Biomedical omics: first insights of a new MSc degree of the University of Milan.

The advent of technologies allowing the global analysis of biological phenomena, referred to as "omics" (genomics, epigenomics, proteomics, metabolomics, microbiomics, radiomics, and radiogenomics), has revolutionized the study of human diseases and traced the path for quantitative personalized medicine. The newly inaugurated Master of Science Program in Biomedical Omics of the University of Milan, Italy, aims at addressing the unmet need to create professionals with a broad understanding of omics disciplines. The course is structured over 2 years and admits students with a bachelor's degree in biotechnology, biology, chemistry, or pharmaceutical sciences. All teaching activities are fully held in English. A total of nine students enrolled in the first academic year and attended the courses of radiomics, genomics and epigenomics, proteomics, and high-throughput screenings, and their feedback was evaluated by means of an online questionnaire. Faculty with different backgrounds were recruited according to the subject. Due to restrictions imposed by the coronavirus disease 2019 (COVID-19) pandemic, laboratory activities were temporarily suspended, while lectures, journal clubs, and examinations were mainly held online. After the end of the first semester, despite the difficulties brought on by the COVID-19 pandemic, the course overall met the expectations of the students, specifically regarding teaching effectiveness, interpersonal interactions with the lecturers, and courses organization. Future efforts will be undertaken to better calibrate the overall workload of the course and to implement the most relevant suggestions from the students together with omics science evolution in order to guarantee state-of-the-art omics teaching and to prepare future omics specialists.

Should 'Omics' education be a part of allied health profession curricula?

Sequencing of human genome followed by monumental progress in omics sciences within last two decades has made personalized nutrition for better health is a reality for near future. The complexity of underlying science in making personalized nutrition recommendation has led to the need for training of health care providers. The International Society of Nutrigenetics/Nutrigenomics (ISNN) has mission to increase the understanding among both professionals and the general public of the role of genetic variation and nutrients in gene expression. To bring this mission to fruition, we need trained healthcare professionals ready to educate public. With this in mind, we have surveyed allied health students for their omics knowledge, desire to learn more and their perception of the need of omics education. The results show a need for training in omics in all allied health disciplines and desire of the students to learn more.

An integrated course based on two dimensional-electrophoresis and mass spectrometry analysis to teach proteomic techniques for undergraduate students.

Here, we developed an integrated course based on two dimensional-electrophoresis and spectrometry mass (2DE-MS) technique for undergraduate students to help them learn proteomic techniques. The soluble proteins in wild type and gene knockout bacteria were separated by 2DE and the differently expressed proteins were identified by MS analysis. The proteomic data was finally confirmed by RT-PCR detection. The separated experiments of 2DE, MS, RNA isolation, RT-PCR, as well as essential bioinformatic analysis, were integrated into a one-week course, which provided students an opportunity to systematically understand the proteomic techniques and their applications in current scientific research. © 2018 by The International Union of Biochemistry and Molecular Biology, 46:354-360, 2018.

Proceedings of the EuBIC Winter School 2017.

The 2017 EuBIC Winter School was held from January 10th to January 13th 2017 in Semmering, Austria. This meeting gathered international researchers in the fields of bioinformatics and proteomics to discuss current challenges in data analysis and biological interpretation. This article outlines the scientific program and exchanges that took place on this occasion and presents the current challenges of this ever-growing field. BIOLOGICAL SIGNIFICANCE: The EUPA bioinformatics community (EuBIC) organized its first winter school in January 2017. This successful event illustrates the growing need of the bioinformatics community in proteomics to gather and discuss current and future challenges in the field. In addition to the organization of yearly meetings, the young and active EuBIC community aims to develop new collaborative open source projects, spread bioinformatics knowledge in Europe, and actively promote data sharing through public repositories.

DEMOCRATIZING MASS SPECTROMETRY.

Mass spectrometry is often seen as a complicated, highly technical technique requiring years of experience to master. Jeffrey Perkel talks to users about the best ways for novices to approach mass spectrometry experiments.

Key players in neurodegenerative disorders in focus-New insights into the proteomic profile of Alzheimer's disease, schizophrenia, ALS, and multiple sclerosis-24th HUPO BPP Workshop: September 29, 2015, Vancouver, Canada.

