formats and has a dynamic userreport system. Finally, Martin Bluggel (ProtagenAG, Dortmund, Germany) described the difficultiesin handling readouts from several different ana-lytical machines. The company have developed aseries of algorithms to enable high-throughput datato be collected, compared and fed into a singledata management system. The scores are boostedby meta-scoring techniques that rely on knowncontaminants and internal calibrants. The impor-tance of involving instrument manufacturers froman early stage in any attempt to establish a com-mon standard was heavily stressed throughout themeeting. A decision was taken at this point to usean existing effort, PEDRo, as a starting point forsystem design, rather than beginning anew.

The meeting then divided into two sessionsto concentrate on the more immediate goals ofdeveloping standards for mass spectrometry andPPIs.

Mass spectrometry group

The mass spectrometry group, chaired by WeiminZhu (EBI), heard a report of a preliminary meet-ing that had been held between lead players in thefirst PSI meeting and hardware (Micromass, Brukerand Ciphergen) and software (Water and Mascot)vendors. The vendors had expressed a strong will-ingness to establish and support a standard repre-sentation for proteomics-related mass spectrometrydata. Randall Julian (Eli Lilly), the chair of theASTM (American Society for Tests and Measure-ments) committee E01.25, which is responsible foran existing mass spectrometry standard, presentedthis to both the preliminary meeting and the opensession. The E01.25 standard has strong vendorsupport, but its scope does not cover all types ofmass spectrometry experiments, and it is imple-mented in netCDF, which is not a highly descrip-tive format. Recently two other putative standards,SpectroML and GAML, have emerged, both usingXML representations: and a second ASTM com-mittee, E13, is looking at expanding their scope tocreate a general standard for mass spectrometry toreplace the E01.25 standard. However, all existingstandards focus on the direct output produced by

an instrument and not on its subsequent extensionto proteomics.

In general discussions, it was decided to define astandard representation for annotated peak lists (i.e.peak lists plus peptide and protein identifications)and to insert such a representation into the emerg-ing standard for raw mass spectrometry data. Ran-dall Julian agreed to steer a collaborative sharingof the XML schemas already developed by partici-pating vendors, with the intention of reporting backto the PSI within 3 months. PSI will contribute tothe process by providing a specification of whatinformation researchers in the field of proteomicswould find useful to have captured within such astandard.

Mass spectrometry and proteomics

The minimum requirements for a possible reposi-tory of spectrometric data were discussed. To max-imize the interpretability of the results, the fullbiological context of an experiment, as describedin a paper, would need to be deposited; to maxi-mize reproducibility, the full details of the exper-iment would need to be captured down to theinstrument level. However, such a system wouldbe too complex to be practical, and compro-mises will be made to achieve a practicablesystem.

Using the prototypic PEDRo data model (asdefined in PEML) as a concrete starting point forworking on the definition of data structures to holdinformation on mass spectrometry experiments, thegroup designed a flexible structure for proteomicsexperiments, with both separation and analyticalphases, to support configurable workflows. Thegroup also developed detailed models for manyparticular separation techniques. Discussions tookplace on clearly defining the many different levelsat which data is produced or interpreted duringa mass spectrometry experiment, and focused inparticular on the key question of the representationof peak lists.

Future developments

The working groups will continue to refine and for-malize their data models and hope to collaboratewith MGED in developing common guidelines forexperimental description. Hardware and softwaremanufacturers have committed to work to ensure

Copyright 2003 John Wiley & Sons, Ltd. Comp Funct Genom 2003; 4: 203–206.

Meeting Review 205

that a proteomics-specific extension is created forthe emerging ASTM mass spectrometry standard.The aim is for a draft specification to be presentedto the ASMS (American Society for Mass Spec-trometry) meeting in June 2003.

Protein–protein interactions group

The session opened with a number of presenta-tions describing the analysis of existing PPI data(Michael Lappe, EBI, and Christian von Mering,EMBL) and detailing a number of both PPI andpathway databases (Yves Deville, ULB) that areinterested in utilizing the protein interaction dataexchange format. Gary Bader described the work ofBioPAX, a group formed by a number of databasesstoring and displaying data on biological pathways(signalling and metabolic) that is also looking fora common format with which to exchange data.BioPAX hope to integrate the standards devel-oped by a number of related projects, such asthe PPI data exchange format and chemical mark-up language (CML) to describe small molecules,into their model to ensure that data exchange willremain possible across the widest possible spreadof databases.

