Special Issue "Clinical Proteomics"

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

Deadline for manuscript submissions: closed (15 June 2016)

Special Issue Editor

Guest Editor
Assoc. Prof. Edwin Lasonder

School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Derriford Research Facility, Research Way, Plymouth PL6 8BU, UK
Website | E-Mail
Interests: mass spectrometry-based proteomics; malaria; Plasmodium falciparum; red blood cells; cancer; phosphorylation; signalling pathways

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 to improve our understanding on the role of proteins involved. These technologies enable biomarker discovery and biomarker validation studies, as well 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 studies covering the analysis of clinical samples by quantitative approaches together with studies presenting novel methodologies for detecting low abundant biomarkers in a complicated matrix as the human body fluid. In addition, we welcome the submission of articles reviewing studies improving our understanding of disease mechanisms by clinical proteomics.

Edwin Lasonder
Guest Editor

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 550 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
  • Biomarkers
  • LC-MS/MS
  • CE-MS/MSord

Published Papers (8 papers)

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Editorial

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Open AccessEditorial Clinical Proteomics: From Biological Sample to Clinical Exploitation
Received: 5 April 2017 / Revised: 5 April 2017 / Accepted: 5 April 2017 / Published: 6 April 2017
Cited by 1 | PDF Full-text (139 KB) | HTML Full-text | XML Full-text
Abstract
Technological advances in mass spectrometry instrumentation and proteomics methodologies are moving the field of clinical proteomics towards the analysis of large numbers of patient samples in a reasonable time. The Special Issue ‘Clinical proteomics’ reviews the current proteomic work flow from biological sample [...] Read more.
Technological advances in mass spectrometry instrumentation and proteomics methodologies are moving the field of clinical proteomics towards the analysis of large numbers of patient samples in a reasonable time. The Special Issue ‘Clinical proteomics’ reviews the current proteomic work flow from biological sample preparation to clinical exploitation with samples collected from human body fluids, tissues or isolated cells, and highlights the trend towards integrated omics approaches for clinical usage.[...] Full article
(This article belongs to the Special Issue Clinical Proteomics)

Research

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Open AccessArticle A Quantitative Proteomics Approach to Clinical Research with Non-Traditional Samples
Received: 28 June 2016 / Revised: 19 September 2016 / Accepted: 21 September 2016 / Published: 17 October 2016
Cited by 2 | PDF Full-text (641 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The proper handling of samples to be analyzed by mass spectrometry (MS) can guarantee excellent results and a greater depth of analysis when working in quantitative proteomics. This is critical when trying to assess non-traditional sources such as ear wax, saliva, vitreous humor, [...] Read more.
The proper handling of samples to be analyzed by mass spectrometry (MS) can guarantee excellent results and a greater depth of analysis when working in quantitative proteomics. This is critical when trying to assess non-traditional sources such as ear wax, saliva, vitreous humor, aqueous humor, tears, nipple aspirate fluid, breast milk/colostrum, cervical-vaginal fluid, nasal secretions, bronco-alveolar lavage fluid, and stools. We intend to provide the investigator with relevant aspects of quantitative proteomics and to recognize the most recent clinical research work conducted with atypical samples and analyzed by quantitative proteomics. Having as reference the most recent and different approaches used with non-traditional sources allows us to compare new strategies in the development of novel experimental models. On the other hand, these references help us to contribute significantly to the understanding of the proportions of proteins in different proteomes of clinical interest and may lead to potential advances in the emerging field of precision medicine. Full article
(This article belongs to the Special Issue Clinical Proteomics)
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Open AccessArticle The Role of Clinical Proteomics, Lipidomics, and Genomics in the Diagnosis of Alzheimer’s Disease
Received: 5 February 2016 / Revised: 24 March 2016 / Accepted: 28 March 2016 / Published: 31 March 2016
Cited by 6 | PDF Full-text (1682 KB) | HTML Full-text | XML Full-text
Abstract
The early diagnosis of Alzheimer’s disease (AD) has become important to the reversal and treatment of neurodegeneration, which may be relevant to premature brain aging that is associated with chronic disease progression. Clinical proteomics allows the detection of various proteins in fluids such [...] Read more.
The early diagnosis of Alzheimer’s disease (AD) has become important to the reversal and treatment of neurodegeneration, which may be relevant to premature brain aging that is associated with chronic disease progression. Clinical proteomics allows the detection of various proteins in fluids such as the urine, plasma, and cerebrospinal fluid for the diagnosis of AD. Interest in lipidomics has accelerated with plasma testing for various lipid biomarkers that may with clinical proteomics provide a more reproducible diagnosis for early brain aging that is connected to other chronic diseases. The combination of proteomics with lipidomics may decrease the biological variability between studies and provide reproducible results that detect a community’s susceptibility to AD. The diagnosis of chronic disease associated with AD that now involves genomics may provide increased sensitivity to avoid inadvertent errors related to plasma versus cerebrospinal fluid testing by proteomics and lipidomics that identify new disease biomarkers in body fluids, cells, and tissues. The diagnosis of AD by various plasma biomarkers with clinical proteomics may now require the involvement of lipidomics and genomics to provide interpretation of proteomic results from various laboratories around the world. Full article
(This article belongs to the Special Issue Clinical Proteomics)
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Review

