Special Issue "Feature Review Papers in Proteomes"

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

Deadline for manuscript submissions: closed (1 August 2021).

Special Issue Editors

Prof. Dr. Jens R. Coorssen
E-Mail Website
Guest Editor
Department of Health Sciences, Faculty of Applied Health Sciences, and Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, 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, Collections and Topics in MDPI journals
Dr. Matthew P. Padula
E-Mail 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, Collections and Topics 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 1600 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 (6 papers)

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Review

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Review
Proteomes Are of Proteoforms: Embracing the Complexity
Proteomes 2021, 9(3), 38; https://doi.org/10.3390/proteomes9030038 - 31 Aug 2021
Cited by 1 | Viewed by 1834
Abstract
Proteomes are complex—much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological [...] Read more.
Proteomes are complex—much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current ‘state-of-the-field’. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy? Full article
(This article belongs to the Special Issue Feature Review Papers in Proteomes)
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Review
Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric
Proteomes 2021, 9(3), 34; https://doi.org/10.3390/proteomes9030034 - 20 Jul 2021
Cited by 2 | Viewed by 1212
Abstract
Proteomic technology has improved at a staggering pace in recent years, with even practitioners challenged to keep up with new methods and hardware. The most common metric used for method performance is the number of peptides and proteins identified. While this metric may [...] Read more.
Proteomic technology has improved at a staggering pace in recent years, with even practitioners challenged to keep up with new methods and hardware. The most common metric used for method performance is the number of peptides and proteins identified. While this metric may be helpful for proteomics researchers shopping for new hardware, this is often not the most biologically relevant metric. Biologists often utilize proteomics in the search for protein regulators that are of a lower relative copy number in the cell. In this review, I re-evaluate untargeted proteomics data using a simple graphical representation of the absolute copy number of proteins present in a single cancer cell as a metric. By comparing single-shot proteomics data to the coverage of the most in-depth proteomic analysis of that cell line acquired to date, we can obtain a rapid metric of method performance. Using a simple copy number metric allows visualization of how proteomics has developed in both sensitivity and overall dynamic range when using both relatively long and short acquisition times. To enable reanalysis beyond what is presented here, two available web applications have been developed for single- and multi-experiment comparisons with reference protein copy number data for multiple cell lines and organisms. Full article
(This article belongs to the Special Issue Feature Review Papers in Proteomes)
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Review
Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics
Proteomes 2021, 9(1), 15; https://doi.org/10.3390/proteomes9010015 - 23 Mar 2021
Cited by 10 | Viewed by 1943
Abstract
Proteomics researchers today face an interesting challenge: how to choose among the dozens of data processing and analysis pipelines available for converting tandem mass spectrometry files to protein identifications. Due to the dominance of Orbitrap technology in proteomics in recent history, many researchers [...] Read more.
Proteomics researchers today face an interesting challenge: how to choose among the dozens of data processing and analysis pipelines available for converting tandem mass spectrometry files to protein identifications. Due to the dominance of Orbitrap technology in proteomics in recent history, many researchers have defaulted to the vendor software Proteome Discoverer. Over the fourteen years since the initial release of the software, it has evolved in parallel with the increasingly complex demands faced by proteomics researchers. Today, Proteome Discoverer exists in two distinct forms with both powerful commercial versions and fully functional free versions in use in many labs today. Throughout the 11 main versions released to date, a central theme of the software has always been the ability to easily view and verify the spectra from which identifications are made. This ability is, even today, a key differentiator from other data analysis solutions. In this review I will attempt to summarize the history and evolution of Proteome Discoverer from its first launch to the versions in use today. Full article
(This article belongs to the Special Issue Feature Review Papers in Proteomes)
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Review
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
Cited by 3 | Viewed by 1406
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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Review
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 27 | Viewed by 4105
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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Other

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Commentary
Reporting of Hybrid Data and the Difficulties with Cross-Discipline Research Techniques
Proteomes 2020, 8(4), 35; https://doi.org/10.3390/proteomes8040035 - 23 Nov 2020
Viewed by 906
Abstract
Peer review is the way in which we, as scientists, criticise, check, and confirm the findings of our colleagues. The process of peer review relies on individuals in all fields applying their particular expertise and determining if they agree with the findings submitted [...] Read more.
Peer review is the way in which we, as scientists, criticise, check, and confirm the findings of our colleagues. The process of peer review relies on individuals in all fields applying their particular expertise and determining if they agree with the findings submitted for publication. In recent years, there has been a significant rise in the number of manuscripts submitted for publication that draw from a range of disparate and complementary fields. This has created the curious situation where an expert may be requested to review a manuscript that is only partially within their immediate field of expertise. The issue that arises is that, without full knowledge of the data, techniques, methodologies, and principles that are presented, it is difficult for reviewers to make properly informed decisions, especially when it can take an entire career to reach that specific level of expertise in a single field. From this perspective, we explore these issues and also provide a commentary on how peer review could evolve in the context of a changing cross-disciplinarily-focused scientific landscape. Full article
(This article belongs to the Special Issue Feature Review Papers in Proteomes)
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