Final Report Summary - PRIME-XS (Proteomics Research Infrastructure Maximising knowledge EXchange and access (XS))
Executive Summary:
The availability of full genome sequences initiated a new era in biomedical research, with the emphasis shifting to the interpretation of the biological functioning of the gene products, the proteins, from which the thriving and rapidly evolving field of proteomics emerged. The technologies that are required to analyze proteins on a global scale require significant investments and expertise and are therefore not always readily available to researchers in life sciences that could benefit from proteomics technologies applied to their research. Over the years, various local and national proteomics facilities and consortia have been established with the aim to provide the technology to their defined user base. In 2011, PRIME-XS, a consortium of twelve partners, all leading in the field of proteomics, joined forces to provide their state-of-the-art proteomics technologies to the entire European biological and biomedical research community.
The PRIME-XS consortium (www.prime-xs.eu) also organized a wide range of meetings, courses and training events to train more researchers that can take full benefit of proteomics technology. Together with an industrial platform, users as well as other stakeholders, the consortium worked towards a sustainable, Europe wide, proteomics community to maintain the high level of proteomics access and world-leading status of European proteomics research.
Following a widely distributed public announcement in July 2011, PRIME-XS continuously received submissions of new proposals for projects using the offered proteomics technologies. Up until January 2015, which marked the end of the project, a total of 145 user projects had been submitted. Of these projects, which came from 23 different European countries, 122 were been approved by external reviewers. In total, PRIME-XS provided 2262.8 “days of access” to users throughout the project, showing the clear need for access to proteomics facilities in Europe.
The Joint Research Activities (JRAs) in PRIME-XS were aimed to facilitate development and further advancement of proteomics enabling technologies to the critical next level. To this end, the JRAs addressed present research bottlenecks in proteomics technologies for streamlining of bioinformatics and workflows for high-throughput proteomics information handling, the unraveling of protein interaction networks and subcellular location, the characterization of posttranslational modification on proteins (JRA3) and the detection of biomarkers for disease. To use the tools developed by the JRAs to improve the quality and quantity of the access provided at the infrastructures, the technologies developed were transferred to the access sites and thus made available to life science researchers in Europe.
The research in the JRAs and the transnational access user projects in PRIME-XS resulted in over 200 scientific publications that acknowledge the support of the PRIME-XS project. Of particular note is the August 2014 issue of the journal Molecular & Cellular Proteomic, which featured a substantial collection of articles describing recent research findings from investigators of the PRIME-XS transnational access and JRA projects as well as an opinion piece from the consortium about the impact PRIME-XS has had on the European proteomics community.
The European proteomics community and research has clearly being strengthened by the PRIME-XS consortium. That recognition, combined with the very positive feedback PRIME-XS received from its users and the potential for new scientific breakthroughs provided by the research activities in PRIME-XS, means the PRIME-XS community sees a positive future for proteomics in Europe and is making efforts to continue some of the activities also beyond the lifetime of the project.
Project Context and Objectives:
The scientific community and the European society as a whole are dealing with great challenges regarding health and disease of its population. The sequencing of the human genome in particular, has initiated a new age in biology, offering unique opportunities to improve health and to stimulate scientific, and industrial activity. With extensive knowledge of the genomes available, emphasis is now rapidly moving to the biological interpretation of the genome sequence information. This biological interpretation encompasses the immense task of identifying structure, function and interactions of the gene-products, i.e. the proteins, and their role in biological processes, and is heavily reliant on the field of proteomics. Proteomics encompasses the analysis of proteins within any given biological sample on a global scale. It demands the application of evolving multidisciplinary technologies to enable the measurement and characterisation of protein expression profiles, protein localisation, modifications and networks related to development, health/disease and other biological processes.
Successful (i.e. biologically meaningful) high-throughput mass spectrometry based proteomics is a highly specialized activity that calls for a supra-national approach to increase its impact on European society. Currently the bottleneck in state of the art proteomics is not only dependent on the availability of hardware infrastructure, but more even on the expertise required for its efficient and innovative use.
Only few laboratories are able to use these instruments to their full potential. The key to their success is the critical mass of proteomics researchers with advanced analytical skills, bioinformatics support, and expertise in various areas of molecular biology, biochemistry, and protein chemistry. In proteomics the experimental design and preparation of biological samples are of paramount importance. Only when these issues have been well-addressed are state-of-the-art mass spectrometers able to achieve the depth required to answer important biological questions.
PRIME-XS brought together global leaders within the field of proteomics collectively with their existing infrastructures and expertise. PRIME-XS provided a world-class research infrastructure for high-throughput proteome analysis aimed at resolving genuine biomedical research questions. The groups brought together in PRIME-XS will have a track record of high impact on not only the European proteomics research community, but also on the biomedical and biological research communities at large. Their combined scientific and technological expertise was used in the JRAs to facilitate development of and further advancement of proteomics enabling technologies to the critical next level
The PRIME-XS project had three overarching aims:
* PRIME-XS aimed to strengthen, increase and optimise the (open and competitive) access to state-of-the-art proteomics infrastructure and expertise for researchers in Europe
* PRIME-XS planned joint research activities to tackle the most relevant technical and bioinformatics bottlenecks in proteomics to further improve quality and quantity of high-throughput proteomics.
* PRIME-XS worked to ensure the long-term sustainability of proteomics in Europe through targeted networking activities in a pan-European fashion.
The objectives of PRIME-XS were to shape coherence, provide wide access and promote collaboration in proteomics research in Europe. PRIME-XS aimed to be recognized as an outstanding partner in proteomics research in Europe and beyond. PRIME-XS brought together the key proteomics infrastructures in Europe, with a track record in providing access. By further opening the access to these centres, PRIME-XS enabled the generation of high-quality proteomics data to top European researchers. PRIME-XS improved and widened fundamental technological tools in proteomics and proteomics related bioinformatics research, and made them available to the wider proteomics research community, by transferring these tools to its access sites, by making available protocols, and by organizing training sessions and workshops for the biological and biomedical research communities. With the help of the new tools developed in the JRAs and the access centers, users of the transnational access sites were enabled to improve our understanding of processes of health and disease, and pave the way for the generation of new means for intervention and prevention of undesired life-processes.
The original objectives of the three major activities of PRIME-XS are summarized below:
Networking Activities
* To strengthen the European research community and enhance technology and expertise transfer to proteomics researchers and the biological and biomedical research communities at large.
* To raise public awareness about proteome research, its research infrastructures and European research infrastructures in general.
* To liaise with public authorities, biologists, the health sector, industries and funding authorities, in collaboration with other European molecular life science projects and research infrastructures, in order to explore the long-term sustainability of the proteomics European research infrastructure.
Transnational Access
* To provide coordinated and transparent pan-European access to excellent biomedical research projects requiring world-class proteomics instrumentation and expertise, evaluated by an independent International Access Board.