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Open AccessReview Phosphoproteome Discovery in Human Biological Fluids
Received: 9 June 2016 / Revised: 11 November 2016 / Accepted: 23 November 2016 / Published: 1 December 2016
Cited by 4 | PDF Full-text (857 KB) | HTML Full-text | XML Full-text
Abstract
Phosphorylation plays a critical role in regulating protein function and thus influences a vast spectrum of cellular processes. With the advent of modern bioanalytical technologies, examination of protein phosphorylation on a global scale has become one of the major research areas. Phosphoproteins are [...] Read more.
Phosphorylation plays a critical role in regulating protein function and thus influences a vast spectrum of cellular processes. With the advent of modern bioanalytical technologies, examination of protein phosphorylation on a global scale has become one of the major research areas. Phosphoproteins are found in biological fluids and interrogation of the phosphoproteome in biological fluids presents an exciting opportunity for discoveries that hold great potential for novel mechanistic insights into protein function in health and disease, and for translation to improved diagnostic and therapeutic approaches for the clinical setting. This review focuses on phosphoproteome discovery in selected human biological fluids: serum/plasma, urine, cerebrospinal fluid, saliva, and bronchoalveolar lavage fluid. Bioanalytical workflows pertinent to phosphoproteomics of biological fluids are discussed with emphasis on mass spectrometry-based approaches, and summaries of studies on phosphoproteome discovery in major fluids are presented. Full article
(This article belongs to the Special Issue Clinical Proteomics)
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Open AccessReview The Proteome of the Red Blood Cell: An Auspicious Source of New Insights into Membrane-Centered Regulation of Homeostasis
Received: 16 September 2016 / Revised: 3 November 2016 / Accepted: 17 November 2016 / Published: 25 November 2016
Cited by 6 | PDF Full-text (191 KB) | HTML Full-text | XML Full-text
Abstract
During the past decade, the hand-in-hand development of biotechnology and bioinformatics has enabled a view of the function of the red blood cell that surpasses the supply of oxygen and removal of carbon dioxide. Comparative proteomic inventories have yielded new clues to the [...] Read more.
During the past decade, the hand-in-hand development of biotechnology and bioinformatics has enabled a view of the function of the red blood cell that surpasses the supply of oxygen and removal of carbon dioxide. Comparative proteomic inventories have yielded new clues to the processes that regulate membrane–cytoskeleton interactions in health and disease, and to the ways by which red blood cells communicate with their environment. In addition, proteomic data have revealed the possibility that many, hitherto unsuspected, metabolic processes are active in the red blood cell cytoplasm. Recent metabolomic studies have confirmed and expanded this notion. Taken together, the presently available data point towards the red blood cell membrane as the hub at which all regulatory processes come together. Thus, alterations in the association of regulatory proteins with the cell membrane may be a sine qua non for the functional relevance of any postulated molecular mechanism. From this perspective, comparative proteomics centered on the red blood cell membrane constitute a powerful tool for the identification and elucidation of the physiologically and pathologically relevant pathways that regulate red blood cell homeostasis. Additionally, this perspective provides a focus for the interpretation of metabolomic studies, especially in the development of biomarkers in the blood. Full article
(This article belongs to the Special Issue Clinical Proteomics)
Open AccessReview Personalized Proteomics: The Future of Precision Medicine
Received: 11 July 2016 / Revised: 9 September 2016 / Accepted: 23 September 2016 / Published: 1 October 2016
Cited by 24 | PDF Full-text (710 KB) | HTML Full-text | XML Full-text
Abstract
Medical diagnostics and treatment has advanced from a one size fits all science to treatment of the patient as a unique individual. Currently, this is limited solely to genetic analysis. However, epigenetic, transcriptional, proteomic, posttranslational modifications, metabolic, and environmental factors influence a patient’s [...] Read more.
