Proteomics of Body Fluids: Principles, Methods, and Applications

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

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 21453

Special Issue Editor


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Guest Editor
1. Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
2. UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, 4200-319 Porto, Portugal
3. LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
Interests: proteomics; body fluids; peptidome; antimicrobial peptides; bioinformatics
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Special Issue Information

Dear Colleagues,

The routine work of most clinical laboratories involves, at least for the most part, the analysis of conventional biological matrices such as whole blood, serum, plasma, and urine. Therefore, the analysis of body fluids plays a critical role in the diagnosis and prognosis of disease. A change in the concentration or composition of a particular biochemical constituent in body fluids is used as an indicator of a physiological or pathological condition. Thus, a particular constituent in body fluids can be considered a marker for the detection of a disease. Driven by new biological discoveries and recent analytical breakthroughs, such as small volume aspiration and automated sample quality assessment, the analysis of body fluids such as saliva, semen, cerebrospinal fluid, peritoneal, pleural, pericardial, pancreatic, synovial, cystic, wound, drainage, and washout fluids, is becoming increasingly popular for the diagnosis and management of a kaleidoscope of human diseases. Therefore, this Special issue of Proteomes on “Proteomics of Body Fluids: Principles, Methods, and Applications” welcomes submissions of original research or review articles that monitor a particular chemical species during disease progression, either an endogenous or exogenous compound that may also provide insight into the efficacy of a particular therapy. Health assessments and therapeutic screenings are also performed by analyzing body fluids. Many medical decisions depend on the results provided by the clinical laboratory in the analysis of body fluids. The clinical laboratory is thus tasked with providing reliable information for the detection, diagnosis, prognosis, prevention, and/or treatment of human diseases. It is therefore extremely important that the clinical laboratory be equipped with the latest and most appropriate analytical method for measuring chemical species in biological fluids.

Dr. Rui Vitorino
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 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

  • Mass spectrometry
  • Global and targeted proteome and peptidome
  • Secretome
  • Body fluids
  • Saliva, urine, plasma, and serum proteome and peptidome
  • Microbial proteome
  • Protein-protein and peptide-protein interactions
  • Inflammation and cell signaling
  • Bioinformatics tools
  • Omics data integration
  • Proteomics and human health
  • Proteome and peptidome dynamics
  • Protein synthesis
  • Micropeptides
  • ORF
  • Text mining tools
  • The Cancer Genome Atlas (TCGA)
  • Gene Expression Omnibus

Published Papers (5 papers)

