Editor Profile: Albert Heck.

In this special interview series, we profile members of The FEBS Journal editorial board to highlight their research and perspectives on the journal and more. Albert Heck is Professor of Chemistry and Pharmaceutical Sciences at Utrecht University, Scientific Director of the Netherlands Proteomics Center, and Head of the Biomolecular Mass Spectrometry and Proteomics group in Utrecht University since September 1998. He has served as Editorial Board Member of The FEBS Journal since 2020.

Asia-Oceania HUPO: Past, Present, and Future.

The Asia-Oceania Human Proteome Organization (AOHUPO; www.aohupo.org) was officially founded on June 7, 2001, by Richard J. Simpson (Australia), Akira Tsugita (Japan), and Young-Ki Paik (Korea) and launched on October 1-4, 2001, at the second scientific meeting of the International Proteomics Conference held in Canberra, Australia. Inaugural council members of the AOHUPO elected were Richard J. Simpson (Australia, president), Qi-Chang Xia (China), Kazuyuki Nakamura (Japan), Akira Tsugita (Japan, VIce President), Young-Ki Paik (Korea, secretary general), Mike Hubbard (New Zealand), Max C. M. Chung (Singapore), Shui-Tien Chen (Taiwan), and John Bennett (Philippines). The first AOHUPO conference was held on March 26-27, 2002, at the Seoul National University, Seoul, Korea, conjointly with the second Annual Meeting of KHUPO. Since then, biennial AOHUPO conferences have been held in Taipei (2004), Singapore (2006), Cairns (2008), Hyderabad (2010), Beijing (2012), Bangkok (2014), Sun Moon Lake (2016), and Osaka (2018). The 10th AOHUPO conference is scheduled to be held in Busan on June 30 to July 2, 2021, to celebrate our 20th anniversary.

Membrane proteomic profiling of the heart: past, present, and future.

Cardiovascular diseases remain the most rapidly rising contributing factor of all-cause mortality and the leading cause of inpatient hospitalization worldwide, with costs exceeding $30 billion annually in North America. Cell surface and membrane-associated proteins play an important role in cardiomyocyte biology and are involved in the pathogenesis of many human heart diseases. In cardiomyocytes, membrane proteins serve as critical signaling receptors, Ca2+ cycling regulators, and electrical propagation regulators, all functioning in concert to maintain spontaneous and synchronous contractions of cardiomyocytes. Membrane proteins are excellent pharmaceutical targets due to their uniquely exposed position within the cell. Perturbations in cardiac membrane protein localization and function have been implicated in the progression and pathogenesis of many heart diseases. However, previous attempts at profiling the cardiac membrane proteome have yielded limited results due to poor technological developments for isolating hydrophobic, low-abundance membrane proteins. Comprehensive mapping and characterization of the cardiac membrane proteome thereby remains incomplete. This review will focus on recent advances in mapping the cardiac membrane proteome and the role of novel cardiac membrane proteins in the healthy and the diseased heart.

Mass cytometry and type 1 diabetes research in the age of single-cell data science.

PURPOSE OF REVIEW: New single-cell tec. hnologies developed over the past decade have considerably reshaped the biomedical research landscape, and more recently have found their way into studies probing the pathogenesis of type 1 diabetes (T1D). In this context, the emergence of mass cytometry in 2009 revolutionized immunological research in two fundamental ways that also affect the T1D world: first, its ready embrace by the community and rapid dissemination across academic and private science centers alike established a new standard of analytical complexity for the high-dimensional proteomic stratification of single-cell populations; and second, the somewhat unexpected arrival of mass cytometry awoke the flow cytometry field from its seeming sleeping beauty stupor and precipitated substantial technological advances that by now approach a degree of analytical dimensionality comparable to mass cytometry. RECENT FINDINGS: Here, we summarize in detail how mass cytometry has thus far been harnessed for the pursuit of discovery studies in T1D science; we provide a succinct overview of other single-cell analysis platforms that already have been or soon will be integrated into various T1D investigations; and we briefly consider how effective adoption of these technologies requires an adjusted model for expense allocation, prioritization of experimental questions, division of labor, and recognition of scientific contributions. SUMMARY: The introduction of contemporary single-cell technologies in general, and of mass cytometry, in particular, provides important new opportunities for current and future T1D research; the necessary reconfiguration of research strategies to accommodate implementation of these technologies, however, may both broaden research endeavors by fostering genuine team science, and constrain their actual practice because of the need for considerable investments into infrastructure and technical expertise.

Fundamentals of Ion Mobility-Mass Spectrometry for the Analysis of Biomolecules.

