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Proteomes, Volume 8, Issue 3 (September 2020) – 13 articles

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19 pages, 3614 KiB  
Article
Glycoproteomic Analysis Reveals Aberrant Expression of Complement C9 and Fibronectin in the Plasma of Patients with Colorectal Cancer
by Juthamard Chantaraamporn, Voraratt Champattanachai, Amnart Khongmanee, Chris Verathamjamras, Naiyarat Prasongsook, Kanokwan Mingkwan, Virat Luevisadpibul, Somchai Chutipongtanate and Jisnuson Svasti
Proteomes 2020, 8(3), 26; https://doi.org/10.3390/proteomes8030026 - 22 Sep 2020
Cited by 18 | Viewed by 3433
Abstract
Colorectal cancer (CRC) is a major cause of cancer mortality. Currently used CRC biomarkers provide insufficient sensitivity and specificity; therefore, novel biomarkers are needed to improve the CRC detection. Label-free quantitative proteomics were used to identify and compare glycoproteins, enriched by wheat germ [...] Read more.
Colorectal cancer (CRC) is a major cause of cancer mortality. Currently used CRC biomarkers provide insufficient sensitivity and specificity; therefore, novel biomarkers are needed to improve the CRC detection. Label-free quantitative proteomics were used to identify and compare glycoproteins, enriched by wheat germ agglutinin, from plasma of CRC patients and age-matched healthy controls. Among 189 identified glycoproteins, the levels of 7 and 15 glycoproteins were significantly altered in the non-metastatic and metastatic CRC groups, respectively. Protein-protein interaction analysis revealed that they were predominantly involved in immune responses, complement pathways, wound healing and coagulation. Of these, the levels of complement C9 (C9) was increased and fibronectin (FN1) was decreased in both CRC states in comparison to those of the healthy controls. Moreover, their levels detected by immunoblotting were validated in another independent cohort and the results were consistent with in the study cohort. Combination of CEA, a commercial CRC biomarker, with C9 and FN1 showed better diagnostic performance. Interestingly, predominant glycoforms associated with acetylneuraminic acid were obviously detected in alpha-2 macroglobulin, haptoglobin, alpha-1-acid glycoprotein 1, and complement C4-A of CRC patient groups. This glycoproteomic approach provides invaluable information of plasma proteome profiles of CRC patients and identification of CRC biomarker candidates. Full article
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16 pages, 5249 KiB  
Article
Serum Glycoproteomic Alterations in Patients with Diabetic Retinopathy
by Ashok Sharma, James Cox, Joshua Glass, Tae Jin Lee, Sai Karthik Kodeboyina, Wenbo Zhi, Lane Ulrich, Zachary Lukowski and Shruti Sharma
Proteomes 2020, 8(3), 25; https://doi.org/10.3390/proteomes8030025 - 13 Sep 2020
Cited by 6 | Viewed by 3482
Abstract
The precise molecular mechanisms of diabetic retinopathy (DR) pathogenesis are unclear, and treatment options are limited. There is an urgent need to discover and develop novel therapeutic targets for the treatment of this disease. Glycosylation is a post-translational modification that plays a critical [...] Read more.
The precise molecular mechanisms of diabetic retinopathy (DR) pathogenesis are unclear, and treatment options are limited. There is an urgent need to discover and develop novel therapeutic targets for the treatment of this disease. Glycosylation is a post-translational modification that plays a critical role in determining protein structure, function, and stability. Recent studies have found that serum glycoproteomic changes are associated with the presence or progression of several inflammatory diseases. However, very little is known about the glycoproteomic changes associated with DR. In this study, glycoproteomic profiling of the serum of diabetic patients with and without DR was performed. A total of 15 glycopeptides from 11 glycoproteins were found to be significantly altered (5 upregulated and 10 downregulated) within the serum glycoproteome of DR patients. These glycoproteins are known to be involved in the maintenance of the extracellular matrix and complement system through peptidolytic activity or regulation. Full article
(This article belongs to the Special Issue Human Proteomics)
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14 pages, 2095 KiB  
Article
Profiling of Inflammatory Proteins in Plasma of HIV-1-Infected Children Receiving Antiretroviral Therapy
by Mahlet Lemma, Stefan Petkov, Yonas Bekele, Beyene Petros, Rawleigh Howe and Francesca Chiodi
Proteomes 2020, 8(3), 24; https://doi.org/10.3390/proteomes8030024 - 7 Sep 2020
Cited by 7 | Viewed by 3187
Abstract
Treatment of HIV-1-infected patients results in improved clinical and immunological conditions, but severe non-AIDS-related conditions still persist. Novel proteomic platforms have identified inflammatory proteins where abundance is dysregulated in adult treated patients, whereas limited data are available in treated HIV-1 infection of children. [...] Read more.
