Immunopeptidomics: Reading the Immune Signal That Defines Self From NonselfFifty years have passed since the study of Benacerraf and McDevitt (1) describing the exquisite regulation of the immune response by the major histocompatibility complex (MHC). The landmark discovery that T-cell activation requires corecognition of peptide antigens and self-MHC molecules (2) revealed not only a unique receptor–ligand interaction but also a delicate balance between autoimmune response and effective protection against infection. These seminal studies laid the foundation to our current understanding of how immune cells distinguish between self and nonself.
Glycoproteomics: Making the Study of the Most Structurally Diverse and Most Abundant Post-Translational Modifications More Accessible to the Scientific CommunityIn 2013, we served as guest editors for the Glycomics special issue where the Athens guidelines for glycomic analyses were first revealed that have since been adopted by multiple journals (1). At that moment in time, we could not have easily conceived of a special issue dedicated to glycoproteomics. However, just 8 years later, we find ourselves presenting a special issue of Molecular & Cellular Proteomics on Glycoproteomics that introduces the reader to the recent explosion in front-end enrichment methods, analytical approaches, and back-end software solutions dedicated to glycoproteomics.
Opening ASBMB publications freely to allWe are extremely excited to announce on behalf of the American Society for Biochemistry and Molecular Biology (ASBMB) that the Journal of Biological Chemistry (JBC), Molecular & Cellular Proteomics (MCP), and the Journal of Lipid Research (JLR) will be published as fully open-access journals beginning in January 2021. This is a landmark decision that will have huge impact for readers and authors. As many of you know, many researchers have called for journals to become open access to facilitate scientific progress, and many funding agencies across the globe are either already requiring or considering a requirement that all scientific publications based on research they support be published in open access journals.
The Data Must Be Accessible to AllScience relies on data acquisition via well-described, rigorous, reproducible procedures; statistically defensible interpretation of these data; and transparent reporting of the interpretations and conclusions reached based on these data. Each of these steps must be communicated to the broader scientific community in such a way that others can critically evaluate the studies, draw conclusions based on the reported findings, design subsequent experiments, and replicate and extend those observations.
Compliance Checklists No Longer Required at Initial Manuscript SubmissionIn our continuing effort to simplify the submission process and ease the burden on authors, effective April 1, 2020, the editors will no longer require authors to provide the appropriate checklists when submitting a new manuscript. However, authors will be required to satisfy compliance with the journal guidelines before acceptance of the reviewed, revised final manuscript. This will be achieved by the author working in concert with the manuscript integrity editor's assistance during the manuscript revision stage.
Virtual Issue: Technological InnovationsThe mission of Molecular and Cellular Proteomics since its creation in 2002 has been to “foster the development and applications of proteomics in both basic and translational research.” Our mission statement mandates that Research Articles “report significant new biological or clinical discoveries underpinned by proteomic observations across all kingdoms of life” and that “manuscripts must define the biological roles played by the proteins investigated or their mechanisms of action.” This governing principle still forms the basis of a Research Article's acceptance in the journal.
For the Sake of ScienceThe world of scientific publishing has been invigorated and challenged by a variety of new proposals and initiatives over the past few years. With each new model for the publishing process, there have been opportunities to reimagine the future of research articles and journals. However, without a deadline for when the future begins, systematic change has been slow in coming.
Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic AnalysisProteomic research began largely as an approach for characterizing sample compositions, but most contemporary studies involve a quantitative aspect. Quantification enables comparing sample classes (e.g. healthy versus disease) to uncover markers of dysregulation, or comparing protein pull-down experiments to mock pull-downs to determine specific interaction partners. For small-scale comparisons, isotopic labeling, whether introduced metabolically or chemically, is very effective and allows comparison of multiple samples mixed together.
Editorial focus on the current MCP Mission Statement and ScopeAs a follow-up to our editorial of January 2018, we have updated the MCP Mission Statement and Scope to 1) re-emphasize our interest in advancing technological and computational tools, and 2) to provide clarification of our new interest in metabolomics that are supportive and complementary to our primary focus on deciphering and understanding the nature and functions of proteins of all living systems.