The PSI PPI data exchange format

As previously described [1], the PSI data exchangeformat is multi-levelled, with Level 1 designed tofulfil basic requirements and be suitable for rapidimplementation. The current status of the Level 1XML model produced as a result of discussionsat the first PSI meeting was described by HenningHermjakob (EBI). The model was then extensivelyreworked during the open session of the meeting. Inaddition to the structural changes, researchers alsonow have the option of ascribing confidence lev-els to the data at various points throughout the dataentry process, dating the entry and adding free com-ments in appropriate places. Wherever possible, thepossible values of attributes in the data model aredefined by controlled vocabularies (Figure 1). Anumber of controlled vocabularies originally devel-oped by Luisa Montecchi (University of Rome) forthe IntAct project will be made available as partof the PPI data exchange format. A procedure toadd new terms was discussed, which will be imple-mented before the schema is released.

It is intended to publish the data exchange formatand accompanying controlled vocabularies, docu-mentation, examples and use-cases in early summer2003. A number of the databases represented at the

Figure 1. (a) A detail of the PSI XML schema for protein interaction data, the description of the experimental parameters.Wherever possible, attributes in the data model are controlled by external controlled vocabularies, which are representedin GO format. (b) An extract of the controlled vocabulary for experimental methods; the arrow illustrates the choiceof a value from the controlled vocabulary. The XML schema representation has been generated by XMLSpy 5.3, therepresentation of the controlled vocabulary by DAG-Edit 1.311


206 Meeting Review

meeting, e.g. BIND, DIP, MINT, IntAct and Hybri-genics, intend to offer their publicly available datain this format during 2003, and confirmation from anumber of other PPI databases is currently awaited.

Future developments

Additional features, which will be implemented atLevel 2, were briefly discussed during the meet-ing but it was decided it would not be appropriateto commence this work until Level 1 had beenpublished. The progress of Level 1 and the devel-opment of Level 2 will be addressed at the next PSImeeting at the 2nd HUPO congress in Montreal, inOctober 2003.

Conclusions

Concrete progress has been made since the initialPSI meeting in October 2002. The mass spectrom-etry group have aligned themselves with existingefforts to standardize instrumentation, and manu-facturers have agreed to support the needs of theproteomics community. Advances have also beenmade in defining the working model to describe aproteomics experiment. The PPI group are readyto publish Level 1 of the PPI data exchange for-mat by early summer 2003 and the infrastructureto support this initiative is already largely in place.

As previously stated, all such efforts requiresupport from the user community and the PSI isactively seeking input and advice from all quarters.

Anyone wishing to become involved is invitedto visit http://psidev.sf.net, to participate in thediscussion groups listed, and to contribute to thefurther development of community standards forproteomics data.

Acknowledgements

Supported by European Community Contract No. QLRI-CT-2001-00015 for ‘TEMBLOR’ under the specific RTDprogramme ‘Quality of Life and Management of LivingResources’.

Related websites

BIND, http://bind.ca/BioPAX, http://www.biopax.orgDIP, http://dip.doe-mbi.ucla.edu/Hybrigenics, http://www.hybrigenics.frMINT, http://cbm.bio.uniroma2.it/mint/MGED, http://www.mged.orgPEDRo, http://pedro.man.ac.uk/PSI, http://psidev.sf.net/

References

1. Orchard S, Kersey P, Hermjakob H, Apweiler R. 2003. Meet-ing Review: the HUPO Proteomics Standards Initiative meet-ing: towards common standards for exchanging proteomicsdata. Comp Funct Genom 4(1): 16–17.

2. Taylor CF, Paton NW, Garwood KL, et al. 2003. A systematicapproach to modelling, capturing and disseminating proteomicsexperimental data. Nature Biotechnol 21: 247–254.


http://psidev.sf.net

http://bind.ca/

http://www.biopax.org

http://dip.doe-mbi.ucla.edu/

http://www.hybrigenics.fr

http://cbm.bio.uniroma2.it/mint/

http://www.mged.org

http://pedro.man.ac.uk/

http://psidev.sf.net/

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Feature Meeting Review: Progress in Establishing Common ...downloads.hindawi.com/journals/ijg/2003/[email protected] Received: 3 February 2003 Revised: 6 February