Joint Research Activities
* To address present research bottlenecks in proteomics technologies for the characterization of post-translational modification on proteins, the unraveling of protein interaction networks, the detection of biomarkers for disease and the streamlining of bioinformatics and workflows for high-throughput proteomics information handling.
* To use the results of such research activities to improve the quality and quantity of the access provided at the infrastructures within the course of the project.
Project Results:
The PRIME-XS consortium consisted of the following partners and access sites:
Partners
* Utrecht University (UU, coordinator), Utrecht, the Netherlands
* Flemish Institute for Biotechnology (VIB), Gent, Belgium
* University of Zurich (UZH), Zurich, Switzerland
* Eidgenössische Technische Hochschule Zurich (ETHZ), Zurich, Switzerland
* University of Copenhagen (UCPH), Copenhagen, Denmark
* Center for Genomic Regulation (CRG), Barcelona, Spain
* University of Cambridge (UCAM), Cambridge, United Kingdom
* Research Institute of Molecular Pathology (IMP), Vienna Austria
* Commissariat à l'énergie atomique (CEA), Grenoble, France
* Eberhard Karls Universität Tübingen (EKUT), Tübingen, Germany
* European Bioinformatics Institute (EBI), Hinxton, United Kingdom
* Max Planck Institute of Biochemistry (MPI), Martinsried, Germany
Access Sites
* Netherlands Proteomics Center (UU)
* VIB Proteomics Unit (VIB)
* Functional Genomics Center Zurich (ETHZ)
* CRG Proteomics Unit (CRG)
* Cambridge Centre for Proteomics (UCAM)
* CEA Proteomics Unit (CEA)
Below are the main results of the PRIME-XS project in the Transnational Access (TA) programme and the Joint Research Activities (JRA).
Transnational Access programme
Proposal submission system
In order to make it as easy as possible for users to submit their user proposal and to provide reviewers and access sites with a simple way of reviewing and handling the submitted projects, an online project submission system was developed that allowed this process to be carried out fully online. Originally, the system was implemented in Actionscript as a web-based front-end that could be run from any internet browser with Flash player installed. The actionscript front-end generated the submission system web pages and interacted with a MySQL database. After about 1.5 years into the project, the decision was made to develop a new GUI for the system. As Flash is being used less and less on websites and in browsers in favour of other technologies such as HTML5, this meant that some newer and mobile browsers would no longer be able to display the online submission system correctly. In addition, maintenance of the Flash system turned out to be relatively tedious and troubleshooting was difficult. The choice was therefore made to generate a new interface, fully developed in modern web technology, namely HTML5 combined with PHP, which was used for the last 2.5 years of PRIME-XS.
When submitting a proposal, the user submitted a completed template with details about the proposed project, such as sample details, the required technology and the requested access site. At the request of multiple users, an option was later introduced that allowed users submitting a project to leave the choice of access site to the consortium. What happened in such a case was that the PRIME-XS project office, based on the project that the user submitted, inquired which access sites had the requested technology available and which of them was able to allocate measurement time within a reasonable timeframe.
The template for project proposals covered the following project aspects:
* User details
* Title of the project
* Background
* Description of the experiments proposed
* Details of the sample(s) to be analysed
* Expected outcome
* References
Following the submission of the user proposal, a so-called editor from the consortium checked if the project proposal submission was done correctly and assigned reviewers from a list. These reviewers were invited by email to review the proposal with the following questions in the online system:
* Is the execution of the proteomics experiments critical to the success of the project?
* Please comment on the scientific or technological relevance and originality of the project.
* Does the project have a clear goal?
* Are the suggested experiments suitable for the question to be answered?
* How do you rate the overall quality of the proposed project?
* Is the project in your opinion suitable for execution in PRIME-XS?
* Do you have any other comments or suggestions related to the project?
Based on the feedback from the external reviewers, the editor accepted or rejected a proposal, upon which the users were notified and if the project was accepted, were brought in contact with the access site to start planinng the user project.
Access provided
Over entire course of the PRIME-XS access programme (first with a beta stage for early adopters in May 2011 and fully open in July 2011) a total of 145 user projects was submitted. Of those, 122 were accepted for execution, 15 were rejected, and 8 were flagged as incorrect submission. Altogether, the resulting acceptance rate is 84% (122/145), and the rejection rate 16% (23/145).
Because submissions of projects were continuously accepted, it was important to monitor this process over time to be able to take action or change this process if necessary. The submission of user projects was pretty much continuous since the start of the access programme in May 2011, with a clear peaks around the time of some public announcements or events. The submission of new projects was put on hold for a few months in 2013, due to all access sites operating at their maximum capacity, and mid-2014 the submission of projects was closed definitely to allow the accepted projects to be completed during the PRIME-XS project lifetime. The submitted projects came from 23 different European countries, with five countries (Portugal, Spain, Germany, United Kingdom and Italy) submitting most of the access proposals.
As stated above, a total of 122 user projects were accepted throughout the PRIME-XS period. By the end of PRIME-XS, not all of those projects were completed and a few had not even started yet. However, the PRIME-XS partners committed to execute these remaining projects after the end of PRIME-XS.
During the 4 years of the PRIME-XS project, a total of 2262.8 days of access were delivered by the PRIME-XS access sites. This is 15% more than the original planned amount of access for the entire project period (1971 access days). Of these, 675.5 days were provided by partner UU, 419 days by partner VIB, 498.8 days by partner ETHZ, 265 days by partner CRG, 180.5 days by partner UCAM and 224 days by partner CEA.
Scientific results
At the end of PRIME-XS, the project had resulted in around 20 publications from the transnational access projects, equaling to about 20% of all user projects. This is not unexpected, as proteomics experiments are often one of the first steps for large research projects and many of the user projects are expected to publish their results in the coming year(s). This expectation was already voiced by the Scientific Advisory Board of the project as early as the first Annual User Meeting, which was held in Palma de Mallorca in Spain in 2012. To account for this fact, the PRIME-XS website will be kept live and updated with the publications related to the project that will come out in the coming year(s) and an up-to-date overview of publications is provided at http://www.primexs.eu/prime-xs-publications.html.
Joint Research Activities
The Joint Research Activities (JRAs) in PRIME-XS were aimed to facilitate development and further advancement of proteomics enabling technologies to the critical next level. To this end, the JRAs addressed research bottlenecks in proteomics technologies for streamlining of bioinformatics and workflows for high-throughput proteomics information handling (JRA1), the unraveling of protein interaction networks and subcellular location (JRA2), the characterization of posttranslational modification on proteins (JRA3) and the detection of biomarkers for disease (JRA4). To use the tools developed by the JRAs to improve the quality and quantity of the access provided at the infrastructures, the technologies developed were transferred to the access sites and thus made available to life science researchers in Europe. The main results of the JRAs from PRIME-XS are described below.
