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.     

A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies

The pilot phase of the Brain Proteome Project (BPP), the Human Proteome Organization (HUPO) initiative that focuses on studies of the brain of both humans and mice, has now been completed. Participating laboratories studied the proteomes of two human samples derived from biopsy and autopsy as well as three mouse samples from various developmental stages. With the combined and centrally reprocessed data now available, a comparison in terms of protein identifications and project organization is made between the HUPO BPP pilot and three other proteomics studies: the HUPO Plasma Proteome Project (PPP) pilot, a proteome of human blood platelets and a recently published comprehensive mouse proteome. Finally, as any comparison between large-scale proteomics datasets is decidedly non-trivial, we also evaluate and discuss several ways to go about comparing such different result sets.     

The time is right: proteome biology of stem cells

In stem cell biology, there is a growing need for advanced technologies that may help to unravel the molecular mechanisms of self-renewal and differentiation. Proteomics, the comprehensive analysis of proteins, is such an emerging technique. To facilitate interactions between specialists in proteomics and stem cell biology,a new initiative has been undertaken, supported by the Human Proteome Organization (HUPO) and the International Society for Stem Cell Research (ISSCR). Here we present the Proteome Biology of Stem Cells Initiative (PBSCI) and report on its goals and future activities.     

Utility of electrophoretically derived protein mass estimates as additional constraints in proteome analysis of human serum based on MS/MS analysis

The proteome of a HUPO human serum reference sample was analyzed using multidimensional separation techniques at both the protein and the peptide levels. To eliminate false-positive identifications from the search results, we employed a data filtering method using molecular weight (MW) correlations derived from denaturing 1-DE. First, the six most abundant serum proteins were removed from the sample using immunoaffinity chromatography. 1-DE was then used to fractionate the remaining serum proteins according to the MW. Gel bands were isolated and in-gel digested with trypsin, and the resulting peptides were analyzed by 2-D LC/ESI-MS/MS. A SEQUEST search using the MS/MS results identified 494 proteins. Of these, 202 were excluded formally using protein data filtering as they were single-assignment proteins and their theoretical and electrophoretically-derived MWs did not correlate at high confidence. To evaluate this method, the results were compared with those of 1-D LC/MALDI-TOF/TOF and HUPO Plasma Proteome Project analyses. Our data filtering approach proved valuable in analysis of complex, large-scale proteomes such as human serum.     

Comparative glycoproteomics based on lectins affinity capture of N-linked glycoproteins from human Chang liver cells and MHCC97-H cells

We present here an effective technique for the large-scale separation and identification of N-linked glycoproteins from Chang liver cells, the human normal liver cells. To enrich N-linked glycoproteins from the whole cells, a procedure containing the lysis of human liver cells, the solubilization of total proteins, lectin affinity chromatography including Concanavalin A and wheat germ agglutinin was established. Furthermore, captured N-linked glycoproteins were separated by 2-DE, and identified by MS and database searching. Finally, we found 63 N-glycoproteins in Chang liver cells. In addition, using the above method, we identified 7 remarkably up-regulated glycoproteins from MHCC97-H cells, highly metastatic liver cancer cells, compared to Chang liver cells. These up-regulated glycoproteins were associated with liver cancer and might be used as biomarkers for tumor diagnosis. Results showed that we established a high-throughput proteomic analysis for separating N-linked glycoproteins from human liver cells. This strategy greatly improved the glycoprotein analysis method associated with proteome-wide glycosylation changes related to liver cancer. Our work was part of the HUPO Human Liver Proteome Project (HLPP) studies and was supported by CHINA HUPO.     

Bridging Proteomics and Medical Science - the 5th HUPO Brain Proteome Workshop in Dublin, Ireland

More than 70 interested colleagues attended the 5th Workshop of the HUPO Brain Proteome Project (HUPO BPP) at the UCD Conway Institute, Dublin, Ireland. An overview of the outcome of the pilot study was presented and the new subprojects "Clinical Neuroproteomics of Human Body Fluids" as well as "Cerebellum 2D-mapping" were announced. In addition the election of the HUPO BPP committees and the future directions of this project were discussed and decided. The meeting was enhanced by several talks highlighting the application of proteomics in biomedical research.     

