Proteomics Data Collection – 4th ProDaC Workshop 15 August 2008, Amsterdam,The Netherlands

ProDaC (Proteomics Data Collection), a “Coordination Action” within the 6^th EU framework programme, was created to support the collection, distribution and public availability of data from proteomics experiments. Within the consortium standards are created and maintained enabling an extensive data collection within the proteomics community. Important elements of ProDaC are workshops held twice a year to allow communication between the ProDaC partners and to report the ongoing progress. The most recent assembly was the 4^th ProDaC workshop on August 15^th, 2008, in Amsterdam, The Netherlands. It took place directly before the 7^th HUPO Annual World Congress (Human Proteome Organisation). Work package coordinators and partners presented the progress achieved since the last meeting. Additionally, an EU official presented funding opportunities for proteomics in the next EU framework programme and five external speakers presented talks about their work in relation to ProDaC.     

Proteomics Data Collection – 5th ProDaC Workshop 4 March 2009, Kolympari,Crete, Greece

The Proteomics Data Collection (ProDaC) consortium, a “Coordination Action” funded by the 6th EU Framework Programme, started in October 2006. Its aim was to facilitate the collection and distribution of proteomics data and the public availability of data sets from proteomics experiments. Within the consortium standard formats are created and tools are developed to allow extensive data collection within the proteomics community. An important part of ProDaC is the organization of workshops twice a year to inform about the consortium's progress and to stimulate communication between the ProDaC partners and between partners and interested members of the proteomics community. ProDaC ends on March 31, 2009. The most recent (and final) workshop was the 5th ProDaC workshop held on March 4, 2009 in Kolympari, Crete, Greece. The progress since the last meeting and an overall summary was presented by the work package coordinators and partners. Four external speakers presented talks about their work in relation to ProDaC.     

Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea

Proteomics Data Collection (ProDaC) is an EU-funded "Coordination Action" within the 6th framework programme. It aims to simplify the publication, dissemination and utilization of proteomics data by establishing standards that will support broad data collection from the research community. As a part of ProDaC, regular workshops are organized on a half-yearly basis to enable communication and discussion of the involved partners and to report on project progress. After the kick-off meeting (October 2006) in Long Beach, CA, USA and the 1st workshop in Lyon, France (April 2007), the 2nd ProDaC workshop took place at the COEX InterContinental Hotel in Seoul, Korea, on 5th October 2007, shortly before the HUPO World Congress. The progress achieved within the first year was presented by the leaders of the work packages. Additionally, a Journal's representative talked about his experiences and future plans concerning Proteomics standards; and two further external speakers presented their research related to data handling and Proteomics repositories.     

Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain

The "Coordination Action" ProDaC (Proteomics Data Collection) - funded by the EU within the 6th framework programme - was created to support the dissemination, utilization and publication of proteomics data. Within this international consortium, standards are developed and maintained to support extensive data collection by the proteomics community. An important part of ProDaC are workshops organized on a regular basis (two per year) to allow discussions and communication between the ProDaC partners and to report on the progress of the project. The kick-off meeting took place in October 2006 in Long Beach, CA, USA. The 1st ProDaC workshop was held in Lyon, France (April 2007) and the 2nd in Seoul, Korea in October 2007. ProDaC organized the 3rd ProDaC workshop at the Beatriz Hotel, Toledo, on 22nd April, 2008, directly before the HUPO - PSI spring meeting (Human Proteome Organisation - Proteomics Standards Initiative). The work package coordinators presented talks about the progress achieved during the past six months. Additionally four external speakers presented their work on data conversion and data repositories. The concluding discussion session was chaired by the Journal's representative.     

A guide to the Proteomics Identifications Database proteomics data repository

The Proteomics Identifications Database (PRIDE, www.ebi.ac.uk/pride ) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through the PRIDE web and BioMart interfaces. We also highlight the mechanism by which tailored queries in the BioMart can join PRIDE to other resources such as Reactome, Ensembl or UniProt to execute extremely powerful across‐domain queries. We then present the latest improvements in the PRIDE submission process, using the new easy‐to‐use, platform‐independent graphical user interface submission tool PRIDE Converter. Finally, we speak about future plans and the role of PRIDE in the ProteomExchange consortium.     

