The International Proteomics Tutorial Programme (IPTP): a teaching tool box for the proteomics community

The most critical functions of the various proteomics organisations are the training of young scientists and the dissemination of information to the general scientific community. The education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) together with their national counterparts are therefore launching the International Proteomics Tutorial Programme to meet these needs. The programme is being led by Peter James (Sweden), Thierry Rabilloud (France) and Kazuyuki Nakamura (Japan). It involves collaboration between the leading proteomics journals: Journal of Proteome Research, Journal of Proteomics, Molecular and Cellular Proteomics, and Proteomics. The overall level is aimed at Masters/PhD level students who are starting out their research and who would benefit from a solid grounding in the techniques used in modern protein-based research. The tutorial program will cover core techniques and basics as an introduction to scientists new to the field. At a later stage the programme may be expanded with a series of more advanced topics focussing on the application of proteomics techniques to biological problem solving. The entire series of articles and slides will be made freely available for teaching use at the Journals and Organisations homepages and at a special website, www.proteomicstutorials.org.     

Virtual Labs in proteomics: new E-learning tools

Web-based educational resources have gained enormous popularity recently and are increasingly becoming a part of modern educational systems. Virtual Labs are E-learning platforms where learners can gain the experience of practical experimentation without any direct physical involvement on real bench work. They use computerized simulations, models, videos, animations and other instructional technologies to create interactive content. Proteomics being one of the most rapidly growing fields of the biological sciences is now an important part of college and university curriculums. Consequently, many E-learning programs have started incorporating the theoretical and practical aspects of different proteomic techniques as an element of their course work in the form of Video Lectures and Virtual Labs. To this end, recently we have developed a Virtual Proteomics Lab at the Indian Institute of Technology Bombay, which demonstrates different proteomics techniques, including basic and advanced gel and MS-based protein separation and identification techniques, bioinformatics tools and molecular docking methods, and their applications in different biological samples. This Tutorial will discuss the prominent Virtual Labs featuring proteomics content, including the Virtual Proteomics Lab of IIT-Bombay, and E-resources available for proteomics study that are striving to make proteomic techniques and concepts available and accessible to the student and research community. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 14). Details can be found at: http://www.proteomicstutorials.org/.     

First Systematic Plant Proteomics Workshop in Botany Department,University of Delhi: Transferring Proteomics Knowledge to Next‐generation Researchers and Students

International Plant Proteomics Organization (INPPO) outlined ten initiatives to promote plant proteomics in each and every country. With greater emphasis in developing countries, one of those was to “organize workshops at national and international levels to train manpower and exchange information”. This third INPPO highlights covers the workshop organized for the very first time in a developing country, India, at the Department of Botany in University of Delhi on December 26–30, 2013 titled – “1^st Plant Proteomics Workshop / Training Program” under the umbrella of INPPO India‐Nepal chapter. Selected 20 participants received on‐hand training mainly on gel‐based proteomics approach along with manual booklet and parallel lectures on this and associated topics. In house, as well as invited experts drawn from other Universities and Institutes (national and international), delivered talks on different aspects of gel‐based and gel‐free proteomics. Importance of gel‐free proteomics approach, translational proteomics, and INPPO roles were presented and interactively discussed by a group of three invited speakers Drs. Ganesh Kumar Agrawal (Nepal), Randeep Rakwal (Japan), and Antonio Masi (Italy). Given the output of this systematic workshop, it was proposed and thereafter decided to be organized every alternate year; the next workshop will be held in 2015. Furthermore, possibilities on providing advanced training to those students / researchers / teachers with basic knowledge in proteomics theory and experiments at national and international levels were discussed. INPPO is committed to generating next‐generation trained manpower in proteomics, and it would only happen by the firm determination of scientists to come forward and do it.     