The HUPO Brain Proteome Project (HUPO BPP) held its 24th workshop in Vancouver, Canada, September 29, 2015. The focus of the autumn workshop was on new insights into the proteomic profile of Alzheimer's disease, schizophrenia, ALS and multiple sclerosis.

Proteomics in Argentina - limitations and future perspectives: A special emphasis on meat proteomics.

Argentina is one of the most relevant countries in Latin America, playing a major role in regional economics, culture and science. Over the last 80 years, Argentinean history has been characterized by several upward and downward phases that had major consequences on the development of science in the country and most recently on proteomics. In this article, we characterize the evolution of Proteomics sciences in Argentina over the last decade and a half. We describe the proteomics publication output of the country in the framework of the regional and international contexts, demonstrating that Argentina is solidly anchored in a regional context, showing results similar to other emergent and Latin American countries, albeit still far from the European, American or Australian realities. We also provide a case-study on the importance of Proteomics to a specific sector in the area of food science: the use of bacteria of technological interest, highlighting major achievements obtained by Argentinean proteomics scientists. Finally, we provide a general picture of the endeavors being undertaken by Argentinean Proteomics scientists and their international collaborators to promote the Proteomics-based research with the new generation of scientists and PhD students in both Argentina and other countries in the Southern cone.

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.

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.

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.

PRIME-XS, a European infrastructure for proteomics.

The PRIME-XS consortium is a pan-European infrastructure for proteomics. As a prologue to this special issue of Molecular & Cellular Proteomics on the research activities of the PRIME-XS consortium, we, as the guest editors of this issue, provide an overview of the structure and activities of this consortium, which is funded by the European Union's 7th Framework Programme for Research and Technological Development.

Simulation of two dimensional electrophoresis and tandem mass spectrometry for teaching proteomics.

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations-2D electrophoresis and tandem mass spectrometry. The two simulations are integrated together and are designed to teach the concept of proteome analysis of prokaryotic and eukaryotic organisms. 2DE-Tandem MS can be used as a freestanding simulation, or in conjunction with a wet lab, to introduce proteomics in the undergraduate classroom. 2DE Tandem MS is a free program available on Sourceforge at https://sourceforge.net/projects/jbf/. It was developed using Java Swing and functions in Mac OSX, Windows, and Linux, ensuring that every student sees a consistent and informative graphical user interface no matter the computer platform they choose. Java must be installed on the host computer to run 2DE Tandem MS. Example classroom exercises are provided in the Supporting Information.

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.

New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences.

This White Paper sets out a Life Sciences Grand Challenge for Proteomics Technologies to enhance our understanding of complex biological systems, link genomes with phenotypes, and bring broad benefits to the biosciences and the US economy. The paper is based on a workshop hosted by the National Institute of Standards and Technology (NIST) in Gaithersburg, MD, 14-15 February 2011, with participants from many federal R&D agencies and research communities, under the aegis of the US National Science and Technology Council (NSTC). Opportunities are identified for a coordinated R&D effort to achieve major technology-based goals and address societal challenges in health, agriculture, nutrition, energy, environment, national security, and economic development.

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/.

Analyzing protein-protein interaction networks.

The advent of the "omics" era in biology research has brought new challenges and requires the development of novel strategies to answer previously intractable questions. Molecular interaction networks provide a framework to visualize cellular processes, but their complexity often makes their interpretation an overwhelming task. The inherently artificial nature of interaction detection methods and the incompleteness of currently available interaction maps call for a careful and well-informed utilization of this valuable data. In this tutorial, we aim to give an overview of the key aspects that any researcher needs to consider when working with molecular interaction data sets and we outline an example for interactome analysis. Using the molecular interaction database IntAct, the software platform Cytoscape, and its plugins BiNGO and clusterMaker, and taking as a starting point a list of proteins identified in a mass spectrometry-based proteomics experiment, we show how to build, visualize, and analyze a protein-protein interaction network.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed upon two primary needs for the wide use of quality metrics: (i) an evolving list of comprehensive quality metrics and (ii) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in Proteomics, Proteomics Clinical Applications, Journal of Proteome Research, and Molecular and Cellular Proteomics, as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.