JRA1
One of the most significant result of this JRA arguable was a standardised quality control analysis pipeline and output format for proteomics experiments, since this work is likely to have considerable impact on the field at large. In order to develop a quality control pipeline that truly fits the purpose of the access sites of PRIME-XS, the metrics defined in this deliverable where selected together with people representing a majority of the access sites and the proposed pipeline was a joint effort between many partners, along with contributions by other project participants. Joint workshops between the various partners of JRA1, along with any interested PRIME-XS Consortium members were organized to be able to effectively come to this jointly proposed pipeline and an accompanying standardized storage format in XML format, termed qcML.
Several other notable results included for example the development of a freely available, open source and cross-platform software tool (Prioritizer) for sample scheduling and workflow tracking of projects which was made available on the internet, but also the development of two sets of tools, PhenoDisco and pRoloc to support organelle proteomics data sets. PhenoDisco is an algorithm which allows identification of both large and small organelle-related protein clusters in complex organelle proteomics data sets beyond those sufficiently annotated for use as training data. pRoloc is a unifying bioinformatics framework for organelle proteomics which facilitates storage and analysis of data from multiple technologies , and application of a variety of machine learning algorithms. Other methods developed included tools to support the identification and validation of post-translational modifications on proteins and the identification and validation of biomarkers
Finally, a collaboration with the ProteomeXchange consortium led to the development of the PRIDE Converter 2 tool to easily upload proteomics data into the PRIDE data repository.
All tools have been disseminated within the project, and several algorithms and tools were used by various PRIME-XS participants. However, the outreach efforts of JRA1 were projected beyond the project participants as well, targeting the scientific community at large. To this end, all software tools developed in JRA1 have been made available for download online as freely available open source projects, and many systems are also directly usable as web applications online, or are integrated into popular third-party tools such as R/Bioconductor and KNIME. A lot of effort has been invested into making these tools user-friendly, which further lowers the threshold of adoption.
JRA2
The work carried out within JRA2 can be divided into three broad areas: methods to facilitate isolation of protein complexes including capturing complexes based on their interaction with small molecules; quantification of proteins within multi-protein complexes in low abundance; simultaneous mapping of the sub-cellular location of thousands of proteins and determination of the sub-cellular location of multi-protein complexes within these maps.
The JRA2 partners were involved in developing several novel proteomics methods. These included a fast immuno-precipitation protocol for GFP tagged bait proteins and their interacting partners, the development of a cross linking protocol to capture transient and weakly interacting protein partners, development of a lipid-protein interaction methodology suitable for interrogating phosphoinositide binding proteins, a method to characterize protein kinase A and protein kinase G interacting proteins using differential binding to cAMP derivatised matrices, the creation of a detail sub organelle map of the plant chloroplast, a detailed sub-cellular map of 7000 mouse embryonic cells and peptide-centric assays that allow targeted and quantitative measurements of more than 3000 low abundant proteins in Drosophila using either SRM or SWATH –based mass spectrometry technologies.
One of the main exercises in JRA2 was the extensive cross laboratory validation of several of the protocols developed. These cross laboratory studies involved researchers active in the access sites and thus methodologies developed in JRA2 have readily been incorporated into the repertoire of methods available to the PRIME-XS transnational access users
JRA3
In a collaborative effort, several PRIME-XS partners jointly developed an optimized phosphopeptide enrichment and phosphopeptide analysis protocol ‘Phosphopeptide enrichment using titanium dioxide (TiO2) affinity chromatography’ that is available for download through the PRIME-XS website. The protocol included a detailed section about phosphopeptide sequencing either by collision-induced dissociation, electron transfer dissociation or higher energy collision-induced dissociation and an optimized algorithm ‘phosphoRS’ for confident localization of phosphosites and other PTMs in modified peptides based on fragmentation spectra.
In addition, novel COFRADIC-based methods for the enrichment of peptides containing nitrated tyrosine residues, the selective enrichment of modified peptides carrying oxidized methionine, to enrich for ubiquitylated peptides or for characterizing the specificity of carboxypeptidases were developed.
Other major development included the generation of unbiased PTM analysis algorithms, methodology for the detection of arginine-phosphorylation and an optimized protocol for in-solution digestion using the metalloendopeptidase Lys-N.
The developed JRA3 phosphopeptide technology protocol has been successfully implemented in all access labs and two dedicated hands-on workshops on ‘Phosphopeptide enrichment, labeling strategies and proteomics data analysis’ were organized to train access site personnel on how to make use of these methods.
JRA4
This JRA generated and validated a comprehensive set of robust biomarker enrichment methods (i.e. N-glyco, non-glyco, phospho-tyrosine, acetyl-lysine peptide/protein captures as well as a hydrazide-based glyco-depletion method). The methods have been published and transferred to access sites where they were implemented and, in part, used in the context of specific user projects. The aim to generate and validate proteotypic peptide- based SRM and SWATH-MS assays for quantitative biomarker discovery was also successfully completed. Furthermore, JRA4 generated software for the determination of the relative and automated absolute biomarker concentrations in collaboration with JRA1. Moreover, the JRA resulted in validation and publication of a generic protein standard (termed DIGESTIF) that enhances the quality and reproducibility of MS-based biomarker studies. Finally, a LC-MRM-MS workflow with isotope dilution assay for the multiplexed measurement of 8 potential cancer biomarkers in human bile was developed.
These methods were successfully transfered and implementated at some of the Transnational Access sites and have been used in selected user projects.
Potential Impact:
Networking Activities
Annual Meetings
In order to establish opportunities for the PRIME-XS partners to share experiences with user projects and knowledge generated in the JRA activities, a Kickoff Meeting was organised in April 2011. To maintain a close relationship with the users of the facilities, several mechanisms have been put in place. Most importantly, all users with approved projects were invited to attend Annual User Meetings of PRIME-XS. Four of such meetings were organized over the course of the PRIME-XS project.
The first Annual User Meeting of PRIME-XS was held in April 2012 on Mallorca in Spain (organized by partner UCAM, together with UU). The meeting was attended by approximately 70 people. Of those, 15 were users representing a total of 8 different user projects and over 50 were representatives of all partners in the project and the project management. Finally, the meeting was attended by one member of the Scientific Advisory Board (SAB), Matthias Selbach and the EU Project Officer, Brigitte Sambain. All user projects represented at this meeting were presented by one of the users.
The second Annual User Meeting was held from 29 January to 1 February 2013 in Menthon St. Bernard (near Annecy), France France (organized by partner CEA, together with UU). The meeting was attended by in total 66 people, among which 46 from the different partners in PRIME-XS, 16 users of the facilities, 2 SAB members (Brian Chait and Matthias Selbach), the project reviewer (Roman Zubarev) and the EU project officer (Brigitte Sambain). Eight different user projects were presented at the meeting.