EuPA achieves visibility - an activity report on the first three years

Plans for the European Proteomics Association (EuPA) were conceived and established during 2004 and 2005, and culminated in the formal inception of the organisation during the 4th HUPO World Congress held in Munich in 2005. The mission from the outset has been three-tiered and is to: i) strengthen the national Proteomics organizations in their efforts; ii) to co-ordinate and provide educational programs, and iii) to advance the networking of scientists through meetings, workshops and student exchange. Linked to the mission were objectives to emphasise the benefits and contributions of Proteomics to biological and industrial researchers, the general public and science policy makers in Europe. In addition, the EuPA set out to promote scientific exchange for all applications and technology development related to Proteomics, and coordinate joint activities of national Proteomics societies at the European level. To achieve these tasks an organisational structure was conceived whereby four Activity Committees (Conferences/Communications, Education, EuPA-HUPO-Interactions and Funding) were implemented and a General Council consisting of all member countries. The remarkable rise and progress the EuPA has achieved in this small time frame is reported here.     

Protein identification using MS/MS data

The subject of this tutorial is protein identification and characterisation by database searching of MS/MS Data. Peptide Mass Fingerprinting is excluded because it is covered in a separate tutorial. Practical aspects of database searching are emphasised, such as choice of sequence database, effect of mass tolerance, and how to identify post-translational modifications. The relationship between sensitivity and specificity is discussed, as is the challenge of using peptide match information to infer which proteins were present in the sample. Since these tutorials are introductory in nature, most references are to reviews, rather than primary research papers. Some familiarity with mass spectrometry and protein chemistry is assumed. There is an accompanying slide presentation, including speaker notes, and a collection of web-based, practical exercises, designed to reinforce key points. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 6).     

Reactome pathway analysis to enrich biological discovery in proteomics data sets

Reactome (http://www.reactome.org) is an open-source, expert-authored, peer-reviewed, manually curated database of reactions, pathways and biological processes. We provide an intuitive web-based user interface to pathway knowledge and a suite of data analysis tools. The Pathway Browser is a Systems Biology Graphical Notation-like visualization system that supports manual navigation of pathways by zooming, scrolling and event highlighting, and that exploits PSI Common Query Interface web services to overlay pathways with molecular interaction data from the Reactome Functional Interaction Network and interaction databases such as IntAct, ChEMBL and BioGRID. Pathway and expression analysis tools employ web services to provide ID mapping, pathway assignment and over-representation analysis of user-supplied data sets. By applying Ensembl Compara to curated human proteins and reactions, Reactome generates pathway inferences for 20 other species. The Species Comparison tool provides a summary of results for each of these species as a table showing numbers of orthologous proteins found by pathway from which users can navigate to inferred details for specific proteins and reactions. Reactome's diverse pathway knowledge and suite of data analysis tools provide a platform for data mining, modeling and analysis of large-scale proteomics data sets. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 8).     

An Introduction to Biological NMR Spectroscopy

NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP).     

Protein extraction from plant tissues for 2DE and its application in proteomic analysis

Plant tissues contain large amounts of secondary compounds that significantly interfere with protein extraction and 2DE analysis. Thus, sample preparation is a crucial step prior to 2DE in plant proteomics. This tutorial highlights the guidelines that need to be followed to perform an adequate total protein extraction before 2DE in plant proteomics. We briefly describe the history, development, and feature of major sample preparation methods for the 2DE analysis of plant tissues, that is, trichloroacetic acid/acetone precipitation and phenol extraction. We introduce the interfering compounds in plant tissues and the general guidelines for tissue disruption, protein precipitation and resolubilization. We describe in details the advantages, limitations, and application of the trichloroacetic acid/acetone precipitation and phenol extraction methods to enable the readers to select the appropriate method for a specific species, tissue, or cell type. The current applications of the sample preparation methods in plant proteomics in the literature are analyzed. A comparative proteomic analysis between male and female plants of Pistacia chinensis is used as an example to represent the sample preparation methodology in 2DE‐based proteomics. Finally, the current limitations and future development of these sample preparation methods are discussed. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP17).     