Ion mobility-mass spectrometry (IM-MS) combines complementary size- and mass-selective separations into a single analytical platform. This chapter provides context for both the instrumental arrangements and key application areas that are commonly encountered in bioanalytical settings. New advances in these high-throughput strategies are described with description of complementary informatics tools to effectively utilize these data-intensive measurements. Rapid separations such as these are especially important in systems, synthetic, and chemical biology in which many small molecules are transient and correspond to various biological classes for integrated omics measurements. This chapter highlights the fundamentals of IM-MS and its applications toward biomolecular separations and discusses methods currently being used in the fields of proteomics, lipidomics, and metabolomics.

The Human Brain Proteome Project: Biological and Technological Challenges.

Brain proteomics has become a method of choice that allows zooming-in where neuropathophysiological alterations are taking place, detecting protein mediators that might eventually be measured in cerebrospinal fluid (CSF) as potential neuropathologically derived biomarkers. Following this hypothesis, mass spectrometry-based neuroproteomics has emerged as a powerful approach to profile neural proteomes derived from brain structures and CSF in order to map the extensive protein catalog of the human brain. This chapter provides a historical perspective on the Human Brain Proteome Project (HBPP), some recommendation to the experimental design in neuroproteomic projects, and a brief description of relevant technological and computational innovations that are emerging in the neurobiology field thanks to the proteomics community. Importantly, this chapter highlights recent discoveries from the biology- and disease-oriented branch of the HBPP (B/D-HBPP) focused on spatiotemporal proteomic characterizations of mouse models of neurodegenerative diseases, elucidation of proteostatic networks in different types of dementia, the characterization of unresolved clinical phenotypes, and the discovery of novel biomarker candidates in CSF.

Gel electrophoresis-based plant proteomics: Past, present, and future. Happy 10th anniversary Journal of Proteomics!

In this century we have assisted at an unimaginable expansion of proteomics, with continuous innovations and optimizations in methods, techniques, protocols, equipment, and associated bioinformatics tools. We have moved forward very fast from first (gel electrophoresis based), to second (based on isotopic or isobaric labelling), to third (shotgun or gel-free, label-free), and to fourth (targeted, mass-western, or SRM/MRM) generation techniques. This evolution is clearly observed in the literature since 1994, when the term "proteome" was first coined, with plant proteomics progressing at a much lower speed than human and other model organisms. The question behind this review is: Is gel electrophoresis an obsolete technique? Is it still alive? The answer is that gel electrophoresis is still a valid technique, with its own particularities, strengths, and weaknesses, "irreplaceable" in top-down experiments directed at investigating protein species, loci and allelic variants, and isoforms, as well as in the post-translational modifications and interactions studies; it is an excellent complementary and alternative approach that could lead us to achieve a deeper visualization and knowledge of the cell proteome. The past, present, and future of this technique is being reviewed. It is not pretended to discuss in detail technical aspects, referring to key original papers or previous reviews, but instead, how it has contributed, from a historical perspective, to plant proteomics and biology research. It is our personal congratulations to "Journal of Proteomics" that celebrates this year its 10th anniversary, and, at the same time, a tribute to those scientists who have contributed to the establishment and development of the gel electrophoresis technique and its application to proteomics and plant biology research. Their direct or indirect teaching has been very valuable to those of us who once decided to enter proteomics, with no access to any sophisticated and expensive equipment. This gel electrophoresis-based plant proteomics review is divided into the following sections: introduction, history, methodology, contribution to plant biology research, and future directions.

IMass Time: The Future, in Future!

Joseph John Thomson discovered and proved the existence of electrons through a series of experiments. His work earned him a Nobel Prize in 1906 and initiated the era of mass spectrometry (MS). In the intervening time, other researchers have also been awarded the Nobel Prize for significant advances in MS technology. The development of soft ionization techniques was central to the application of MS to large biological molecules and led to an unprecedented interest in the study of biomolecules such as proteins (proteomics), metabolites (metabolomics), carbohydrates (glycomics), and lipids (lipidomics), allowing a better understanding of the molecular underpinnings of health and disease. The interest in large molecules drove improvements in MS resolution and now the challenge is in data deconvolution, intelligent exploitation of heterogeneous data, and interpretation, all of which can be ameliorated with a proposed IMass technology. We define IMass as a combination of MS and artificial intelligence, with each performing a specific role. IMass will offer advantages such as improving speed, sensitivity, and analyses of large data that are presently not possible with MS alone. In this study, we present an overview of the MS considering historical perspectives and applications, challenges, as well as insightful highlights of IMass.

The Evolution and Metamorphosis of Arthropod Proteomics and Genomics.

This article presents an overview of the development of techniques for analyzing cuticular proteins (CPs), their transcripts, and their genes over the past 50 years based primarily on experience in the laboratory of J.H. Willis. It emphasizes changes in the kind of data that can be gathered and how such data provided insights into the molecular underpinnings of insect metamorphosis and cuticle structure. It describes the techniques that allowed visualization of the location of CPs at both the anatomical and intracuticular levels and measurement of the appearance and deployment of transcripts from CP genes as well as what was learned from genomic and transcriptomic data. Most of the early work was done with the cecropia silkmoth, Hyalophora cecropia, and later work was with Anopheles gambiae.