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Research

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15 pages, 2481 KiB  
Article
Optimization of a Protocol for Protein Extraction from Calcified Aortic Valves for Proteomics Applications: Development of a Standard Operating Procedure
by Fábio Trindade, Ana F. Ferreira, Francisca Saraiva, Diana Martins, Vera M. Mendes, Carla Sousa, Cristina Gavina, Adelino Leite-Moreira, Bruno Manadas, Inês Falcão-Pires and Rui Vitorino
Proteomes 2022, 10(3), 30; https://doi.org/10.3390/proteomes10030030 - 01 Sep 2022
Viewed by 4337
Abstract
The comprehension of the pathophysiological mechanisms, the identification of druggable targets, and putative biomarkers for aortic valve stenosis can be pursued through holistic approaches such as proteomics. However, tissue homogenization and protein extraction are made difficult by tissue calcification. The reproducibility of proteome [...] Read more.
The comprehension of the pathophysiological mechanisms, the identification of druggable targets, and putative biomarkers for aortic valve stenosis can be pursued through holistic approaches such as proteomics. However, tissue homogenization and protein extraction are made difficult by tissue calcification. The reproducibility of proteome studies is key in clinical translation of the findings. Thus, we aimed to optimize a protocol for aortic valve homogenization and protein extraction and to develop a standard operating procedure (SOP), which researchers can use to maximize protein yield while reducing inter-laboratory variability. We have compared the protein yield between conventional tissue grinding in nitrogen followed by homogenization with a Potter apparatus with a more advanced bead-beating system. Once we confirmed the superiority of the latter, we further optimized it by testing the effect of beads size, the number of homogenization cycles, tube capacity, lysis buffer/tissue mass ratio, and two different lysis buffers. Optimal protein extraction was achieved with 2.8 mm zirconium dioxide beads, in two homogenization cycles, in the presence of 20 µL RIPA buffer/mg tissue, using 2 mL O-ring cryotubes. As a proof of concept of the usefulness of this SOP for proteomics, the AV proteome of men and women with aortic stenosis was characterized, resulting in the quantification of proteins across six orders of magnitude and uncovering some putative proteins dysregulated by sex. Full article
(This article belongs to the Special Issue Proteomics of Body Fluids: Principles, Methods, and Applications)
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14 pages, 1722 KiB  
Article
Molecular Mapping of Urinary Complement Peptides in Kidney Diseases
by Ralph Wendt, Justyna Siwy, Tianlin He, Agnieszka Latosinska, Thorsten Wiech, Peter F. Zipfel, Aggeliki Tserga, Antonia Vlahou, Harald Rupprecht, Lorenzo Catanese, Harald Mischak and Joachim Beige
Proteomes 2021, 9(4), 49; https://doi.org/10.3390/proteomes9040049 - 13 Dec 2021
Cited by 10 | Viewed by 3280
Abstract
Defective complement activation has been associated with various types of kidney disease. This led to the hypothesis that specific urine complement fragments may be associated with kidney disease etiologies, and disease progression may be reflected by changes in these complement fragments. We investigated [...] Read more.
Defective complement activation has been associated with various types of kidney disease. This led to the hypothesis that specific urine complement fragments may be associated with kidney disease etiologies, and disease progression may be reflected by changes in these complement fragments. We investigated the occurrence of complement fragments in urine, their association with kidney function and disease etiology in 16,027 subjects, using mass spectrometry based peptidomics data from the Human Urinary Proteome/Peptidome Database. Twenty-three different urinary peptides originating from complement proteins C3, C4 and factor B (CFB) could be identified. Most C3-derived peptides showed inverse association with estimated glomerular filtration rate (eGFR), while the majority of peptides derived from CFB demonstrated positive association with eGFR. Several peptides derived from the complement proteins C3, C4 and CFB were found significantly associated with specific kidney disease etiologies. These peptides may depict disease-specific complement activation and could serve as non-invasive biomarkers to support development of complement interventions through assessing complement activity for patients’ stratification and monitoring of drug impact. Further investigation of these complement peptides may provide additional insight into disease pathophysiology and could possibly guide therapeutic decisions, especially when targeting complement factors. Full article
(This article belongs to the Special Issue Proteomics of Body Fluids: Principles, Methods, and Applications)
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17 pages, 1825 KiB  
Article
Downregulation of Salivary Proteins, Protective against Dental Caries, in Type 1 Diabetes
by Eftychia Pappa, Konstantinos Vougas, Jerome Zoidakis, William Papaioannou, Christos Rahiotis and Heleni Vastardis
Proteomes 2021, 9(3), 33; https://doi.org/10.3390/proteomes9030033 - 19 Jul 2021
Cited by 9 | Viewed by 4248
Abstract
Saliva, an essential oral secretion involved in protecting the oral cavity’s hard and soft tissues, is readily available and straightforward to collect. Recent studies have analyzed the salivary proteome in children and adolescents with extensive carious lesions to identify diagnostic and prognostic biomarkers. [...] Read more.
Saliva, an essential oral secretion involved in protecting the oral cavity’s hard and soft tissues, is readily available and straightforward to collect. Recent studies have analyzed the salivary proteome in children and adolescents with extensive carious lesions to identify diagnostic and prognostic biomarkers. The current study aimed to investigate saliva’s diagnostic ability through proteomics to detect the potential differential expression of proteins specific for the occurrence of carious lesions. For this study, we performed bioinformatics and functional analysis of proteomic datasets, previously examined by our group, from samples of adolescents with regulated and unregulated type 1 diabetes, as they compare with healthy controls. Among the differentially expressed proteins relevant to caries pathology, alpha-amylase 2B, beta-defensin 4A, BPI fold containing family B member 2, protein S100-A7, mucin 5B, statherin, salivary proline-rich protein 2, and interleukin 36 gamma were significantly downregulated in poorly-controlled patients compared to healthy subjects. In addition, significant biological pathways (defense response to the bacterium, beta-defensin activity, proline-rich protein activity, oxygen binding, calcium binding, and glycosylation) were deregulated in this comparison, highlighting specific molecular characteristics in the cariogenic process. This analysis contributes to a better understanding of the mechanisms involved in caries vulnerability in adolescents with unregulated diabetes. Full article
(This article belongs to the Special Issue Proteomics of Body Fluids: Principles, Methods, and Applications)
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Review