Treatment of HIV-1-infected patients results in improved clinical and immunological conditions, but severe non-AIDS-related conditions still persist. Novel proteomic platforms have identified inflammatory proteins where abundance is dysregulated in adult treated patients, whereas limited data are available in treated HIV-1 infection of children. Using a proteomic plasma profiling approach comprising 92 inflammation-related molecules, we analyzed specimens from 43 vertically HIV-1-infected children receiving antiretroviral treatment (ART) and matched controls in Ethiopia. The infected children were analyzed as a group and separately, according to age of treatment initiation. Proteins displaying a significantly different abundance between groups were hierarchically clustered and presented in heat maps. Random forest analysis was performed to pin-point proteins discriminating between groups; five proteins (STAMBP, CD5, TFG-α, TRANCE, AXIN1) were the strongest prediction factors for treated HIV-1 infection. TRANCE was previously linked to reduced bone mass levels in HIV-1-infected children. CCL4 chemokine, ligand to HIV-1 co-receptor CCR5, was the most critical protein for successful classification between children who initiated ART at different time points. Our data provide evidence that a dysregulated expression of proteins linked to immunological abnormalities and bone metabolism can be found in HIV-1-infected children with prolonged exposure to ART. Full article
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15 pages, 620 KiB  
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
by Katrin Marcus and Thierry Rabilloud
Proteomes 2020, 8(3), 23; https://doi.org/10.3390/proteomes8030023 - 3 Sep 2020
Cited by 8 | Viewed by 3399
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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22 pages, 2440 KiB  
Article
Diurnal Differences in Human Muscle Isometric Force In Vivo Are Associated with Differential Phosphorylation of Sarcomeric M-Band Proteins
by Zulezwan Ab Malik, Kelly A. Bowden Davies, Elliott C. R. Hall, Jennifer Barrett, Samuel A. Pullinger, Robert M. Erskine, Sam O. Shepherd, Zafar Iqbal, Ben J. Edwards and Jatin G. Burniston
Proteomes 2020, 8(3), 22; https://doi.org/10.3390/proteomes8030022 - 26 Aug 2020
Cited by 8 | Viewed by 3669
Abstract
We investigated whether diurnal differences in muscle force output are associated with the post-translational state of muscle proteins. Ten physically active men (mean ± SD; age 26.7 ± 3.7 y) performed experimental sessions in the morning (08:00 h) and evening (17:00 h), which [...] Read more.
We investigated whether diurnal differences in muscle force output are associated with the post-translational state of muscle proteins. Ten physically active men (mean ± SD; age 26.7 ± 3.7 y) performed experimental sessions in the morning (08:00 h) and evening (17:00 h), which were counterbalanced in order of administration and separated by at least 72 h. Knee extensor maximal voluntary isometric contraction (MVIC) force and peak rate of force development (RFD) were measured, and samples of vastus lateralis were collected immediately after exercise. MVIC force was greater in the evening (mean difference of 67 N, 10.2%; p < 0.05). Two-dimensional (2D) gel analysis encompassed 122 proteoforms and discovered 6 significant (p < 0.05; false discovery rate [FDR] = 10%) diurnal differences. Phosphopeptide analysis identified 1693 phosphopeptides and detected 140 phosphopeptides from 104 proteins that were more (p < 0.05, FDR = 22%) phosphorylated in the morning. Myomesin 2, muscle creatine kinase, and the C-terminus of titin exhibited the most robust (FDR < 10%) diurnal differences. Exercise in the morning, compared to the evening, coincided with a greater phosphorylation of M-band-associated proteins in human muscle. These protein modifications may alter the M-band structure and disrupt force transmission, thus potentially explaining the lower force output in the morning. Full article
(This article belongs to the Special Issue Striated Muscle Proteomics II)
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11 pages, 2013 KiB  
Article
PeptideWitch–A Software Package to Produce High-Stringency Proteomics Data Visualizations from Label-Free Shotgun Proteomics Data
by David C. L. Handler, Flora Cheng, Abdulrahman M. Shathili and Paul A. Haynes
Proteomes 2020, 8(3), 21; https://doi.org/10.3390/proteomes8030021 - 21 Aug 2020
Cited by 2 | Viewed by 3306
Abstract
PeptideWitch is a python-based web module that introduces several key graphical and technical improvements to the Scrappy software platform, which is designed for label-free quantitative shotgun proteomics analysis using normalised spectral abundance factors. The program inputs are low stringency protein identification lists output [...] Read more.
