Clinical Proteomics 2018

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

Deadline for manuscript submissions: closed (15 October 2018) | Viewed by 13640

Special Issue Editors


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Guest Editor
Department of Applied Sciences, Faculty of Life and Health Sciences, Northumbria University, Newcastle-Upon-Tyne NE1 8ST, UK
Interests: mass spectrometry-based proteomics; malaria; Plasmodium falciparum; red blood cells; cancer; phosphorylation; signalling pathways; clinical proteomics
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Guest Editor
School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
Interests: proteomics; mass spectrometry; signaling pathways; cancer; phosphorylation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Technological advances in mass spectrometry instrumentation and in proteomics methods are moving the field of clinical proteomics towards the analysis of large numbers of patient samples in a reasonable time. State-of-the art protein quantification is achieved by applying chemical labelling technologies incorporating multiple isobaric tags (Isobaric tags for relative and absolute quantitation—iTRAQ, Tandem Mass Tags—TMT), by targeted methods (Multiple reaction monitoring/Selected reaction monitoring—MRM/SRM, SWATH), or by label free approaches (extracted ion chromatograms—XICs, spectral counts) in bottom–up proteomics combining tandem mass spectrometry with liquid chromatography or capillary electrophoresis for online peptide fractionation. This offers the opportunity to systematically study disease mechanisms using gel free approaches and improve our understanding on the role of proteins involved. These technologies enable biomarker discovery and biomarker validation studies with samples collected from human body fluids (e.g., blood, urine, saliva, and Cerebrospinal Fluid—CSF), from tissues, or from isolated cells. Current challenges for the utilisation of these technologies in the clinic, for prognosis, diagnosis, and for therapy monitoring, are (1) the large dynamic range of proteins present in body fluids, which is exceeding the capabilities of modern mass spectrometers with several orders of magnitude, and (2) reproducibility between laboratories, requiring standardization in the proteomic work flow encompassing standard operating procedures (SOPs) for sample collection, sample storage, sample processing techniques, MS data acquisition, and analysis methods.

In this Special Issue, we are looking forward to receive original clinical proteomics studies and review articles focussed on (1) the underlying mechanisms of disease pathways, (2) biomarker discovery studies using quantitative proteomics, and (3) mass spectrometry-based biomarker validation studies.

Dr. Edwin Lasonder
Dr. Vikram Sharma
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 submissions that pass pre-check are 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 1800 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.

Keywords

  • Clinical proteomics
  • Human body fluids
  • Disease mechanisms
  • Biomarker discovery
  • Biomarker validation

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Published Papers (3 papers)

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Research

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9 pages, 509 KiB  
Article
Identification of Potential Plasma Biomarkers for Abdominal Aortic Aneurysm Using Tandem Mass Tag Quantitative Proteomics
by Anders E. Henriksson, Markus Lindqvist, Carina Sihlbom, Jörgen Bergström and Dan Bylund
Proteomes 2018, 6(4), 43; https://doi.org/10.3390/proteomes6040043 - 18 Oct 2018
Cited by 9 | Viewed by 3265
Abstract
Plasma biomarkers that identify abdominal aortic aneurysm (AAA) rupture risk would greatly assist in stratifying patients with small aneurysms. Identification of such biomarkers has hitherto been unsuccessful over a range of studies using different methods. The present study used an alternative proteomic approach [...] Read more.
Plasma biomarkers that identify abdominal aortic aneurysm (AAA) rupture risk would greatly assist in stratifying patients with small aneurysms. Identification of such biomarkers has hitherto been unsuccessful over a range of studies using different methods. The present study used an alternative proteomic approach to find new, potential plasma AAA biomarker candidates. Pre-fractionated plasma samples from twelve patients with AAA and eight matched controls without aneurysm were analyzed by mass spectrometry applying a tandem mass tag (TMT) technique. Eight proteins were differentially regulated in patients compared to controls, including decreased levels of the enzyme bleomycin hydrolase. The down-regulation of this enzyme was confirmed in an extended validation study using an enzyme-linked immunosorbent assay (ELISA). The TMT-based proteomic approach thus identified novel potential plasma biomarkers for AAA. Full article
(This article belongs to the Special Issue Clinical Proteomics 2018)
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Review

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16 pages, 1821 KiB  
Review
Clinical Proteomics in Colorectal Cancer, a Promising Tool for Improving Personalised Medicine
by Anaïs Chauvin and François-Michel Boisvert
Proteomes 2018, 6(4), 49; https://doi.org/10.3390/proteomes6040049 - 02 Dec 2018
Cited by 28 | Viewed by 4555
Abstract
Colorectal cancer is the third most common and the fourth most lethal cancer worldwide. In most of cases, patients are diagnosed at an advanced or even metastatic stage, thus explaining the high mortality. The lack of proper clinical tests and the complicated procedures [...] Read more.
Colorectal cancer is the third most common and the fourth most lethal cancer worldwide. In most of cases, patients are diagnosed at an advanced or even metastatic stage, thus explaining the high mortality. The lack of proper clinical tests and the complicated procedures currently used for detecting this cancer, as well as for predicting the response to treatment and the outcome of a patient’s resistance in guiding clinical practice, are key elements driving the search for biomarkers. In the present overview, the different biomarkers (diagnostic, prognostic, treatment resistance) discovered through proteomics studies in various colorectal cancer study models (blood, stool, biopsies), including the different proteomic techniques used for the discovery of these biomarkers, are reviewed, as well as the various tests used in clinical practice and those currently in clinical phase. These studies define the limits and perspectives related to proteomic biomarker research for personalised medicine in colorectal cancer. Full article
(This article belongs to the Special Issue Clinical Proteomics 2018)
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9 pages, 404 KiB  
Review
Potential Alternative Strategy against Drug Resistant Tuberculosis: A Proteomics Prospect
by Divakar Sharma, Deepa Bisht and Asad U. Khan
Proteomes 2018, 6(2), 26; https://doi.org/10.3390/proteomes6020026 - 28 May 2018
Cited by 26 | Viewed by 5297
Abstract
Mycobacterium tuberculosis is one of the deadliest human pathogen of the tuberculosis diseases. Drug resistance leads to emergence of multidrug-resistant and extremely drug resistant strains of M. tuberculosis. Apart from principal targets of resistance, many explanations have been proposed for drug resistance [...] Read more.
Mycobacterium tuberculosis is one of the deadliest human pathogen of the tuberculosis diseases. Drug resistance leads to emergence of multidrug-resistant and extremely drug resistant strains of M. tuberculosis. Apart from principal targets of resistance, many explanations have been proposed for drug resistance but some resistance mechanisms are still unknown. Recently approved line probe assay (LPA) diagnostics for detecting the resistance to first and second line drugs are unable to diagnose the drug resistance in M. tuberculosis isolates which do not have the mutations in particular genes responsible for resistance. Proteomics and bioinformatic tools emerged as direct approaches for identification and characterization of novel proteins which are directly and indirectly involved in drug resistance that could be used as potential targets in future. In future, these novel targets might reveal new mechanism of resistance and can be used in diagnostics or as drug targets. Full article
(This article belongs to the Special Issue Clinical Proteomics 2018)
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