The dawn and the first twenty-five years of proteomics in Mexico: a personal chronicle / El nacimiento y los 25 primeros años de la proteómica en México: una crónica personal

Abstract: This review does not aim to be an up-to-date of proteomics in Mexico; it simply tries to trace its development, exposing the story of the researchers, laboratories and some institutions that have contributed to the establishment and development of this science in Mexico.

Resumen: Esta revisión no pretende cubrir el panorama actual de la proteómica en México, simplemente intenta describir su nacimiento y desarrollo, exponiendo la historia de algunos investigadores, laboratorios e Instituciones que han contribuido al establecimiento y crecimiento de esta ciencia en México.

Clinical Proteomics in Kidney Disease: From Discovery to Clinical Application.

Proteome analysis has been applied in multiple studies in the context of chronic kidney disease, aiming at improving our knowledge on the molecular pathophysiology of the disease. The approach is generally based on the hypothesis that proteins are key in maintaining kidney function, and disease is a clinical consequence of a significant change of the protein level. Knowledge on critical proteins and their alteration in disease should in turn enable identification of ideal biomarkers that could guide patient management. In addition, all drugs currently employed target proteins. Hence, proteome analysis also promises to enable identifying the best suited therapeutic target, and, in combination with biomarkers, could be used as the rationale basis for personalized intervention. To assess the current status of proteome analysis in the context of CKD, we present the results of a systematic review, of up-to-date scientific research, and give an outlook on the developments that can be expected in near future. Based on the current literature, proteome analysis has already seen implementation in the management of CKD patients, and it is expected that this approach, also supported by the positive results generated to date, will see advanced high-throughput application.

The dawn and the first twenty-five years of proteomics in Mexico: a personal chronicle.

This review does not aim to be an up-to-date of proteomics in Mexico; it simply tries to trace its development, exposing the story of the researchers, laboratories and some institutions that have contributed to the establishment and development of this science in Mexico.

Concepts and Methodologies to Study Protein SUMOylation: An Overview.

Protein modification by the small ubiquitin-related modifier (SUMO) was simultaneously discovered by several groups at the middle of the 1990s. Although distinct names were proposed including Sentrin, GMP1, PIC1, or SMT3, SUMO became the most popular. Early studies on the functions of SUMOylation focused on activities in the nucleus, including transcription activation, chromatin structure, and DNA repair. However, it is now recognized that SUMOylation affects a large diversity of cellular processes both in the nucleus and the cytoplasm and functions of SUMOylation appear to have undefined limits. SUMO-conjugating enzymes and specific proteases actively regulate the modification status of target proteins. The recent discoveries of ubiquitin-SUMO hybrid chains, multiple SUMO-interacting motifs, and macromolecular complexes regulated by SUMOylation underscore the high complexity of this dynamic reversible system. New conceptual frameworks suggested by these findings have motivated the development of new methodologies to study pre- and post-SUMOylation events in vitro and in vivo, using distinct model organisms. Here we summarize some of the new developments and methodologies in the field, particularly those that will be further elaborated on in the chapters integrating this book.

Constructing failure in big biology: The socio-technical anatomy of Japan's Protein 3000 Project.

This study focuses on the 5-year Protein 3000 Project launched in 2002, the largest biological project in Japan. The project aimed to overcome Japan's alleged failure to contribute fully to the Human Genome Project, by determining 3000 protein structures, 30 percent of the global target. Despite its achievement of this goal, the project was fiercely criticized in various sectors of society and was often branded an awkward failure. This article tries to solve the mystery of why such failure discourse was prevalent. Three explanatory factors are offered: first, because some goals were excluded during project development, there was a dynamic of failed expectations; second, structural genomics, while promoting collaboration with the international community, became an 'anti-boundary object', only the absence of which bound heterogeneous domestic actors; third, there developed an urgent sense of international competition in order to obtain patents on such structural information.

The 20th anniversary of proteomics and some of its origins.

The term "proteome" was first introduced into the scientific literature in July 1995. Almost 20 years ago attempts to characterize the "total protein complement able to be encoded by a given genome" only became possible due to privileged access to what were then the world's most complete sets of genomic data. Today, proteomics has become an important pillar in the fields of disease diagnosis and drug research and development, while also playing a critical role in the much larger field of Healthcare Analytics and Biomarker Discovery and Detection. It is important to note that this industry originated mostly from building blocks in analytical science that predated the term "proteomics" by many decades. However, proteomics, as a discipline, has allowed protein scientists to more favorably compete in the face of highly fashionable Big Science and, more specifically, genomics.