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21 pages, 4968 KiB  
Review
Insights on Proteomics-Driven Body Fluid-Based Biomarkers of Cervical Cancer
by Amrita Mukherjee, Chinmayi Bhagwan Pednekar, Siddhant Sujit Kolke, Megha Kattimani, Subhiksha Duraisamy, Ananya Raghu Burli, Sudeep Gupta and Sanjeeva Srivastava
Proteomes 2022, 10(2), 13; https://doi.org/10.3390/proteomes10020013 - 29 Apr 2022
Cited by 2 | Viewed by 6565
Abstract
Cervical cancer is one of the top malignancies in women around the globe, which still holds its place despite being preventable at early stages. Gynecological conditions, even maladies like cervical cancer, still experience scrutiny from society owing to prevalent taboo and invasive screening [...] Read more.
Cervical cancer is one of the top malignancies in women around the globe, which still holds its place despite being preventable at early stages. Gynecological conditions, even maladies like cervical cancer, still experience scrutiny from society owing to prevalent taboo and invasive screening methods, especially in developing economies. Additionally, current diagnoses lack specificity and sensitivity, which prolong diagnosis until it is too late. Advances in omics-based technologies aid in discovering differential multi-omics profiles between healthy individuals and cancer patients, which could be utilized for the discovery of body fluid-based biomarkers. Body fluids are a promising potential alternative for early disease detection and counteracting the problems of invasiveness while also serving as a pool of potential biomarkers. In this review, we will provide details of the body fluids-based biomarkers that have been reported in cervical cancer. Here, we have presented our perspective on proteomics for global biomarker discovery by addressing several pertinent problems, including the challenges that are confronted in cervical cancer. Further, we also used bioinformatic methods to undertake a meta-analysis of significantly up-regulated biomolecular profiles in CVF from cervical cancer patients. Our analysis deciphered alterations in the biological pathways in CVF such as immune response, glycolytic processes, regulation of cell death, regulation of structural size, protein polymerization disease, and other pathways that can cumulatively contribute to cervical cancer malignancy. We believe, more extensive research on such biomarkers, will speed up the road to early identification and prevention of cervical cancer in the near future. Full article
(This article belongs to the Special Issue Proteomics of Body Fluids: Principles, Methods, and Applications)
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13 pages, 2494 KiB  
Technical Note
Urine-HILIC: Automated Sample Preparation for Bottom-Up Urinary Proteome Profiling in Clinical Proteomics
by Ireshyn Selvan Govender, Rethabile Mokoena, Stoyan Stoychev and Previn Naicker
Proteomes 2023, 11(4), 29; https://doi.org/10.3390/proteomes11040029 - 28 Sep 2023
Cited by 1 | Viewed by 1614
Abstract
Urine provides a diverse source of information related to a patient’s health status and is ideal for clinical proteomics due to its ease of collection. To date, most methods for the preparation of urine samples lack the throughput required to analyze large clinical [...] Read more.
Urine provides a diverse source of information related to a patient’s health status and is ideal for clinical proteomics due to its ease of collection. To date, most methods for the preparation of urine samples lack the throughput required to analyze large clinical cohorts. To this end, we developed a novel workflow, urine-HILIC (uHLC), based on an on-bead protein capture, clean-up, and digestion without the need for bottleneck processing steps such as protein precipitation or centrifugation. The workflow was applied to an acute kidney injury (AKI) pilot study. Urine from clinical samples and a pooled sample was subjected to automated sample preparation in a KingFisher™ Flex magnetic handling station using the novel approach based on MagReSyn® HILIC microspheres. For benchmarking, the pooled sample was also prepared using a published protocol based on an on-membrane (OM) protein capture and digestion workflow. Peptides were analyzed by LCMS in data-independent acquisition (DIA) mode using a Dionex Ultimate 3000 UPLC coupled to a Sciex 5600 mass spectrometer. The data were searched in Spectronaut™ 17. Both workflows showed similar peptide and protein identifications in the pooled sample. The uHLC workflow was easier to set up and complete, having less hands-on time than the OM method, with fewer manual processing steps. Lower peptide and protein coefficient of variation was observed in the uHLC technical replicates. Following statistical analysis, candidate protein markers were filtered, at ≥8.35-fold change in abundance, ≥2 unique peptides and ≤1% false discovery rate, and revealed 121 significant, differentially abundant proteins, some of which have known associations with kidney injury. The pilot data derived using this novel workflow provide information on the urinary proteome of patients with AKI. Further exploration in a larger cohort using this novel high-throughput method is warranted. Full article
(This article belongs to the Special Issue Proteomics of Body Fluids: Principles, Methods, and Applications)
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