The third Annual User Meeting was held from 23-25 October 2013, in Split, Croatia (organized by partner VIB, together with UU and EKUT). The was attended by in total 82 people, among which 60 from the different partners in PRIME-XS, 21 users of the facilities and 1 SAB member (Matthias Selbach). Eight different user projects were presented at the meeting.
The fourth Annual User Meeting was held from 8-9 October 2014, in Avila, Spain (organized by partner CRG, together with UU). The meeting was attended by in total 88 people, among which 51 from the different partners in PRIME-XS and 37 users of the facilities. Eleven different user projects were presented at the meeting.
Feedback that was received from users at the Annual User Meetings, or other occasions, has been very positive and constructive overall. Below are some (anonymized) quotes from users that we have received, which show their involvement in the project and how PRIME-XS was of benefit to them:
* “Just coming back to the lab, i want to send an email to express our gratitude for our inclusion in the PRIME-XS consortium as a user. It has been an incomparable chance to expand our research in agro-food area, were proteomics approaches still being underrepresented. It had allow the opportunity to obtain an instrument for our university under new university research policies.”
* “Thanks for organizing the great meeting in Split”
* “…thank you once again for taking care about us on workshop. we had really good time there in Split”
On January 26 and 27, 2015, partner UU organized, jointly with the Netherlands Proteomics Center, the final meeting of PRIME-XS, with the topic “Proteomics in a European Context”, in Utrecht, the Netherlands. The meeting was broadly advertised, open to all interested scientists and featured many speakers from the PRIME-XS consortium. The meeting was attended by around 200 participants, including many PRIME-XS partners and users and was also covered in the April 2015 edition of the NPC Highlights journal of the Netherlands Proteomics Center.
Local operator meetings
To ensure smooth implementation of the access provision in PRIME-XS, to maintain consistency between the operational procedures of the various access sites and to share knowledge and experiences between the sites, four local operator meetings were held over the entire project period. These meetings also served to address the possibilities for using standards and best practices, and to adopt common procedures and protocols.
Workshops
In order to allow the researchers involved in the various JRA workpackages to collaborate and share ideas and experiences as efficiently as possible, regular meetings and workshops between the scientists of a particular JRA were held. In some cases these meetings coincided with other meetings, like the kickoff meeting and the annual user, whereas in other cases dedicated workshops of a single or multiple days have been held.
To strengthen the efforts in training of users in state-of-the-art proteomics technologies and to extend the outreach towards new member states, two workshops were organized as satellite meetings to two PRIME-XS Annual User Meetings. These meetings were very broadly advertised, by distributing the announcements through various mailing lists, contacting national proteomics societies, and announcements on a large number of websites.
The first workshop was on “Quantitative Proteomics of Biomarkers for Medical Applications and Basic Research” and was held in Annecy, France from 29-30 January 2013. The workshop was attended by 19 postdocs and PhD students from 9 different countries.
The second workshop on “phosphopeptide enrichment, proteomics labeling strategies and proteomics data analysis” and was in Split, Croatia from 22-23 October 2013. The workshop was hosted by dr. Janoš Terzic at the premises of the Medical Faculty of the University of Split. The programme also included practical sessions in the laboratories of the Medical Faculty of the University of Split. The workshop was attended by 30 postdocs and PhD students from 11 different countries, of which approximately 50% from EU new members states.
In addition to these dedicated PRIME-XS workshops, the PRIME-XS partners (co-)organized around 30 other workshops about proteomics technology, for either local, national or international scientific audiences and presented the results from the project at over 80 scientific meetings.
Protocols
As a service to the broader scientific community, but also towards all users, partners and access sites in PRIME-XS, a large number of protocols has been made freely available on the project website. These protocols cover a wide range of different techniques, ranging from simple protein determination methods to advanced enrichment technologies for specific post-transnationally modified peptides. By the end of the project, 20 protocols were available for download on the PRIME-XS website and those had been downloaded more than 2500 times in total.
Publications
At this moment, the project has results in more than 230 publications, of which ~10% has resulted from the transnational access projects (equaling to about 20% of all user projects). This is not unexpected, as proteomics experiments are often one of the first steps for large research projects and many of the user projects are expected to publish their results in the coming year(s). More publications acknowledging the project are expected in the coming year(s).
Of all publications, around 30 have been in journals with an impact factor higher than 10, and the average impact of all publication is around 7.5 much higher than the average impact of publications in the life science field.
PRIME-XS also ensured that all publications are present in the database of publications resulting from EU funded projects that is maintained by the OpenAIRE project (http://www.openaire.eu). OpenAIRE is particularly focused on making the results of EU funded research open to the public, for example by stimulating Open Access publications, depositing of pre- or post-prints in public repositories and by collecting an overview of the results of many EU funded projects. Currently, around 50% of all PRIME-XS publications are available through Open Access.
To disseminate the results of PRIME-XS to a broader audience than just the involved partners and users, the PRIME-XS consortium negotiated with the proteomics journal Molecular & Cellular Proteomics (MCP) a dedicated issue with papers that were the direct result from the PRIME-XS project (albeit still going through the regular peer-review process of the journal). In total about 30 papers from the consortium and its users were submitted to MCP for that special issue. The special issue of the journal Molecular & Cellular Proteomics was published in August 2014 and featured nineteen research articles describing research findings from investigators of the PRIME-XS transnational access user projects and the JRAs. This MCP issue was broadly distributed, as it for example was included in the conference bag of all over 2000 participants at the HUPO 2014 Meeting in Madrid.
Industrial Platform
Industry plays an important role in the field of proteomics. Not just due to the strong technical nature of the work that often depends on access to state-of-the-art mass spectrometry equipment, but also because proteomics technology is used by companies involved in life science research. Therefore, members of the industrial platform were already selected during the preparation of the proposal of the PRIME-XS project and the Industrial Platform has been operational since the start of the project. The industrial platform was represented at the first and fourth Annual User Meeting of PRIME-XS, and its members have been active in several courses organized by the PRIME-XS partners and in the International Access Board that reviewed submitted proposals. Collaborative research with members of the Industrial Platform resulted in 11 joint publications.
Sustainability
Also after the end of the PRIME-XS project, life science researchers throughout Europe will encounter biological or biomedical research questions that can be addressed with proteomics technology and might not always have access to suitable proteomics facilities locally, or nationally. In addition, and as also described by Scientific Advisory Board member Brian Chait in a recent opinion piece, the PRIME-XS project has really brought together the European proteomics community, at the level of the research groups that are at the front end of proteomics technology developments, but also at the level of the interaction of these groups with life science researchers that benefit from using proteomics technology to further their biological or biomedical research. The PRIME-XS community sees a positive future for proteomics in Europe and is making efforts to continue some of its activities also beyond the lifetime of the project.
