Special Issue "Feature Review Papers in Proteomes"

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: 15 November 2020.

Special Issue Editors

Prof. Dr. Jens R. Coorssen
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Guest Editor
Department of Health Sciences, Faculty of Applied Health Sciences, and Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, ON, Canada
Interests: analytical proteomics; high-resolution discovery proteomics; top-down proteomics; two-dimensional gel electrophoresis; 2DE/MS/MS; proteoforms/protein species; molecular mechanisms; biomarkers; membrane proteomes; synaptic function; lipidomics; metabolomics; translational proteomics; systems biology; exocytosis; preterm labor; spinal cord injury; neurodegenerative disorders
Special Issues and Collections in MDPI journals
Dr. Matthew P. Padula
Website
Guest Editor
School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
Interests: high-resolution discovery proteomics; methodology development; top-down proteomics; two-dimensional gel electrophoresis; 2DE/MS/MS; proteoforms; lipidomics; metabolomics; data-independent acquisition
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

Proteomics as an identifiable discipline is between 25 and 40 years old, depending on who one asks, but one might suggest it to be a discipline that has yet to fulfil its promise.

While great advances have been made in techniques and technologies, the complete coverage and quantification of all proteoforms in a proteome would still appear to be in the distant future. Current methodologies for analyzing the diversity of proteoforms leverage evolving rather than revolutionary technologies, despite how welcome a genuine, quantitative revolution might be. Nonetheless, proteoforms, despite being the key to understanding fundamental molecular mechanisms and thus providing new biomarkers and drug targets, do not lend themselves to ‘high-throughput’ analyses. Thus, it is time to meaningfully reflect on the current state of proteomics, its genuine objectives, and intimate relationship to inter-related fields, including glycoproteomics, lipoproteomics, metabolomics, interactomics, bioinformatics, and, in the end, systems biology to celebrate all that has been achieved. Nonetheless, rather than stopping at the celebration, it is very much time for the field to critically reflect on the practical effect of those achievements and ask very hard, direct questions about what is stopping proteomics from being a more broadly implemented research approach.

This Special Issue targets the critical observations and opinions of the engaged scientists who have contributed to driving the field to its current state and status, and who thus wish to see it advance accordingly. We have asked that they document the progress, reflect on the achievements, and objectively discuss the future demands and realistic critical expectations of the field within the next 5–10 years, and thus, its potential impact on biomedical, agricultural, and environmental states. More importantly, though, we want these scientists to tell us what is ‘wrong’ with the field of proteomics and what we should be doing better, even if the opinions are controversial or not immediately achievable with our current resources. Speculation is warranted to drive innovation in unpredictable and productive directions. We thus do not necessarily want these reviews and opinions to be ‘balanced’ but rather to openly reveal, for our full consideration, all the things that need to be said and critically evaluated to further enable the most productive and meaningful future research.

Prof. Jens Coorssen
Dr. Matthew P. Padula
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Proteomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (2 papers)

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Review

Open AccessFeature PaperReview
How Do the Different Proteomic Strategies Cope with the Complexity of Biological Regulations in a Multi-Omic World? Critical Appraisal and Suggestions for Improvements
Proteomes 2020, 8(3), 23; https://doi.org/10.3390/proteomes8030023 - 03 Sep 2020
Abstract
In this second decade of the 21st century, we are lucky enough to have different types of proteomic analyses at our disposal. Furthermore, other functional omics such as transcriptomics have also undergone major developments, resulting in mature tools. However, choice equals questions, and [...] Read more.
In this second decade of the 21st century, we are lucky enough to have different types of proteomic analyses at our disposal. Furthermore, other functional omics such as transcriptomics have also undergone major developments, resulting in mature tools. However, choice equals questions, and the major question is how each proteomic strategy is fit for which purpose. The aim of this opinion paper is to reposition the various proteomic strategies in the frame of what is known in terms of biological regulations in order to shed light on the power, limitations, and paths for improvement for the different proteomic setups. This should help biologists to select the best-suited proteomic strategy for their purposes in order not to be driven by raw availability or fashion arguments but rather by the best fitness for purpose. In particular, knowing the limitations of the different proteomic strategies helps in interpreting the results correctly and in devising the validation experiments that should be made downstream of the proteomic analyses. Full article
(This article belongs to the Special Issue Feature Review Papers in Proteomes)
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Open AccessReview
A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field
Proteomes 2020, 8(3), 14; https://doi.org/10.3390/proteomes8030014 - 06 Jul 2020
Cited by 1
Abstract
Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one. Proteins can be investigated for their abundance, variety of proteoforms due to post-translational modifications (PTMs), and their stable or transient protein–protein [...] Read more.
Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one. Proteins can be investigated for their abundance, variety of proteoforms due to post-translational modifications (PTMs), and their stable or transient protein–protein interactions. This can be especially beneficial in the clinical setting when studying proteins involved in different diseases and conditions. Here, we aim to describe a bottom-up proteomics workflow from sample preparation to data analysis, including all of its benefits and pitfalls. We also describe potential improvements in this type of proteomics workflow for the future. Full article
(This article belongs to the Special Issue Feature Review Papers in Proteomes)
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