Reduction through education: the insight of a trainer

One of the articles contained within European Council Directive 86/609/EEC states that "Persons who carry out experiments or take part in them, and persons who take care of animals used for experiments, including duties of a supervisory nature, shall have appropriate training". In effect, this article stipulates that only competent individuals are allowed to work with laboratory animals. At least three groups of individuals can be identified with different responsibilities toward experimental animals: animal technicians, scientists, and veterinarians/animal welfare officers. The responsibilities and duties of the individuals within each of these categories differ. This paper focuses on the training of scientists. The scientist designs, and often also performs, animal experiments. Therefore, scientists must be educated to develop an attitude of respect toward laboratory animals, and must be trained so that, if an experiment must be performed with animals, it is designed according to the highest possible scientific and ethical standards. In The Netherlands, the law stipulates that scientists intending to work with animals must have completed a course in laboratory animal science. This compulsory course started in 1986. The Department of Laboratory Animal Science at Utrecht University is responsible for the national coordination of this course. Participants must have an academic degree (at the level of MSc) in one of the biomedical sciences, such as biology, medicine or veterinary medicine. Although the course is an intensive 3-week, 120-hour long course, which covers both technical and ethical aspects of laboratory animal experimentation, it cannot provide full competence. It is designed to provide sufficient basic training and knowledge to enable students to design animal experiments, and to develop an attitude that will be conducive to the implementation of the Three Rs. However, full competence will always require further training that can only be acquired as a result of practical experience gained while working in the field of laboratory animal research. Evaluations subsequent to the course have revealed that more than 98% of the students regard the course as indispensable for all scientists working in a research area where animal experiments are performed. They agree that the course not only contributes to the quality of experiments and to the welfare of animals, but also to a decrease in the number of animals used in experiments.     

Two-dimensional gel electrophoresis in proteomics: a tutorial

Two-dimensional electrophoresis of proteins has preceded, and accompanied, the birth of proteomics. Although it is no longer the only experimental scheme used in modern proteomics, it still has distinct features and advantages. The purpose of this tutorial paper is to guide the reader through the history of the field, then through the main steps of the process, from sample preparation to in-gel detection of proteins, commenting the constraints and caveats of the technique. Then the limitations and positive features of two-dimensional electrophoresis are discussed (e.g. its unique ability to separate complete proteins and its easy interfacing with immunoblotting techniques), so that the optimal type of applications of this technique in current and future proteomics can be perceived. This is illustrated by a detailed example taken from the literature and commented in detail. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 2).     

Teaching the Fundamentals of Biological Data Integration Using Classroom Games

This article aims to introduce the nature of data integration to life scientists. Generally, the subject of data integration is not discussed outside the field of computational science and is not covered in any detail, or even neglected, when teaching/training trainees. End users (hereby defined as wet-lab trainees, clinicians, lab researchers) will mostly interact with bioinformatics resources and tools through web interfaces that mask the user from the data integration processes. However, the lack of formal training or acquaintance with even simple database concepts and terminology often results in a real obstacle to the full comprehension of the resources and tools the end users wish to access. Understanding how data integration works is fundamental to empowering trainees to see the limitations as well as the possibilities when exploring, retrieving, and analysing biological data from databases. Here we introduce a game-based learning activity for training/teaching the topic of data integration that trainers/educators can adopt and adapt for their classroom. In particular we provide an example using DAS (Distributed Annotation Systems) as a method for data integration.     

The mzIdentML data standard for mass spectrometry-based proteomics results

We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The format was developed by the Proteomics Standards Initiative in collaboration with instrument and software vendors, and the developers of the major open-source projects in proteomics. Software implementations have been developed to enable conversion from most popular proprietary and open-source formats, and mzIdentML will soon be supported by the major public repositories. These developments enable proteomics scientists to start working with the standard for exchanging and publishing data sets in support of publications and they provide a stable platform for bioinformatics groups and commercial software vendors to work with a single file format for identification data.     

The bench vs. the blackboard: learning to teach during graduate school

Many science, technology, engineering, and mathematics (STEM) graduate students travel through the academic career pipeline without ever learning how to teach effectively, an oversight that negatively affects the quality of undergraduate science education and cheats trainees of valuable professional development. This article argues that all STEM graduate students and postdoctoral fellows should undergo training in teaching to strengthen their resumes, polish their oral presentation skills, and improve STEM teaching at the undergraduate level. Though this may seem like a large undertaking, the author outlines a three-step process that allows busy scientists to fit pedagogical training into their research schedules in order to make a significant investment both in their academic career and in the continuing improvement of science education.     

