24th Annual Meeting of the American Electrophoresis Society

Presentations at the 2007 meeting of the American Electrophoresis Society covered many aspects of this key separation technology. In total there were three plenary speakers, two invited talks, 85 technical talks and 14 posters in a 5-day meeting. The three plenary speakers presented their work with each of them discussing somewhat different multiplexed proteomics approaches. The invited speakers discussed ways to improve resolution and shorten running times in proteomic and genomic separations. The proteomics technical talks described applications of 1D and 2D gel electrophoresis, capillary electrophoresis and micro-scale platforms. This report is limited to a small number of those presentations that discussed proteomics directly.     

24th Annual Meeting of the American Electrophoresis Society

Presentations at the 2007 meeting of the American Electrophoresis Society covered many aspects of this key separation technology. In total there were three plenary speakers, two invited talks, 85 technical talks and 14 posters in a 5-day meeting. The three plenary speakers presented their work with each of them discussing somewhat different multiplexed proteomics approaches. The invited speakers discussed ways to improve resolution and shorten running times in proteomic and genomic separations. The proteomics technical talks described applications of 1D and 2D gel electrophoresis, capillary electrophoresis and micro-scale platforms. This report is limited to a small number of those presentations that discussed proteomics directly.     

High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK

The Wellcome Trust Conference Centre at Hinxton, UK, was the meeting place of the 7th HUPO Brain Proteome Project Workshop entitled "High Performance Proteomics". It started on Wednesday, March 7, 2007 with a steering committee meeting followed by a two days series of talks dealing with the standardization and handling of tissues, body fluids as well as of proteomics data. The presentation and accompanying vivid discussions created a picture of actual strategies and standards in recent proteomics.     

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

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

Proteomics 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.     

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

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

Proteomics in environmental and technical microbiology

Nowadays, the field of proteomics encompasses various techniques for the analysis of the entirety of proteins in biological samples. Not only 2D electrophoresis as the primary method, but also MS‐based workflows and bioinformatic tools are being increasingly applied. In particular, research in microbiology was significantly influenced by proteomics during the last few decades. Hence, this review presents results of proteomic studies carried out in areas, such as fundamental microbiological research and biotechnology. In addition, the emerging field of metaproteomics is addressed because high‐throughput genome sequencing and high‐performance MS facilitate the access to such complex samples from microbial communities as found in sludge from wastewater treatment plants and biogas plants. Both current technical limitations and new concepts in this growing and important area are discussed. Moreover, it was convincingly shown that future prospective applications of proteomics in technical and environmental microbiology might also be closely connected with other Omics approaches as well as bioinformatics for systems biology studies.     

Recent advances in 2D electrophoresis: an array of possibilities

2D electrophoresis is currently the most widespread technique used for performing functional proteomics (i.e., the large-scale analysis of alterations in protein expression levels). Nevertheless, several limitations inherent to this technology have restricted the full potential of this protein differential display methodology for years. This has even led to the abandonment of 2D electrophoresis by several groups that switched to performing gel-free functional proteomics analyses based on liquid chromatography and mass spectrometry. Meanwhile, important recent advances in 2D electrophoresis, such as the introduction of fluorescent 2D difference gel electrophoresis and numerous protein prefractionation techniques, have thoroughly modernized 2D electrophoresis, making it again one of the preferred methods for the analysis of protein expression differences in many laboratories.     

Recent advances in 2D electrophoresis: an array of possibilities

2D electrophoresis is currently the most widespread technique used for performing functional proteomics (i.e., the large-scale analysis of alterations in protein expression levels). Nevertheless, several limitations inherent to this technology have restricted the full potential of this protein differential display methodology for years. This has even led to the abandonment of 2D electrophoresis by several groups that switched to performing gel-free functional proteomics analyses based on liquid chromatography and mass spectrometry. Meanwhile, important recent advances in 2D electrophoresis, such as the introduction of fluorescent 2D difference gel electrophoresis and numerous protein prefractionation techniques, have thoroughly modernized 2D electrophoresis, making it again one of the preferred methods for the analysis of protein expression differences in many laboratories.     

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.     

A streamlined approach to high-throughput proteomics

Proteomics has rapidly become an important tool for life science research, allowing the integrated analysis of global protein expression from a single experiment. To accommodate the complexity and dynamic nature of any proteome, researchers must use a combination of disparate protein biochemistry techniques, often a highly involved and time-consuming process. Whilst highly sophisticated, individual technologies for each step in studying a proteome are available, true high-throughput proteomics that provides a high degree of reproducibility and sensitivity has been difficult to achieve. The development of high-throughput proteomic platforms, encompassing all aspects of proteome analysis and integrated with genomics and bioinformatics technology, therefore represents a crucial step for the advancement of proteomics research. ProteomIQ? (Proteome Systems) is the first fully integrated, start-to-finish proteomics platform to enter the market. Sample preparation and tracking, centralized data acquisition and instrument control, and direct interfacing with genomics and bioinformatics databases are combined into a single suite of integrated hardware and software tools, facilitating high reproducibility and rapid turnaround times. This review will highlight some features of ProteomIQ, with particular emphasis on the analysis of proteins separated by 2D polyacrylamide gel electrophoresis.     