PeptideWitch is a python-based web module that introduces several key graphical and technical improvements to the Scrappy software platform, which is designed for label-free quantitative shotgun proteomics analysis using normalised spectral abundance factors. The program inputs are low stringency protein identification lists output from peptide-to-spectrum matching search engines for ‘control’ and ‘treated’ samples. Through a combination of spectral count summation and inner joins, PeptideWitch processes low stringency data, and outputs high stringency data that are suitable for downstream quantitation. Data quality metrics are generated, and a series of statistical analyses and graphical representations are presented, aimed at defining and presenting the difference between the two sample proteomes. Full article
(This article belongs to the Special Issue Proteomics: Technologies and Their Applications)
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11 pages, 1127 KiB  
Article
Rapid Liquid AP-MALDI MS Profiling of Lipids and Proteins from Goat and Sheep Milk for Speciation and Colostrum Analysis
by Cristian Piras, Carlotta Ceniti, Evita Hartmane, Nicola Costanzo, Valeria Maria Morittu, Paola Roncada, Domenico Britti and Rainer Cramer
Proteomes 2020, 8(3), 20; https://doi.org/10.3390/proteomes8030020 - 21 Aug 2020
Cited by 13 | Viewed by 3989
Abstract
Rapid profiling of the biomolecular components of milk can be useful for food quality assessment and for food fraud detection. Differences in commercial value and availability of milk from specific species are often the reasons for the illicit and fraudulent sale of milk [...] Read more.
Rapid profiling of the biomolecular components of milk can be useful for food quality assessment and for food fraud detection. Differences in commercial value and availability of milk from specific species are often the reasons for the illicit and fraudulent sale of milk whose species origin is wrongly declared. In this study, a fast, MS-based speciation method is presented to distinguish sheep from goat milk and sheep colostrum at different phases. Using liquid atmospheric pressure (AP)-matrix-assisted laser desorption/ionisation (MALDI) MS, it was possible to classify samples of goat and sheep milk with 100% accuracy in one minute of data acquisition per sample. Moreover, an accuracy of 98% was achieved in classifying pure sheep milk samples and sheep milk samples containing 10% goat milk. Evaluating colostrum quality and postnatal stages represents another possible application of this technology. Classification of sheep colostrum samples that were collected within 6 hours after parturition and 48 hours later was achieved with an accuracy of 84.4%. Our data show that substantial changes in the lipid profile can account for the accurate classification of colostrum collected at the early and late time points. This method applied to the analysis of protein orthologs of different species can, as in this case, allow unequivocal speciation analysis. Full article
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14 pages, 3008 KiB  
Article
Cellular and Extracellular Proteome of the Animal Pathogen Corynebacterium silvaticum, a Close Relative of Zoonotic Corynebacterium ulcerans and Corynebacterium pseudotuberculosis
by Jens Möller, Svenja Schorlemmer, Jörg Hofmann and Andreas Burkovski
Proteomes 2020, 8(3), 19; https://doi.org/10.3390/proteomes8030019 - 12 Aug 2020
Cited by 8 | Viewed by 3815
Abstract
Corynebacterium silvaticum is a newly described animal pathogen, closely related to the emerging human pathogen Corynebacterium ulcerans and Corynebacterium pseudotuberculosis, a major pathogen of small ruminants. In this study, proteins of a whole cell and a shaving fraction and the exoproteome of [...] Read more.