List of Websites:
Website: www.prime-xs.eu
Coordinator: A.J.R.Heck@uu.nl
The availability of full genome sequences initiated a new era in biomedical research, with the emphasis shifting to the interpretation of the biological functioning of the gene products, the proteins, from which the thriving and rapidly evolving field of proteomics emerged. The technologies that are required to analyze proteins on a global scale require significant investments and expertise and are therefore not always readily available to researchers in life sciences that could benefit from proteomics technologies applied to their research. Over the years, various local and national proteomics facilities and consortia have been established with the aim to provide the technology to their defined user base. In 2011, PRIME-XS, a consortium of twelve partners, all leading in the field of proteomics, joined forces to provide their state-of-the-art proteomics technologies to the entire European biological and biomedical research community.
The PRIME-XS consortium (www.prime-xs.eu) also organized a wide range of meetings, courses and training events to train more researchers that can take full benefit of proteomics technology. Together with an industrial platform, users as well as other stakeholders, the consortium worked towards a sustainable, Europe wide, proteomics community to maintain the high level of proteomics access and world-leading status of European proteomics research.
Following a widely distributed public announcement in July 2011, PRIME-XS continuously received submissions of new proposals for projects using the offered proteomics technologies. Up until January 2015, which marked the end of the project, a total of 145 user projects had been submitted. Of these projects, which came from 23 different European countries, 122 were been approved by external reviewers. In total, PRIME-XS provided 2262.8 “days of access” to users throughout the project, showing the clear need for access to proteomics facilities in Europe.
The Joint Research Activities (JRAs) in PRIME-XS were aimed to facilitate development and further advancement of proteomics enabling technologies to the critical next level. To this end, the JRAs addressed present research bottlenecks in proteomics technologies for streamlining of bioinformatics and workflows for high-throughput proteomics information handling, the unraveling of protein interaction networks and subcellular location, the characterization of posttranslational modification on proteins (JRA3) and the detection of biomarkers for disease. To use the tools developed by the JRAs to improve the quality and quantity of the access provided at the infrastructures, the technologies developed were transferred to the access sites and thus made available to life science researchers in Europe.
The research in the JRAs and the transnational access user projects in PRIME-XS resulted in over 200 scientific publications that acknowledge the support of the PRIME-XS project. Of particular note is the August 2014 issue of the journal Molecular & Cellular Proteomic, which featured a substantial collection of articles describing recent research findings from investigators of the PRIME-XS transnational access and JRA projects as well as an opinion piece from the consortium about the impact PRIME-XS has had on the European proteomics community.
The European proteomics community and research has clearly being strengthened by the PRIME-XS consortium. That recognition, combined with the very positive feedback PRIME-XS received from its users and the potential for new scientific breakthroughs provided by the research activities in PRIME-XS, means the PRIME-XS community sees a positive future for proteomics in Europe and is making efforts to continue some of the activities also beyond the lifetime of the project.
Project Context and Objectives:
The scientific community and the European society as a whole are dealing with great challenges regarding health and disease of its population. The sequencing of the human genome in particular, has initiated a new age in biology, offering unique opportunities to improve health and to stimulate scientific, and industrial activity. With extensive knowledge of the genomes available, emphasis is now rapidly moving to the biological interpretation of the genome sequence information. This biological interpretation encompasses the immense task of identifying structure, function and interactions of the gene-products, i.e. the proteins, and their role in biological processes, and is heavily reliant on the field of proteomics. Proteomics encompasses the analysis of proteins within any given biological sample on a global scale. It demands the application of evolving multidisciplinary technologies to enable the measurement and characterisation of protein expression profiles, protein localisation, modifications and networks related to development, health/disease and other biological processes.
Successful (i.e. biologically meaningful) high-throughput mass spectrometry based proteomics is a highly specialized activity that calls for a supra-national approach to increase its impact on European society. Currently the bottleneck in state of the art proteomics is not only dependent on the availability of hardware infrastructure, but more even on the expertise required for its efficient and innovative use.
Only few laboratories are able to use these instruments to their full potential. The key to their success is the critical mass of proteomics researchers with advanced analytical skills, bioinformatics support, and expertise in various areas of molecular biology, biochemistry, and protein chemistry. In proteomics the experimental design and preparation of biological samples are of paramount importance. Only when these issues have been well-addressed are state-of-the-art mass spectrometers able to achieve the depth required to answer important biological questions.
PRIME-XS brought together global leaders within the field of proteomics collectively with their existing infrastructures and expertise. PRIME-XS provided a world-class research infrastructure for high-throughput proteome analysis aimed at resolving genuine biomedical research questions. The groups brought together in PRIME-XS will have a track record of high impact on not only the European proteomics research community, but also on the biomedical and biological research communities at large. Their combined scientific and technological expertise was used in the JRAs to facilitate development of and further advancement of proteomics enabling technologies to the critical next level
The PRIME-XS project had three overarching aims:
* PRIME-XS aimed to strengthen, increase and optimise the (open and competitive) access to state-of-the-art proteomics infrastructure and expertise for researchers in Europe
* PRIME-XS planned joint research activities to tackle the most relevant technical and bioinformatics bottlenecks in proteomics to further improve quality and quantity of high-throughput proteomics.
* PRIME-XS worked to ensure the long-term sustainability of proteomics in Europe through targeted networking activities in a pan-European fashion.
The objectives of PRIME-XS were to shape coherence, provide wide access and promote collaboration in proteomics research in Europe. PRIME-XS aimed to be recognized as an outstanding partner in proteomics research in Europe and beyond. PRIME-XS brought together the key proteomics infrastructures in Europe, with a track record in providing access. By further opening the access to these centres, PRIME-XS enabled the generation of high-quality proteomics data to top European researchers. PRIME-XS improved and widened fundamental technological tools in proteomics and proteomics related bioinformatics research, and made them available to the wider proteomics research community, by transferring these tools to its access sites, by making available protocols, and by organizing training sessions and workshops for the biological and biomedical research communities. With the help of the new tools developed in the JRAs and the access centers, users of the transnational access sites were enabled to improve our understanding of processes of health and disease, and pave the way for the generation of new means for intervention and prevention of undesired life-processes.
The original objectives of the three major activities of PRIME-XS are summarized below:
Networking Activities
* To strengthen the European research community and enhance technology and expertise transfer to proteomics researchers and the biological and biomedical research communities at large.
* To raise public awareness about proteome research, its research infrastructures and European research infrastructures in general.
* To liaise with public authorities, biologists, the health sector, industries and funding authorities, in collaboration with other European molecular life science projects and research infrastructures, in order to explore the long-term sustainability of the proteomics European research infrastructure.
Transnational Access
* To provide coordinated and transparent pan-European access to excellent biomedical research projects requiring world-class proteomics instrumentation and expertise, evaluated by an independent International Access Board.