Medical diagnostics and treatment has advanced from a one size fits all science to treatment of the patient as a unique individual. Currently, this is limited solely to genetic analysis. However, epigenetic, transcriptional, proteomic, posttranslational modifications, metabolic, and environmental factors influence a patient’s response to disease and treatment. As more analytical and diagnostic techniques are incorporated into medical practice, the personalized medicine initiative transitions to precision medicine giving a holistic view of the patient’s condition. The high accuracy and sensitivity of mass spectrometric analysis of proteomes is well suited for the incorporation of proteomics into precision medicine. This review begins with an overview of the advance to precision medicine and the current state of the art in technology and instrumentation for mass spectrometry analysis. Thereafter, it focuses on the benefits and potential uses for personalized proteomic analysis in the diagnostic and treatment of individual patients. In conclusion, it calls for a synthesis between basic science and clinical researchers with practicing clinicians to design proteomic studies to generate meaningful and applicable translational medicine. As clinical proteomics is just beginning to come out of its infancy, this overview is provided for the new initiate. Full article
(This article belongs to the Special Issue Clinical Proteomics)
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Open AccessReview Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia
Received: 6 July 2016 / Revised: 9 August 2016 / Accepted: 12 August 2016 / Published: 22 August 2016
Cited by 9 | PDF Full-text (527 KB) | HTML Full-text | XML Full-text
Abstract
Global mass spectrometry (MS)-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML) biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and [...] Read more.
Global mass spectrometry (MS)-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML) biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and selection of patients for bone marrow transplant. MS-based studies require optimal and reproducible workflows that allow a satisfactory coverage of the proteome and its modifications. Preparation of samples for global MS analysis is a crucial step and it usually requires method testing, tuning and optimization. Different proteomic workflows that have been used to prepare AML patient samples for global MS analysis usually include a standard protein in-solution digestion procedure with a urea-based lysis buffer. The enrichment of phosphopeptides from AML patient samples has previously been carried out either with immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC). We have recently tested several methods of sample preparation for MS analysis of the AML proteome and phosphoproteome and introduced filter-aided sample preparation (FASP) as a superior methodology for the sensitive and reproducible generation of peptides from patient samples. FASP-prepared peptides can be further fractionated or IMAC-enriched for proteome or phosphoproteome analyses. Herein, we will review both in-solution and FASP-based sample preparation workflows and encourage the use of the latter for the highest protein and phosphorylation coverage and reproducibility. Full article
(This article belongs to the Special Issue Clinical Proteomics)
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Open AccessReview Mass Spectrometric Immunoassays in Characterization of Clinically Significant Proteoforms
Received: 5 January 2016 / Revised: 10 March 2016 / Accepted: 14 March 2016 / Published: 17 March 2016
Cited by 7 | PDF Full-text (1230 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Proteins can exist as multiple proteoforms in vivo, as a result of alternative splicing and single-nucleotide polymorphisms (SNPs), as well as posttranslational processing. To address their clinical significance in a context of diagnostic information, proteoforms require a more in-depth analysis. Mass spectrometric [...] Read more.
Proteins can exist as multiple proteoforms in vivo, as a result of alternative splicing and single-nucleotide polymorphisms (SNPs), as well as posttranslational processing. To address their clinical significance in a context of diagnostic information, proteoforms require a more in-depth analysis. Mass spectrometric immunoassays (MSIA) have been devised for studying structural diversity in human proteins. MSIA enables protein profiling in a simple and high-throughput manner, by combining the selectivity of targeted immunoassays, with the specificity of mass spectrometric detection. MSIA has been used for qualitative and quantitative analysis of single and multiple proteoforms, distinguishing between normal fluctuations and changes related to clinical conditions. This mini review offers an overview of the development and application of mass spectrometric immunoassays for clinical and population proteomics studies. Provided are examples of some recent developments, and also discussed are the trends and challenges in mass spectrometry-based immunoassays for the next-phase of clinical applications. Full article
(This article belongs to the Special Issue Clinical Proteomics)
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