Towards standard protocols and guidelines for urine proteomics: a report on the Human Kidney and Urine Proteome Project (HKUPP) symposium and workshop, 6 October 2007, Seoul, Korea and 1 November 2007, San Francisco, CA, USA

The Human Kidney and Urine Proteome Project (HKUPP) was initiated in 2005 to promote proteomics research in the nephrology field, to better understand kidney functions as well as pathogenic mechanisms of kidney diseases, and to define novel biomarkers and therapeutic targets. This project was first approved in 2005 by the Human Proteome Organisation (HUPO) as a Kidney Disease Initiative under an umbrella of the HUPO Disease Biomarker Initiative (DBI), and more recently was approved as the HKUPP Initiative in 2007. Several sub-projects have been planned to achieve the ultimate goals. The most pressing is the establishment of "standard protocols and guidelines for urine proteome analysis". This sub-project had been extensively discussed during the first HKUPP symposium (during 6(th) HUPO Annual World Congress--October 2007, Seoul, Korea) and second workshop (during 40(th) American Society of Nephrology Renal Week--November 2007, San Francisco, CA, USA). Additional data and references have been collected after the symposium and workshop. An initial draft of standard protocols and guidelines for proteome analysis of non-proteinuric urine (urine protein excretion < or =150 mg/day) will soon be released as the first HKUPP product.     

The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland

iMOP--the Initiative on Model Organism Proteomes--was accepted as a new HUPO initiative at the Ninth HUPO meeting in Sydney in 2010. A goal of iMOP is to integrate research groups working on a great diversity of species into a model organism community. At the Tenth HUPO meeting in Geneva this variety was reflected in the iMOP session on Tuesday September 6, 2011. The presentations covered the quantitative proteome database PaxDb, proteomics projects studying farm animals, Arabidopsis thaliana, as well as host-pathogen interactions.     

The 6th HUPO Antibody Initiative (HAI) Workshop: Sharing Data About Affinity Reagents and Other Recent Developments September 2009, Toronto,Canada

The Human Antibody Initiative (HAI) aims to promote and facilitate the use of antibodies for proteomics research. The 6th workshop for the HUPO Antibody Initiative (HAI) held in September 2009 was co‐chaired by Michael Snyder and Mathias Uhlen and discussed several aspects of antibody production, their validation, and attempts to standardise this process, in particular, when subsequently described in the literature. An update on the progress of the Human Protein Atlas was also presented to the attendees.     

HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease

A newly reorganized HUPO Cardiovascular Initiative was announced at the HUPO 2011 Cardiovascular Initiative Workshop at Geneva. The new initiative is now part of the biology- and disease-driven component of the HUPO Human Proteome Project (B/D-HPP). Here we report the recent achievements and future directions of the initiative, and offer a perspective on the present challenges of cardiovascular proteomics and its integration with the cardiovascular biology community at large.     

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 2011 Human Liver Proteome Project (HLPP) Workshop September 5, 2011, Geneva, Switzerland

During the 10th HUPO Annual World Congress held in Geneva (Switzerland) from 4th to 7th September, a workshop on Human Liver Proteome Project (HLPP) Initiative took place. Four research groups presented their latest results from different ongoing projects. Later on, during the HLPP executive members' meeting, the status of current projects and the next possible steps to be taken were discussed.     

Meeting New Challenges: The 2014 HUPO‐PSI/COSMOS Workshop

The Annual 2014 Spring Workshop of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) was held this year jointly with the metabolomics COordination of Standards in MetabOlomicS (COSMOS) group. The range of existing MS standards (mzML, mzIdentML, mzQuantML, mzTab, TraML) was reviewed and updated in the light of new methodologies and advances in technologies. Adaptations to meet the needs of the metabolomics community were incorporated and a new data format for NMR, nmrML, was presented. The molecular interactions workgroup began work on a new version of the existing XML data interchange format. PSI‐MI XML3.0 will enable the capture of more abstract data types such as protein complex topology derived from experimental data, allosteric binding, and dynamic interactions. Further information about the work of the HUPO‐PSI can be found at http://www.psidev.info .     

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.     

Further advances in the development of a data interchange standard for proteomics data

The Protein Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Significant progress was made in advancing the design and implementation of a draft standard for exchanging experimental data from proteomics experiments involving mass spectrometry at the 51st Annual Conference of the American Society for Mass Spectrometry. In collaboration with the American Society for Tests and Measurements, the PSI propose to publish this first draft at the forthcoming HUPO 2nd World Congress in Montreal, 8-11 October 2003.     