A streamlined approach to high-throughput proteomics

Proteomics has rapidly become an important tool for life science research, allowing the integrated analysis of global protein expression from a single experiment. To accommodate the complexity and dynamic nature of any proteome, researchers must use a combination of disparate protein biochemistry techniques, often a highly involved and time-consuming process. Whilst highly sophisticated, individual technologies for each step in studying a proteome are available, true high-throughput proteomics that provides a high degree of reproducibility and sensitivity has been difficult to achieve. The development of high-throughput proteomic platforms, encompassing all aspects of proteome analysis and integrated with genomics and bioinformatics technology, therefore represents a crucial step for the advancement of proteomics research. ProteomIQ (Proteome Systems) is the first fully integrated, start-to-finish proteomics platform to enter the market. Sample preparation and tracking, centralized data acquisition and instrument control, and direct interfacing with genomics and bioinformatics databases are combined into a single suite of integrated hardware and software tools, facilitating high reproducibility and rapid turnaround times. This review will highlight some features of ProteomIQ, with particular emphasis on the analysis of proteins separated by 2D polyacrylamide gel electrophoresis.     

An integrated proteomic workflow for two-dimensional differential gel electrophoresis and robotic spot picking

New technologies have advanced the field of proteomics, and a number of companies have developed innovative platforms to drive this research. However, significant challenges are often encountered when trying to integrate complementary technologies from multiple manufacturers. We have developed a software and hardware solution to integrate the Ettan two-dimensional difference gel electrophoresis (2-D DIGE) system (GE Healthcare) with the Investigator ProPic spot picking robot (Genomic Solutions). We have analyzed protein sample preparations from bacterial and mammalian sources to demonstrate a new workflow with increased throughput for gel-based proteomics.     

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

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

Peptidomics: bridging the gap between proteome and metabolome

Studies of naturally occurring peptides and protein profiling by 'classical' proteomics are linked by common analytical objectives and methodologies. The first international workshop "Peptidomics: methods and applications" held on 6-7th September 2005 at Royal Holloway University of London confirmed that the science of peptidomics is a rapidly developing activity of high interest to both academia and industry. This meeting featured talks by over 20 leading international scientists detailing methods and typical applications, including newly-developed capabilities for protein and peptide analyses. It provided a definition of the scope of the subject in terms of current and future technologies together with applications ranging from studies of defined biological extracts to complete ecosystems. The proceedings of this meeting, speakers' contact details and other relevant information can be accessed at: www.rhul.ac.uk/biosci/meetings.     

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

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

All about DIGE: quantification technology for differential-display 2D-gel proteomics

2D polyacrylamide gel electrophoresis has been the traditional workhorse of proteomics, allowing for the resolution of several thousand proteins in a single gel. Difference gel electrophoresis is an emerging technology that allows for accurate quantification with statistical confidence while controlling for nonbiologic variation, and also increases the dynamic range and sensitivity of traditional 2D polyacrylamide gel electrophoresis. With inclusion of an internal standard formed from equal amounts of every sample in an experiment, difference gel electrophoresis technology also allows for repetitive measurements and multivariable analyses to be quantitatively analyzed in one co-ordinated experiment, yielding statistically-significant changes in protein expression related to many disease states. This technique promises to be an important tool in clinical proteomics and the study of the mechanism of disease, investigating diagnostic biomarkers and pinpointing novel therapeutic targets.     

All about DIGE: quantification technology for differential-display 2D-gel proteomics

2D polyacrylamide gel electrophoresis has been the traditional workhorse of proteomics, allowing for the resolution of several thousand proteins in a single gel. Difference gel electrophoresis is an emerging technology that allows for accurate quantification with statistical confidence while controlling for nonbiologic variation, and also increases the dynamic range and sensitivity of traditional 2D polyacrylamide gel electrophoresis. With inclusion of an internal standard formed from equal amounts of every sample in an experiment, difference gel electrophoresis technology also allows for repetitive measurements and multivariable analyses to be quantitatively analyzed in one co-ordinated experiment, yielding statistically-significant changes in protein expression related to many disease states. This technique promises to be an important tool in clinical proteomics and the study of the mechanism of disease, investigating diagnostic biomarkers and pinpointing novel therapeutic targets.     

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.     

牛精子蛋白质组学技术平台的建立及冻融前后精子差异蛋白初步分析

本研究通过探索不同的精子蛋白制备方法、水化液成分和优化2D电泳程序以建立牛精子蛋白质组学研究技术平台,同时以牛鲜冻精为实验材料通过差异凝胶电泳寻找冻融前后精子蛋白的改变。结果表明：使用改进的热TRIzol法裂解精子细胞制备蛋白,结合优化的2D电泳技术可建立稳定的牛精子蛋白质组学研究技术平台。差异凝胶电泳揭示牛精子在冻融后有质和量的改变：冻融后缺失的蛋白点有20个,表达下调的有2个,表达上调的有10个。作为一项阶段性的实验成果,本研究建立的2D平台和所发现的冻融引起的差异表达蛋白质点为揭示冷冻损伤机理和性控精液的差异蛋白质组学研究奠定了较好的基础。