Joint Research Activities
* To address present research bottlenecks in proteomics technologies for the characterization of post-translational modification on proteins, the unraveling of protein interaction networks, the detection of biomarkers for disease and the streamlining of bioinformatics and workflows for high-throughput proteomics information handling.
* To use the results of such research activities to improve the quality and quantity of the access provided at the infrastructures within the course of the project.
Project Results:
The PRIME-XS consortium consisted of the following partners and access sites:
Partners
* Utrecht University (UU, coordinator), Utrecht, the Netherlands
* Flemish Institute for Biotechnology (VIB), Gent, Belgium
* University of Zurich (UZH), Zurich, Switzerland
* Eidgenössische Technische Hochschule Zurich (ETHZ), Zurich, Switzerland
* University of Copenhagen (UCPH), Copenhagen, Denmark
* Center for Genomic Regulation (CRG), Barcelona, Spain
* University of Cambridge (UCAM), Cambridge, United Kingdom
* Research Institute of Molecular Pathology (IMP), Vienna Austria
* Commissariat à l'énergie atomique (CEA), Grenoble, France
* Eberhard Karls Universität Tübingen (EKUT), Tübingen, Germany
* European Bioinformatics Institute (EBI), Hinxton, United Kingdom
* Max Planck Institute of Biochemistry (MPI), Martinsried, Germany
Access Sites
* Netherlands Proteomics Center (UU)
* VIB Proteomics Unit (VIB)
* Functional Genomics Center Zurich (ETHZ)
* CRG Proteomics Unit (CRG)
* Cambridge Centre for Proteomics (UCAM)
* CEA Proteomics Unit (CEA)
Below are the main results of the PRIME-XS project in the Transnational Access (TA) programme and the Joint Research Activities (JRA).
Transnational Access programme
Proposal submission system
In order to make it as easy as possible for users to submit their user proposal and to provide reviewers and access sites with a simple way of reviewing and handling the submitted projects, an online project submission system was developed that allowed this process to be carried out fully online. Originally, the system was implemented in Actionscript as a web-based front-end that could be run from any internet browser with Flash player installed. The actionscript front-end generated the submission system web pages and interacted with a MySQL database. After about 1.5 years into the project, the decision was made to develop a new GUI for the system. As Flash is being used less and less on websites and in browsers in favour of other technologies such as HTML5, this meant that some newer and mobile browsers would no longer be able to display the online submission system correctly. In addition, maintenance of the Flash system turned out to be relatively tedious and troubleshooting was difficult. The choice was therefore made to generate a new interface, fully developed in modern web technology, namely HTML5 combined with PHP, which was used for the last 2.5 years of PRIME-XS.
When submitting a proposal, the user submitted a completed template with details about the proposed project, such as sample details, the required technology and the requested access site. At the request of multiple users, an option was later introduced that allowed users submitting a project to leave the choice of access site to the consortium. What happened in such a case was that the PRIME-XS project office, based on the project that the user submitted, inquired which access sites had the requested technology available and which of them was able to allocate measurement time within a reasonable timeframe.
The template for project proposals covered the following project aspects:
* User details
* Title of the project
* Background
* Description of the experiments proposed
* Details of the sample(s) to be analysed
* Expected outcome
* References
Following the submission of the user proposal, a so-called editor from the consortium checked if the project proposal submission was done correctly and assigned reviewers from a list. These reviewers were invited by email to review the proposal with the following questions in the online system:
* Is the execution of the proteomics experiments critical to the success of the project?
* Please comment on the scientific or technological relevance and originality of the project.
* Does the project have a clear goal?
* Are the suggested experiments suitable for the question to be answered?
* How do you rate the overall quality of the proposed project?
* Is the project in your opinion suitable for execution in PRIME-XS?
* Do you have any other comments or suggestions related to the project?
Based on the feedback from the external reviewers, the editor accepted or rejected a proposal, upon which the users were notified and if the project was accepted, were brought in contact with the access site to start planinng the user project.
Access provided
Over entire course of the PRIME-XS access programme (first with a beta stage for early adopters in May 2011 and fully open in July 2011) a total of 145 user projects was submitted. Of those, 122 were accepted for execution, 15 were rejected, and 8 were flagged as incorrect submission. Altogether, the resulting acceptance rate is 84% (122/145), and the rejection rate 16% (23/145).
Because submissions of projects were continuously accepted, it was important to monitor this process over time to be able to take action or change this process if necessary. The submission of user projects was pretty much continuous since the start of the access programme in May 2011, with a clear peaks around the time of some public announcements or events. The submission of new projects was put on hold for a few months in 2013, due to all access sites operating at their maximum capacity, and mid-2014 the submission of projects was closed definitely to allow the accepted projects to be completed during the PRIME-XS project lifetime. The submitted projects came from 23 different European countries, with five countries (Portugal, Spain, Germany, United Kingdom and Italy) submitting most of the access proposals.
As stated above, a total of 122 user projects were accepted throughout the PRIME-XS period. By the end of PRIME-XS, not all of those projects were completed and a few had not even started yet. However, the PRIME-XS partners committed to execute these remaining projects after the end of PRIME-XS.
During the 4 years of the PRIME-XS project, a total of 2262.8 days of access were delivered by the PRIME-XS access sites. This is 15% more than the original planned amount of access for the entire project period (1971 access days). Of these, 675.5 days were provided by partner UU, 419 days by partner VIB, 498.8 days by partner ETHZ, 265 days by partner CRG, 180.5 days by partner UCAM and 224 days by partner CEA.
Scientific results
At the end of PRIME-XS, the project had resulted in around 20 publications from the transnational access projects, equaling to about 20% of all user projects. This is not unexpected, as proteomics experiments are often one of the first steps for large research projects and many of the user projects are expected to publish their results in the coming year(s). This expectation was already voiced by the Scientific Advisory Board of the project as early as the first Annual User Meeting, which was held in Palma de Mallorca in Spain in 2012. To account for this fact, the PRIME-XS website will be kept live and updated with the publications related to the project that will come out in the coming year(s) and an up-to-date overview of publications is provided at http://www.primexs.eu/prime-xs-publications.html.
Joint Research Activities
The Joint Research Activities (JRAs) in PRIME-XS were aimed to facilitate development and further advancement of proteomics enabling technologies to the critical next level. To this end, the JRAs addressed research bottlenecks in proteomics technologies for streamlining of bioinformatics and workflows for high-throughput proteomics information handling (JRA1), the unraveling of protein interaction networks and subcellular location (JRA2), the characterization of posttranslational modification on proteins (JRA3) and the detection of biomarkers for disease (JRA4). To use the tools developed by the JRAs to improve the quality and quantity of the access provided at the infrastructures, the technologies developed were transferred to the access sites and thus made available to life science researchers in Europe. The main results of the JRAs from PRIME-XS are described below.