Announcing New Editorial Leadership in Clinical Proteomics and Biomarker DiscoveryWe are delighted to announce the appointment of Dr. Michael A. Gillette from the Broad Institute of M.I.T. and Harvard as a new Associate Editor in the expanding area of clinical proteomics and biomarker discovery.
Your technological advances belong hereThe Molecular & Cellular Proteomics editorial leadership team gathered over the summer to discuss the journal's plans for the new year. At that strategy session, we determined it is necessary to re-establish that MCP is where your technological advances belong, and we have made other policy changes about which you should be aware.
The Host-Pathogen Ecosystem Viewed Through the Prism of ProteomicsThe coexistence and coevolution of hosts with pathogens is intrinsic to our ecosystem. Pathogenic infections induce a diverse array of changes in the hosts that are tightly linked to the progression of infection and establishment of disease. At the cellular level, this is reflected in alterations in host cell composition, organization, and ability to communicate with other cells. Thus, changes in the host proteome, metabolome, lipidome, and secretome have started to be recognized as signatures of infectious or disease states.
On Strengthening the MCP Editorial LeadershipWith this issue, a long-standing member of our Editorial Board, Natalie Ahn, becomes President of our Society. Also with this issue, I am delighted to announce a number of editorial changes designed to expand and broaden our scientific leadership. Although a revised Mission Statement follows, our core mission has not changed. MCP will continue to serve the proteomics community with original contributions that enhance our knowledge in the general areas of protein biology of living systems and the biomedical sciences.
Reshaping the Chromatin and Epigenetic Landscapes with Quantitative Mass SpectrometryThe solving of the structure of DNA by Watson and Crick is arguably one of the major breakthroughs in all of science during the 20th century (1). Subsequent feverish research led to the discovery of a DNA genetic code, and that this code was utilized by living cells to encode proteins, the workhorse molecules of most cellular functions (2). The fundamental idea of genetic information transfer encoded by a DNA code has revolutionized the biological sciences and has led to the creation of new related fields and industries such as genomics, proteomics and biotechnology.
Neuroproteomics: How Many Angels can be Identified in an Extract from the Head of a Pin?Oscar Wilde once defined fox hunting as an activity of “the unspeakable in pursuit of the uneatable.” This sentiment may well reflect the reaction of some mass spectrometry laboratories to neuroscience colleagues rushing in with a vial containing a hopelessly inadequate amount of sample originating from a tissue of intractable complexity, or in other words a neuroproteomics project. This issue of Molecular and Cellular Proteomics focuses on application of proteomics to current problems in neuroscience.
On Credibility, Clarity, and ComplianceSince its inception, MCP has recognized the promise of proteomics and its underlying technologies to significantly move the boundaries of knowledge in biology and medicine. As has been noted (1), proteomics represented a paradigm shift in how experiments were designed and executed and how the resultant data were interpreted and stored. But the journal has also recognized that the value of the proteomic approach and the data generated were only as good as the quality and reliability of that data“a corollary of the computational maxim, “garbage in, garbage out.” Thus, in its very earliest stages, the editorial staff of MCP, particularly Steve Carr, Ruedi Aebersold, and Al Burlingame, began earnest discussions about how a journal should evaluate data arising from large scale, often called “shotgun,” mass spectrometric experiments, which ultimately lead to the first set of guidelines (2).
Post-translational Modifications: A Major Focus for the Future of ProteomicsWith 20,000 to 30,000 human genes and only 100,000 expressed proteins, the dynamic complexity of living systems is achieved, in part, through an enormous repertoire of chemical modifications of amino acids that occur during and after protein translation. There are over 400 known post-translational modifications (PTMs), and technical advances in methodology and instrumentation are permitting the discovery of new modifications, enabling the development of a global view of the role of modifications in responding to and regulating biological processes, and revealing the magnitude of complexity that is imparted to protein regulation by combinations of modifications.