Commercializing medical technology

As medicine moves into the 21st century, life saving therapies will move from inception into medical products faster if there is a better synergy between science and business. Medicine appears to have 50-year innovative cycles of education and scientific discoveries. In the 1880’s, the chemical industry in Germany was faced with the dilemma of modernization to exploit the new scientific discoveries. The solution was the spawning of novel technical colleges for training in these new chemical industries. The impact of those new employees and their groundbreaking compounds had a profound influence on medicine and medical education in Germany between 1880 and 1930. Germany dominated international science during this period and was a training center for scientists worldwide. This model of synergy between education and business was envied and admired in Europe, Asia and America. British science soon after evolved to dominate the field of science during the prewar and post World War (1930’s–1970’s) because the German scientists fled Hitler’s government. These expatriated scientists had a profound influence on the teaching and training of British scientists, which lead to advances in medicine such as antibiotics. After the Second World War, the US government wisely funded the development of the medical infrastructure that we see today. British and German scientists in medicine moved to America because of this bountiful funding for their research. These expatriated scientists helped drive these medical advances into commercialized products by the 1980’s. America has been the center of medical education and advances of biotechnology but will it continue? International scientists trained in America have started to return to Europe and Asia. These American-trained scientists and their governments are very aware of the commercial potential of biotechnology. Those governments are now more prepared to play an active role this new science. Germany, Ireland, Britain, Singapore, Taiwan and Israel are such examples of this government support for biotechnology in the 21st century. Will the US continue to maintain its domination of biotechnology in this century? Will the US education system adjust to the new dynamic of synergistic relationships between the education system, industry and government? This article will try to address these questions but also will help the reader understand who will emerge by 2015 as the leader in science and education.     

药物蛋白质组学与药物发现

21世纪,科学家面临着从基因组到蛋白质组的转变,蛋白质组学是基因组和药物发现的效率。药物蛋白质组学研究不仅有助于发现治疗的可能靶点,也将明显提高药物发现的效率。药物蛋白质组学的研究内容,在临床前包括发现新的治疗靶点和发现针对所有靶点的全部化合物,在临床研究方面应包括药物作用的特异蛋白作为诊断和治疗的标志,或以蛋白质谱的差异来分类者。本文主要综述了蛋白质组学在药物靶点的发现和确认,以有药物发现过程中最有关的技术物研究进展。     

Leaf-mining and gall-forming insects: tools for teaching population ecology

Groups of Israeli and Australian science educationists, practising secondary school science teachers, practising scientists, and science graduates preparing to become science teachers were questioned as to the suitability of teleologically and anthropomorphically formulated statements for inclusion in fourth/fifth-form (14–16 year olds) level study material. Respondents' awareness of the dangers involved (i.e. literal acceptance by pupils of such statements) was acute in the science educationist group, but progressively less so with the teachers, the scientists, and the prospective teachers. It was recommended that all persons connected with science teaching become more aware of the problem, in particular persons engaged in teacher training, and those responsible for preparing texts.     

High‐throughput cloning and expression library creation for functional proteomics

The study of protein function usually requires the use of a cloned version of the gene for protein expression and functional assays. This strategy is particularly important when the information available regarding function is limited. The functional characterization of the thousands of newly identified proteins revealed by genomics requires faster methods than traditional single‐gene experiments, creating the need for fast, flexible, and reliable cloning systems. These collections of ORF clones can be coupled with high‐throughput proteomics platforms, such as protein microarrays and cell‐based assays, to answer biological questions. In this tutorial, we provide the background for DNA cloning, discuss the major high‐throughput cloning systems (Gateway® Technology, Flexi® Vector Systems, and Creator^TM DNA Cloning System) and compare them side‐by‐side. We also report an example of high‐throughput cloning study and its application in functional proteomics. This tutorial is part of the International Proteomics Tutorial Programme (IPTP12).