HUPO BPP pilot study: a proteomics analysis of the mouse brain of different developmental stages

This study is a part of the HUPO Brain Proteome Project (BPP) pilot study, which aims at obtaining a reliable database of mouse brain proteome, at the comparison of techniques, laboratories, and approaches as well as at preparing subsequent proteome studies of neurologic diseases. The C57/Bl6 mouse brains of three developmental stages at embryonic day 16 (E16), postnatal day 7 (P7), and 8 wk (P56) (n = 5 in each group) were provided by the HUPO BPP executive committee. The whole brain proteins of each animal were individually prepared using 2-DE coupled with PDQuest software analysis. The protein spots representing developmentally related or stably expressed proteins were then prepared with in-gel digestion followed with MALDI-TOF/TOF MS/MS and analyzed using the MASCOT search engines to search the Swiss-Prot or NCBInr database. The 2-DE gel maps of the mouse brains of all of the developmental stages were obtained and submitted to the Data Collection Centre (DCC). The proteins alpha-enolase, stathmin, actin, C14orf166 homolog, 28,000 kDa heat- and acid-stable phosphoprotein, 3-mercaptopyruvate sulfurtransferase and 40 S ribosomal protein S3a were successfully identified. A further Western blotting analysis demonstrated that enolase is a protein up-regulated in the mouse brain from embryonic stage to adult stage. These data are helpful for understanding the proteome changes in the development of the mouse brain.     

HUPO World Congress Publication Committee Meeting August 2008, Amsterdam,The Netherlands

The plenary session of the Publications Committee of the Human Proteome Organisation at the 7^th annual HUPO world congress examined the relationship between journals, proteomics standardization initiatives, such as the work of the HUPO‐PSI, and the public domain data repositories. Delegates from industry, academia and the publishing houses discussed how best to bring these bodies closer to together and facilitate the publication process for the bench scientist.     

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.     

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.     

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.     

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline

Motivation: The quest for high-throughput proteomics has revealeda number of challenges in recent years. Whilst substantial improvementsin automated protein separation with liquid chromatography andmass spectrometry (LC/MS), aka ‘shotgun’ proteomics,have been achieved, large-scale open initiatives such as theHuman Proteome Organization (HUPO) Brain Proteome Project haveshown that maximal proteome coverage is only possible when LC/MSis complemented by 2D gel electrophoresis (2-DE) studies. Moreover,both separation methods require automated alignment and differentialanalysis to relieve the bioinformatics bottleneck and so makehigh-throughput protein biomarker discovery a reality. The purposeof this article is to describe a fully automatic image alignmentframework for the integration of 2-DE into a high-throughputdifferential expression proteomics pipeline. Results: The proposed method is based on robust automated imagenormalization (RAIN) to circumvent the drawbacks of traditionalapproaches. These use symbolic representation at the very earlystages of the analysis, which introduces persistent errors dueto inaccuracies in modelling and alignment. In RAIN, a third-ordervolume-invariant B-spline model is incorporated into a multi-resolutionschema to correct for geometric and expression inhomogeneityat multiple scales. The normalized images can then be compareddirectly in the image domain for quantitative differential analysis.Through evaluation against an existing state-of-the-art methodon real and synthetically warped 2D gels, the proposed analysisframework demonstrates substantial improvements in matchingaccuracy and differential sensitivity. High-throughput analysisis established through an accelerated GPGPU (general purposecomputation on graphics cards) implementation. Availability: Supplementary material, software and images usedin the validation are available at http://www.proteomegrid.org/rain/ Contact: g.z.yang{at}imperial.ac.uk Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: David Rocke     

Meeting report on the 7th World Congress of the Human Proteome Organization (HUPO) in Amsterdam: Proteome Biology

The 7th World Congress of the Human Proteome Organization HUPO was held in Amsterdam, the Netherlands, from August 16 to 20, 2008. The event offered a very dense 5-day agenda consisting of an exciting scientific program documenting the tremendous progress, the current challenges, and the major recent accomplishments of proteomics, an exhibition in which all the major vendors in the field of proteomics from around the globe showcased their products, technologies, and services, educational and training events in which new proteomic technologies were introduced and taught, and a series of workshops and discussion forums of all HUPO sanctioned initiatives, including a potential Human Proteome project. Around 1200 scientific abstracts were received, 80 companies signed up for and supported the exhibition, and the total number of registrations was just above 1700, with close to 700 also present for the weekend's Pre-Program. More than 60 nationalities were represented at the meeting.     