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland

The plenary session of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization at the Tenth annual HUPO World Congress updated the delegates on the ongoing activities of this group. The Molecular Interactions workgroup described the success of the PSICQUIC web service, which enables users to access multiple interaction resources with a single query. One user instance is the IMEx Consortium, which uses the service to enable users to access a non-redundant set of protein-protein interaction records. The mass spectrometry data formats, mzML for mass spectrometer output files and mzIdentML for the output of search engines, are now successfully established with increasing numbers of implementations. A format for the output of quantitative proteomics data, mzQuantML, and also TraML, for SRM/MRM transition lists, are both currently nearing completion. The corresponding MIAPE documents are being updated in line with advances in the field, as is the shared controlled vocabulary PSI-MS. In addition, the mzTab format was introduced, as a simpler way to report MS proteomics and metabolomics results. Finally, the ProteomeXchange Consortium, which will supply a single entry point for the submission of MS proteomics data to multiple data resources including PRIDE and PeptideAtlas, is currently being established.     

jmzTab: A Java interface to the mzTab data standard

mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab‐delimited file that can capture identification and quantification results coming from MS‐based proteomics and metabolomics approaches. We here present an open‐source Java application programming interface for mzTab called jmzTab. The software allows the efficient processing of mzTab files, providing read and write capabilities, and is designed to be embedded in other software packages. The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table‐based sections in the mzTab files. In this article, as two example implementations, we also describe two stand‐alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab. The library is freely available at http://mztab.googlecode.com .     

Tackling Quantitation: A Report on the Annual Spring Workshop of the HUPO‐PSI 28–30 March 2010, Seoul,South Korea

The annual Spring Workshop of the HUPO‐PSI took place in Korea, where the Mass Spectrometry and Protein Separations groups joined forces to tackle the issue of the consistent reporting of quantitative proteomic data generated by mass‐spectrometry‐based technologies. A preliminary mzQuantML schema was drafted which, when completed and tested, will complement the existing mzIdentML schema for reporting protein identifications. The Molecular Interactions group concentrated on the implementations of the PSICQUIC (PSI Common Query InterfaCe) service that allows users to simultaneously query interaction data across multiple participating resources. Work was also undertaken to update the MIAPE guidelines, in response to feedback from the editors of a number of proteomic journals.     

Data standards for proteomics: mitochondrial two-dimensional polyacrylamide gel electrophoresis data as a model system

Proteomics has emerged as a major discipline that led to a re-examination of the need for consensus and a nationally sanctioned set of proteomics technology standards. Such standards for databases and data reporting may be applied to two-dimensional polyacrylamide gel electrophoresis (2D PAGE) technology as a pilot project for assessing global and national needs in proteomics, and the role of the National Institute of Standards and Technology (NIST) and other similar standards and measurement organizations. The experience of harmonizing the heterogeneous data included in the Protein Data Bank (PDB) provides a paradigm for technology in an area where significant heterogeneity in technical detail and data storage has evolved. Here we propose an approach toward standardizing mitochondrial 2D PAGE data in support of a globally relevant proteomics consensus.     

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA

The theme of the third annual Spring workshop of the HUPO-PSI was "proteomics and beyond" and its underlying goal was to reach beyond the boundaries of the proteomics community to interact with groups working on the similar issues of developing interchange standards and minimal reporting requirements. Significant developments in many of the HUPO-PSI XML interchange formats, minimal reporting requirements and accompanying controlled vocabularies were reported, with many of these now feeding into the broader efforts of the Functional Genomics Experiment (FuGE) data model and Functional Genomics Ontology (FuGO) ontologies.     

Helicobacter pylori proteomics by 2‐DE/MS, 1‐DE‐LC/MS and functional data mining

With its predicted proteome of 1550 proteins (data set Etalon) Helicobacter pylori 26695 represents a perfect model system of medium complexity for investigating basic questions in proteomics. We analyzed urea‐solubilized proteins by 2‐DE/MS (data set 2‐DE) and by 1‐DE‐LC/MS (Supprot); proteins insoluble in 9 M urea but solubilized by SDS (Pellet); proteins precipitating in the Sephadex layer at the application side of IEF (Sephadex) by 1‐DE‐LC/MS; and proteins precipitating close to the application side within the IEF gel by LC/MS (Startline). The experimental proteomics data of H. pylori comprising 567 proteins (protein coverage: 36.6%) were stored in the Proteome Database System for Microbial Research ( http://www.mpiib‐berlin.mpg.de/2D‐PAGE/ ), which gives access to raw mass spectra (MALDI‐TOF/TOF) in T2D format, as well as to text files of peak lists. For data mining the protein mapping and comparison tool PROMPT ( http://webclu.bio.wzw.tum.de/prompt/ ) was used. The percentage of proteins with transmembrane regions, relative to all proteins detected, was 0, 0.2, 0, 0.5, 3.8 and 6.3% for 2‐DE, Supprot, Startline, Sephadex, Pellet, and Etalon, respectively. 2‐DE does not separate membrane proteins because they are insoluble in 9 M urea/70 mM DTT and 2% CHAPS. SDS solubilizes a considerable portion of the urea‐insoluble proteins and makes them accessible for separation by SDS‐PAGE and LC. The 2‐DE/MS analysis with urea‐solubilized proteins and the 1‐DE‐LC/MS analysis with the urea‐insoluble protein fraction (Pellet) are complementary procedures in the pursuit of a complete proteome analysis. Access to the PROMPT‐generated diagrams in the Proteome Database allows the mining of experimental data with respect to other functional aspects.     