HUPO Biological Reference Material Initiative Workshop 26 September 2009, Toronto,Canada

The Biological Reference Material Initiative Workshop held at the Toronto HUPO congress on 26 September 2009, focused on the development of new biological reference materials and tools for the assessment of reproducibility, the solutions to many of the technical challenges in proteomics and protein‐based molecular diagnostics. This half‐day meeting included presentations from leading scientists from the worldwide proteomic community, who shared a common interest in standardization and increased accuracy of proteomic data. The conclusion was that proteomics is highly sensitive to both biological and technical variability. It is this biological and technical variance, when not accounted for by experiment design, that invalidates proteomic experiments, but both of these issues can be dealt with by tackling reproducibility.     

Creating a human brain proteome atlas--14th HUPO BPP workshop September 20-21, 2010, Sydney, Australia

The HUPO Brain Proteome Project (HUPO BPP) held its 14th workshop during the HUPO 9th Annual World Congress in Sydney, Australia. The principal aim of this project is to discover prognostic and diagnostic biomarkers associated with neurodegenerative diseases and brain aging, with the ultimate objective of obtaining a better understanding of these conditions and creating roads for the development of novel diagnostic techniques and effective treatments. The attendees came together to discuss progress in the human clinical neuroproteomics and to define the needs and guidelines required for more advanced proteomics approaches.     

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.     

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.     

Proteomics for everyday use: activities of the HUPO Brain Proteome Project during the 5th HUPO World Congress

Long Beach hosted this year's annual congress of the Human Proteome Organisation (HUPO). In addition to the numerous sessions, talks and poster presentations organized by HUPO itself, several events were arranged by the HUPO initiatives. The Brain Proteome Project (HUPO BPP) was very active, initiating three pre-congress workshops: (i) the kick-off meeting of the EU-funded ProDaC consortium (Proteomics Data Collection) that is aiming at the bioinformatics Standardization in the proteomics field; (ii) the workshop "Standardization Issues in Proteomics: Perspectives from Vendors" giving an overview about the lessons learned by proteomics industrial partners; (iii) the 6th HUPO BPP Workshop "New Proteomics Approaches for further HUPO BPP Studies" offering new concepts for brain-related proteomics studies.     

Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004

The increasing volume of proteomics data currently being generated by increasingly high-throughput methodologies has led to an increasing need for methods by which such data can be accurately described, stored and exchanged between experimental researchers and data repositories. Work by the Proteomics Standards Initiative of the Human Proteome Organisation has laid the foundation for the development of standards by which experimental design can be described and data exchange facilitated. The progress of these efforts, and the direct benefits already accruing from them, were described at a plenary session of the 3(rd) Annual HUPO congress. Parallel sessions allowed the three work groups to present their progress to interested parties and to collect feedback from groups already implementing the available formats.     

Human Brain Proteome Project – 12th HUPO BPP Workshop 26 September 2009, Toronto,Canada

The HUPO Brain Proteome Project (HUPO BPP) held its 12th workshop in Toronto on 26 September 2009 prior to the HUPO VIII World Congress. The principal aim of this project is to obtain a better understanding of neurodiseases and ageing, with the ultimate objective of discovering prognostic and diagnostic biomarkers, in addition to the development of novel diagnostic techniques and new medications. The attendees came together to discuss progress in the human clinical neuroproteomics and to define the needs and guidelines required for more advanced proteomic approaches.     

Creating a human brain proteome atlas--13th HUPO BPP Workshop March 30-31, 2010, Ochang, Korea

The HUPO Brain Proteome Project (HUPO BPP) held its 13th workshop in Ochang from March 30th to 31st, 2010 prior to the Korean HUPO 10th Annual International Proteomics Conference. The principal aim of this project is to obtain a better understanding of neurodiseases and aging with the ultimate objective of discovering prognostic and diagnostic biomarkers, in addition to the development of novel diagnostic techniques and new medications. The attendees came together to discuss progress in the clinical neuroproteomics of human and to define the needs and guidelines required for more advanced proteomics approaches.     

Proteome biology of stem cells

The notion that integration of cutting-edge technologies in stem cell research would be enhanced by proteomic analyses has emanated from rapid advances in proteome technology. These advances have increased the probability that basic properties of stem cells will be elucidated more effectively, leading to acceleration toward novel stem cell therapies. We have therefore sought to establish a world-wide alliance of proteomics and stem cell researchers, which has resulted in the foundation of an initiative supported by the Human Proteome Organisation (HUPO) and the International Society for Stem Cell Research (ISSCR) called the Proteome Biology of Stem Cells Initiative. Here we report on the rationale and goals of this initiative.     

Clinical aspects of neurodegenerative diseases - 15th HUPO BPP Workshop April 8-9, 2011, Bochum, Germany

The HUPO Brain Proteome Project (HUPO BPP) held its 15th workshop in Bochum, Germany, from April 8th to 9th, 2011 directly after the Proteomic Forum 2011 in Berlin. Like on every spring workshop, the focus was more on clinical aspects, so that especially clinicians participated in this workshop.