Western Blots versus Selected Reaction Monitoring Assays: Time to Turn the Tables?As of January 1, 2013, the paper entitled “Electrophoretic Transfer of Proteins from Polyacrylamide Gels to Nitrocellulose Sheets: Procedure and Some Applications,” by Towbin and colleagues (1), had been cited 52,488 times (ISI Web of Knowledge v5.8), placing it among the elite group of papers that have truly transformed life science research. For more than 30 years, the nitrocellulose-based Western blotting technique introduced by this paper has been a principal method for the detection of specific proteins in complex biological samples.
Glycomics: Building Upon Proteomics to Advance GlycosciencesGlycans are among the building blocks of the four major biomolecules of life—carbohydrates, nucleic acids, lipids, and proteins. Intriguingly, the other three major biomolecules of life either contain (ribo- or deoxyribonucleic acids) or can be modified with (glycolipids and glycoproteins) carbohydrates. To quote one of the leaders in the field of glycobiology, Ajit Varki of the University of California at San Diego, “Despite more than 3 billion years since the origin of life on earth, the powerful forces of biological evolution seem to have failed to generate any living cell that is devoid of a dense and complex array of cell surface glycans” (1).
Seven Years of Good LuckThe end of 2008 marks the completion of the first seven years in the life of Molecular & Cellular Proteomics, which began publication in 2002. Although it has a way to go to reach the plateaus of its stable mates (the Journal of Biological Chemistry began its second century in 2005, and the Journal of Lipid Research celebrates its 50th anniversary this year, to which the editors and staff of MCP offer their heartiest congratulations), it has enjoyed some considerable measure of success in its own right.
New Guidelines for Clinical Proteomics ManuscriptsSeveral years ago, the editors of MCP1 , concerned with the widely varying standards in articles reporting large scale protein identifications, undertook the task of drafting and adopting guidelines for manuscripts that laid out what it felt (and strengthened by considerable advice and comments received from numerous experts in the field) were the minimum set of requirements for reporting and analyzing this type of data (1). The purpose was to raise awareness to the fact that if articles were severely flawed by incorrect or incomplete information, the field of proteomics was bound to suffer a major loss of credibility.
Welcome, HUPOWith this issue, we initiate a new phase of the association of MCP with the Human Proteome Organisation (HUPO), a relationship that extends back to the inception of both ventures. Since the now historic first congress in Versailles in November 2002, MCP has been privileged to publish the abstracts/program of every HUPO congress. This was an important decision for a young journal but one that was in keeping with the principles enunciated at the time the journal was founded, to wit, that it meant to strive not only to record the progress of proteomics, as it evolved as a science, but also to support the development of this relatively new field through appropriate ancillary activities.
MCP and HUPOThis issue of MCP marks the progression to a new phase in the relationship between HUPO and MCP. Through the years, the support of MCP to HUPO has been mutually beneficial and, after having been the publisher for the book of abstracts for all the world congresses of HUPO (Versailles 2002, Montreal 2003, Beijing 2004, Munich 2005, Long Beach 2006), MCP now becomes the first publication to be endorsed as an official journal of HUPO.
Biomarkers and Clinical ProteomicsThe landmark completion of the human genome project and the methodological breakthrough that has taken place within proteomics and functional genomics in the last decade promise to have a major impact on clinical practice, as these developments are likely to change the way in which diseases will be diagnosed, treated, and monitored in the near future. Today, we are moving increasingly from the study of cultured cells to the analysis of freshly collected cells, tissue samples, and biofluids, and one of the main challenges we face is how best to apply these powerful novel technologies to the study of clinically relevant samples in a well defined clinical and pathological framework.
First Annual Symposium on Proteome FractionationIn September 2004, the First Annual Symposium on Proteome Fractionation was held at Harvard University, Cambridge. MA. The presentations mainly dealt with the application of multidimensional techniques to the fractionation of various proteomes. As the field of what is now referred to as proteomics has developed, it has become increasingly apparent that traditional separation technologies were not sufficient to dissect proteomes in adequate detail and that new advances were needed. The use of multidimensional techniques offers considerable promise to help meet these needs, and their use has increased markedly over the past few years.