Managing the Data Explosion A Report on the HUPO‐PSI Workshop August 2008, Amsterdam,The Netherlands

The plenary session of the Proteomics Standards Initiative (PSI) of the Human Proteome Organisation at the 7^th annual HUPO world congress updated the delegates on the current status of the ongoing work of this group. The release of the new MS interchange format, mzML, was formally announced and delegates were also updated on the advances in the area of molecular interactions, protein separations, proteomics informatics and also on PEFF, a common sequence database format currently under review in the PSI documentation process. Community input on this initiative was requested. Finally, the impact these new data standards are having on the data submission process, which increasingly is an integral part of the publication process, was reviewed and discussed.     

Preparing to Work with Big Data in Proteomics – A Report on the HUPO‐PSI Spring Workshop

The Human Proteome Organisation Proteomics Standards Initiative (HUPO‐PSI) was established in 2002 with the aim of defining community standards for data representation in proteomics and facilitating data comparison, exchange and verification. The 2013 annual spring workshop was hosted by the University of Liverpool, UK and concentrated on updating and refining the existing standards in the light of new methodologies and technologies. To control the inflation of file sizes, strategies for file compression, particularly for mzML files, were explored. Best practices for encoding information such as protein grouping and PTM localisation were refined and documented. Additional example files for the mzQuantML format were designed to provide support for selected reaction monitoring techniques. Enhancements to the PSI Common Query Interface (PSICQUIC) and PSI‐MI XML were discussed. Finally, the group engaged in discussion on how the existing work of the HUPO‐PSI can be leveraged by the Metabolomics Standards Initiative to improve the capture of metabolite data.     

Implementing Data Standards: A report on the HUPOPSI Workshop September 2009, Toronto,Canada

The plenary session of the Proteomics Standards Initiative of the Human Proteome Organisation at the 8th Annual HUPO World Congress updated the delegates on the current status of the ongoing work of this group. The mass spectrometry group reviewed the progress of mzML since its release last year and detailed new work on providing a common format for SRM/MRM transition lists (TraML). The implementation of mzIdentML, for describing the output of proteomics search engines, was outlined and the release of a new web service PSICQUIC, which allows users to simultaneously search multiple interaction databases, was announced. Finally, the audience participated in a lively debate, discussing both the benefits of these standard formats and issues with their adoption and use in a research environment.     

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed upon two primary needs for the wide use of quality metrics: (i) an evolving list of comprehensive quality metrics and (ii) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in Proteomics, Proteomics Clinical Applications, Journal of Proteome Research, and Molecular and Cellular Proteomics, as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.     

5th BSPR‐EBI Meeting,Proteomics: From Technology to New Biology 8–10 July 2008, Wellcome Trust Conference Centre,Hinxton, Cambridge,UK

This paper reports on the 5^th joint British Society for Proteome Research (BSPR) and European Bioinformatics Institute (EBI) meeting which took place at the Wellcome Trust Conference Centre, Cambridge, UK, from the 8^th to 10^th July, 2008. As in previous years, the meeting attracted leading experts in the field who presented the latest cutting edge in proteomics. The meeting was entitled “Proteomics: From Technology to New Biology” taking into account the major transition proteomics has undergone in the past few years. In particular, the use of multiple reaction monitoring (MRM)‐based targeted experiments for absolute quantification and validation of proteins was the hot topic of the meeting. Attended by some 250 delegates, the conference was extremely well organised and provided a great opportunity for discussion and initiation of new collaborations.     

Ten Years of Standardizing Proteomic Data: A Report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA

The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was established in 2002 with the aim of defining community standards for data representation in proteomics and facilitating data comparison, exchange and verification. Over the last 10 years significant advances have been made, with common data standards now published and implemented in the field of both mass spectrometry and molecular interactions. The 2012 meeting further advanced this work, with the mass spectrometry groups finalising approaches to capturing the output from recent developments in the field, such as quantitative proteomics and SRM. The molecular interaction group focused on improving the integration of data from multiple resources. Both groups united with a guest work track, organized by the HUPO Technology/Standards Committee, to formulate proposals for data submissions from the HUPO Human Proteome Project and to start an initiative to collect standard experimental protocols.     

The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative

The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel‐based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.