The HUPO initiative on Model Organism Proteomes, iMOP

The community working on model organisms is growing steadily and the number of model organisms for which proteome data are being generated is continuously increasing. To standardize efforts and to make optimal use of proteomics data acquired from model organisms, a new Human Proteome Organisation (HUPO) initiative on model organism proteomes (iMOP) was approved at the HUPO Ninth Annual World Congress in Sydney, 2010. iMOP will seek to stimulate scientific exchange and disseminate HUPO best practices. The needs of model organism researchers for central databases will be better represented, catalyzing the integration of proteomics and organism-specific databases. Full details of iMOP activities, members, tools and resources can be found at our website http://www.imop.uzh.ch/ and new members are invited to join us.     

The HUPO Brain Proteome project wish list--summary of the 9(th) HUPO BPP Workshop 9-10 January 2008, Barbados

The Human Brain Proteome Project (HUPO BPP) aims at advancing knowledge and the understanding of neurodiseases and aging with the purpose of identifying prognostic and diagnostic biomarkers, as well as to push new diagnostic approaches and medications. The participating groups meet in semi-annual workshops to discuss the progress, as well as the needs, within the field of proteomics. The 9(th) HUPO BPP workshop took place in Barbados from 9-10 January, 2008. Discussing the future HUPO BPP Roadmap, the attendees drafted the so called HUPO BPP wish list containing timelines, suggestions and missions. This wish list will be updated regularly and will serve as a guideline for the next phase.     

Analyzing large-scale proteomics projects with latent semantic indexing

Since the advent of public data repositories for proteomics data, readily accessible results from high-throughput experiments have been accumulating steadily. Several large-scale projects in particular have contributed substantially to the amount of identifications available to the community. Despite the considerable body of information amassed, very few successful analyses have been performed and published on this data, leveling off the ultimate value of these projects far below their potential. A prominent reason published proteomics data is seldom reanalyzed lies in the heterogeneous nature of the original sample collection and the subsequent data recording and processing. To illustrate that at least part of this heterogeneity can be compensated for, we here apply a latent semantic analysis to the data contributed by the Human Proteome Organization's Plasma Proteome Project (HUPO PPP). Interestingly, despite the broad spectrum of instruments and methodologies applied in the HUPO PPP, our analysis reveals several obvious patterns that can be used to formulate concrete recommendations for optimizing proteomics project planning as well as the choice of technologies used in future experiments. It is clear from these results that the analysis of large bodies of publicly available proteomics data by noise-tolerant algorithms such as the latent semantic analysis holds great promise and is currently underexploited.     

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.     

The proteomes of the human eye,a highly compartmentalized organ

Proteomics has now published a series of Dataset Briefs on the EyeOme from the HUPO Human Proteome Project with high‐quality analyses of the proteomes of these compartments of the human eye: retina, iris, ciliary body, retinal pigment epithelium/choroid, retrobulbar optic nerve, and sclera, with 3436, 2929, 2867, 2755, 2711, and 1945 proteins, respectively. These proteomics resources represent a useful starting point for a broad range of research aimed at developing preventive and therapeutic interventions for the various causes of blindness.     

Human Proteome Organisation’s 7th World Congress, 2008

The annual world congress of Human Proteome Organisation (HUPO) is one of the premier meetings in proteomics. Rotating between Europe, North America and Asia/Oceana, this year’s host city was Amsterdam, The Netherlands. Proteomics still being a rapidly evolving field, HUPO meetings provide a platform for technical advancements in protein purification and separation techniques, innovations in mass spectrometry and applications in bioinformatics and computational biology. A special focus of this year’s meeting was on proteome biology, indicating that the state of technology has progressed to a level permitting interrogation of biological systems in a meaningful way.     

Minimum reporting requirements for proteomics: a MIAPE primer

Amongst other functions, the Human Proteome Organization's Proteomics Standards Initiative (HUPO PSI) facilitates the generation by the proteomics community of guidelines that specify the appropriate level of detail to provide when describing the various components of a proteomics experiment. These guidelines are codified as the MIAPE (Minimum Information About a Proteomics Experiment) specification, the first modules of which are now finalized. This primer describes the structure and scope of MIAPE, places it in context amongst reporting specifications for other domains, briefly discusses related informatics resources and closes by considering the ramifications for the proteomics community.