JRA1
One of the most significant result of this JRA arguable was a standardised quality control analysis pipeline and output format for proteomics experiments, since this work is likely to have considerable impact on the field at large. In order to develop a quality control pipeline that truly fits the purpose of the access sites of PRIME-XS, the metrics defined in this deliverable where selected together with people representing a majority of the access sites and the proposed pipeline was a joint effort between many partners, along with contributions by other project participants. Joint workshops between the various partners of JRA1, along with any interested PRIME-XS Consortium members were organized to be able to effectively come to this jointly proposed pipeline and an accompanying standardized storage format in XML format, termed qcML.
Several other notable results included for example the development of a freely available, open source and cross-platform software tool (Prioritizer) for sample scheduling and workflow tracking of projects which was made available on the internet, but also the development of two sets of tools, PhenoDisco and pRoloc to support organelle proteomics data sets. PhenoDisco is an algorithm which allows identification of both large and small organelle-related protein clusters in complex organelle proteomics data sets beyond those sufficiently annotated for use as training data. pRoloc is a unifying bioinformatics framework for organelle proteomics which facilitates storage and analysis of data from multiple technologies , and application of a variety of machine learning algorithms. Other methods developed included tools to support the identification and validation of post-translational modifications on proteins and the identification and validation of biomarkers
Finally, a collaboration with the ProteomeXchange consortium led to the development of the PRIDE Converter 2 tool to easily upload proteomics data into the PRIDE data repository.
All tools have been disseminated within the project, and several algorithms and tools were used by various PRIME-XS participants. However, the outreach efforts of JRA1 were projected beyond the project participants as well, targeting the scientific community at large. To this end, all software tools developed in JRA1 have been made available for download online as freely available open source projects, and many systems are also directly usable as web applications online, or are integrated into popular third-party tools such as R/Bioconductor and KNIME. A lot of effort has been invested into making these tools user-friendly, which further lowers the threshold of adoption.
JRA2
The work carried out within JRA2 can be divided into three broad areas: methods to facilitate isolation of protein complexes including capturing complexes based on their interaction with small molecules; quantification of proteins within multi-protein complexes in low abundance; simultaneous mapping of the sub-cellular location of thousands of proteins and determination of the sub-cellular location of multi-protein complexes within these maps.
The JRA2 partners were involved in developing several novel proteomics methods. These included a fast immuno-precipitation protocol for GFP tagged bait proteins and their interacting partners, the development of a cross linking protocol to capture transient and weakly interacting protein partners, development of a lipid-protein interaction methodology suitable for interrogating phosphoinositide binding proteins, a method to characterize protein kinase A and protein kinase G interacting proteins using differential binding to cAMP derivatised matrices, the creation of a detail sub organelle map of the plant chloroplast, a detailed sub-cellular map of 7000 mouse embryonic cells and peptide-centric assays that allow targeted and quantitative measurements of more than 3000 low abundant proteins in Drosophila using either SRM or SWATH –based mass spectrometry technologies.
One of the main exercises in JRA2 was the extensive cross laboratory validation of several of the protocols developed. These cross laboratory studies involved researchers active in the access sites and thus methodologies developed in JRA2 have readily been incorporated into the repertoire of methods available to the PRIME-XS transnational access users
JRA3
In a collaborative effort, several PRIME-XS partners jointly developed an optimized phosphopeptide enrichment and phosphopeptide analysis protocol ‘Phosphopeptide enrichment using titanium dioxide (TiO2) affinity chromatography’ that is available for download through the PRIME-XS website. The protocol included a detailed section about phosphopeptide sequencing either by collision-induced dissociation, electron transfer dissociation or higher energy collision-induced dissociation and an optimized algorithm ‘phosphoRS’ for confident localization of phosphosites and other PTMs in modified peptides based on fragmentation spectra.
In addition, novel COFRADIC-based methods for the enrichment of peptides containing nitrated tyrosine residues, the selective enrichment of modified peptides carrying oxidized methionine, to enrich for ubiquitylated peptides or for characterizing the specificity of carboxypeptidases were developed.
Other major development included the generation of unbiased PTM analysis algorithms, methodology for the detection of arginine-phosphorylation and an optimized protocol for in-solution digestion using the metalloendopeptidase Lys-N.
The developed JRA3 phosphopeptide technology protocol has been successfully implemented in all access labs and two dedicated hands-on workshops on ‘Phosphopeptide enrichment, labeling strategies and proteomics data analysis’ were organized to train access site personnel on how to make use of these methods.
JRA4
This JRA generated and validated a comprehensive set of robust biomarker enrichment methods (i.e. N-glyco, non-glyco, phospho-tyrosine, acetyl-lysine peptide/protein captures as well as a hydrazide-based glyco-depletion method). The methods have been published and transferred to access sites where they were implemented and, in part, used in the context of specific user projects. The aim to generate and validate proteotypic peptide- based SRM and SWATH-MS assays for quantitative biomarker discovery was also successfully completed. Furthermore, JRA4 generated software for the determination of the relative and automated absolute biomarker concentrations in collaboration with JRA1. Moreover, the JRA resulted in validation and publication of a generic protein standard (termed DIGESTIF) that enhances the quality and reproducibility of MS-based biomarker studies. Finally, a LC-MRM-MS workflow with isotope dilution assay for the multiplexed measurement of 8 potential cancer biomarkers in human bile was developed.
These methods were successfully transfered and implementated at some of the Transnational Access sites and have been used in selected user projects.
Potential Impact:
Networking Activities
Annual Meetings
In order to establish opportunities for the PRIME-XS partners to share experiences with user projects and knowledge generated in the JRA activities, a Kickoff Meeting was organised in April 2011. To maintain a close relationship with the users of the facilities, several mechanisms have been put in place. Most importantly, all users with approved projects were invited to attend Annual User Meetings of PRIME-XS. Four of such meetings were organized over the course of the PRIME-XS project.
The first Annual User Meeting of PRIME-XS was held in April 2012 on Mallorca in Spain (organized by partner UCAM, together with UU). The meeting was attended by approximately 70 people. Of those, 15 were users representing a total of 8 different user projects and over 50 were representatives of all partners in the project and the project management. Finally, the meeting was attended by one member of the Scientific Advisory Board (SAB), Matthias Selbach and the EU Project Officer, Brigitte Sambain. All user projects represented at this meeting were presented by one of the users.
The second Annual User Meeting was held from 29 January to 1 February 2013 in Menthon St. Bernard (near Annecy), France France (organized by partner CEA, together with UU). The meeting was attended by in total 66 people, among which 46 from the different partners in PRIME-XS, 16 users of the facilities, 2 SAB members (Brian Chait and Matthias Selbach), the project reviewer (Roman Zubarev) and the EU project officer (Brigitte Sambain). Eight different user projects were presented at the meeting.
The third Annual User Meeting was held from 23-25 October 2013, in Split, Croatia (organized by partner VIB, together with UU and EKUT). The was attended by in total 82 people, among which 60 from the different partners in PRIME-XS, 21 users of the facilities and 1 SAB member (Matthias Selbach). Eight different user projects were presented at the meeting.
The fourth Annual User Meeting was held from 8-9 October 2014, in Avila, Spain (organized by partner CRG, together with UU). The meeting was attended by in total 88 people, among which 51 from the different partners in PRIME-XS and 37 users of the facilities. Eleven different user projects were presented at the meeting.
Feedback that was received from users at the Annual User Meetings, or other occasions, has been very positive and constructive overall. Below are some (anonymized) quotes from users that we have received, which show their involvement in the project and how PRIME-XS was of benefit to them:
* “Just coming back to the lab, i want to send an email to express our gratitude for our inclusion in the PRIME-XS consortium as a user. It has been an incomparable chance to expand our research in agro-food area, were proteomics approaches still being underrepresented. It had allow the opportunity to obtain an instrument for our university under new university research policies.”
* “Thanks for organizing the great meeting in Split”
* “…thank you once again for taking care about us on workshop. we had really good time there in Split”
On January 26 and 27, 2015, partner UU organized, jointly with the Netherlands Proteomics Center, the final meeting of PRIME-XS, with the topic “Proteomics in a European Context”, in Utrecht, the Netherlands. The meeting was broadly advertised, open to all interested scientists and featured many speakers from the PRIME-XS consortium. The meeting was attended by around 200 participants, including many PRIME-XS partners and users and was also covered in the April 2015 edition of the NPC Highlights journal of the Netherlands Proteomics Center.
Local operator meetings
To ensure smooth implementation of the access provision in PRIME-XS, to maintain consistency between the operational procedures of the various access sites and to share knowledge and experiences between the sites, four local operator meetings were held over the entire project period. These meetings also served to address the possibilities for using standards and best practices, and to adopt common procedures and protocols.
Workshops
In order to allow the researchers involved in the various JRA workpackages to collaborate and share ideas and experiences as efficiently as possible, regular meetings and workshops between the scientists of a particular JRA were held. In some cases these meetings coincided with other meetings, like the kickoff meeting and the annual user, whereas in other cases dedicated workshops of a single or multiple days have been held.
To strengthen the efforts in training of users in state-of-the-art proteomics technologies and to extend the outreach towards new member states, two workshops were organized as satellite meetings to two PRIME-XS Annual User Meetings. These meetings were very broadly advertised, by distributing the announcements through various mailing lists, contacting national proteomics societies, and announcements on a large number of websites.
The first workshop was on “Quantitative Proteomics of Biomarkers for Medical Applications and Basic Research” and was held in Annecy, France from 29-30 January 2013. The workshop was attended by 19 postdocs and PhD students from 9 different countries.
The second workshop on “phosphopeptide enrichment, proteomics labeling strategies and proteomics data analysis” and was in Split, Croatia from 22-23 October 2013. The workshop was hosted by dr. Janoš Terzic at the premises of the Medical Faculty of the University of Split. The programme also included practical sessions in the laboratories of the Medical Faculty of the University of Split. The workshop was attended by 30 postdocs and PhD students from 11 different countries, of which approximately 50% from EU new members states.
In addition to these dedicated PRIME-XS workshops, the PRIME-XS partners (co-)organized around 30 other workshops about proteomics technology, for either local, national or international scientific audiences and presented the results from the project at over 80 scientific meetings.
Protocols
As a service to the broader scientific community, but also towards all users, partners and access sites in PRIME-XS, a large number of protocols has been made freely available on the project website. These protocols cover a wide range of different techniques, ranging from simple protein determination methods to advanced enrichment technologies for specific post-transnationally modified peptides. By the end of the project, 20 protocols were available for download on the PRIME-XS website and those had been downloaded more than 2500 times in total.
Publications
At this moment, the project has results in more than 230 publications, of which ~10% has resulted from the transnational access projects (equaling to about 20% of all user projects). This is not unexpected, as proteomics experiments are often one of the first steps for large research projects and many of the user projects are expected to publish their results in the coming year(s). More publications acknowledging the project are expected in the coming year(s).
Of all publications, around 30 have been in journals with an impact factor higher than 10, and the average impact of all publication is around 7.5 much higher than the average impact of publications in the life science field.
PRIME-XS also ensured that all publications are present in the database of publications resulting from EU funded projects that is maintained by the OpenAIRE project (http://www.openaire.eu). OpenAIRE is particularly focused on making the results of EU funded research open to the public, for example by stimulating Open Access publications, depositing of pre- or post-prints in public repositories and by collecting an overview of the results of many EU funded projects. Currently, around 50% of all PRIME-XS publications are available through Open Access.
To disseminate the results of PRIME-XS to a broader audience than just the involved partners and users, the PRIME-XS consortium negotiated with the proteomics journal Molecular & Cellular Proteomics (MCP) a dedicated issue with papers that were the direct result from the PRIME-XS project (albeit still going through the regular peer-review process of the journal). In total about 30 papers from the consortium and its users were submitted to MCP for that special issue. The special issue of the journal Molecular & Cellular Proteomics was published in August 2014 and featured nineteen research articles describing research findings from investigators of the PRIME-XS transnational access user projects and the JRAs. This MCP issue was broadly distributed, as it for example was included in the conference bag of all over 2000 participants at the HUPO 2014 Meeting in Madrid.
Industrial Platform
Industry plays an important role in the field of proteomics. Not just due to the strong technical nature of the work that often depends on access to state-of-the-art mass spectrometry equipment, but also because proteomics technology is used by companies involved in life science research. Therefore, members of the industrial platform were already selected during the preparation of the proposal of the PRIME-XS project and the Industrial Platform has been operational since the start of the project. The industrial platform was represented at the first and fourth Annual User Meeting of PRIME-XS, and its members have been active in several courses organized by the PRIME-XS partners and in the International Access Board that reviewed submitted proposals. Collaborative research with members of the Industrial Platform resulted in 11 joint publications.
Sustainability
Also after the end of the PRIME-XS project, life science researchers throughout Europe will encounter biological or biomedical research questions that can be addressed with proteomics technology and might not always have access to suitable proteomics facilities locally, or nationally. In addition, and as also described by Scientific Advisory Board member Brian Chait in a recent opinion piece, the PRIME-XS project has really brought together the European proteomics community, at the level of the research groups that are at the front end of proteomics technology developments, but also at the level of the interaction of these groups with life science researchers that benefit from using proteomics technology to further their biological or biomedical research. The PRIME-XS community sees a positive future for proteomics in Europe and is making efforts to continue some of its activities also beyond the lifetime of the project.
List of Websites:
Website: www.prime-xs.eu
Coordinator: A.J.R.Heck@uu.nl