Corynebacterium silvaticum is a newly described animal pathogen, closely related to the emerging human pathogen Corynebacterium ulcerans and Corynebacterium pseudotuberculosis, a major pathogen of small ruminants. In this study, proteins of a whole cell and a shaving fraction and the exoproteome of C. silvaticum strain W25 were analyzed as a first proteome study of this species. In total, 1305 proteins were identified out of 2013 proteins encoded by the W25 genome sequence and number of putative virulence factors were detected already under standard growth conditions including phospholipase D and sialidase. An up to now uncharacterized trypsin-like protease is by far the most secreted protein in this species, indicating a putative role in pathogenicity. Furthermore, the proteome analyses carried out in this study support the recently published taxonomical delineation of C. silvaticum from the closely related zoonotic Corynebacterium species. Full article
(This article belongs to the Special Issue Microbial Proteomics II)
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16 pages, 955 KiB  
Review
New Insights into Inflammatory Bowel Diseases from Proteomic and Lipidomic Studies
by Serena Longo, Marcello Chieppa, Luca G. Cossa, Chiara C. Spinelli, Marco Greco, Michele Maffia and Anna M. Giudetti
Proteomes 2020, 8(3), 18; https://doi.org/10.3390/proteomes8030018 - 10 Aug 2020
Cited by 9 | Viewed by 6561
Abstract
Ulcerative colitis (UC) and Crohn’s disease (CD) represent the two main forms of chronic inflammatory bowel diseases (IBD). The exact IBD etiology is not yet revealed but CD and UC are likely induced by an excessive immune response against normal constituents of the [...] Read more.
Ulcerative colitis (UC) and Crohn’s disease (CD) represent the two main forms of chronic inflammatory bowel diseases (IBD). The exact IBD etiology is not yet revealed but CD and UC are likely induced by an excessive immune response against normal constituents of the intestinal microbial flora. IBD diagnosis is based on clinical symptoms often combined with invasive and costly procedures. Thus, the need for more non-invasive markers is urgent. Several routine laboratory investigations have been explored as indicators of intestinal inflammation in IBD, including blood testing for C-reactive protein, erythrocyte sedimentation rate, and specific antibodies, in addition to stool testing for calprotectin and lactoferrin. However, none has been universally adopted, some have been well-characterized, and others hold great promise. In recent years, the technological developments within the field of mass spectrometry (MS) and bioinformatics have greatly enhanced the ability to retrieve, characterize, and analyze large amounts of data. High-throughput research allowed enhancing the understanding of the biology of IBD permitting a more accurate biomarker discovery than ever before. In this review, we summarize currently used IBD serological and stool biomarkers and how proteomics and lipidomics are contributing to the identification of IBD biomarkers. Full article
(This article belongs to the Special Issue Human Proteomics)
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26 pages, 1010 KiB  
Review
What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World?
by Katrin Marcus, Cécile Lelong and Thierry Rabilloud
Proteomes 2020, 8(3), 17; https://doi.org/10.3390/proteomes8030017 - 6 Aug 2020
Cited by 45 | Viewed by 5382
Abstract
Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis [...] Read more.
Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis depth is of critical importance, for many others, two-dimensional gel electrophoresis-based proteomics still has a lot to offer. This is because of its robustness, its ability to separate proteoforms, and its easy interface with many powerful biochemistry techniques (including western blotting). This paper reviews where and why two-dimensional gel electrophoresis-based proteomics can still be profitably used. It emerges that, rather than being a thing of the past, two-dimensional gel electrophoresis-based proteomics is still highly valuable for many studies. Thus, its use cannot be dismissed on simple fashion arguments and, as usual, in science, the tree is to be judged by the fruit. Full article
(This article belongs to the Special Issue Proteomics: Technologies and Their Applications)
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13 pages, 1349 KiB  
Article
High-Throughput Identification of the Rhodnius prolixus Midgut Proteome Unravels a Sophisticated Hematophagic Machinery
by Radouane Ouali, Karen Caroline Valentim de Brito, Didier Salmon and Sabrina Bousbata
Proteomes 2020, 8(3), 16; https://doi.org/10.3390/proteomes8030016 - 24 Jul 2020
Cited by 12 | Viewed by 3348
Abstract
Chagas disease is one of the most common parasitic infections in Latin America, which is transmitted by hematophagous triatomine bugs, of which Rhodnius prolixus is the vector prototype for the study of this disease. The protozoan parasite Trypanosoma cruzi, the etiologic agent [...] Read more.
Chagas disease is one of the most common parasitic infections in Latin America, which is transmitted by hematophagous triatomine bugs, of which Rhodnius prolixus is the vector prototype for the study of this disease. The protozoan parasite Trypanosoma cruzi, the etiologic agent of this disease, is transmitted by the vector to humans through the bite wound or mucosa. The passage of the parasite through the digestive tract of its vector constitutes a key step in its developmental cycle. Herewith, by a using high-throughput proteomic tool in order to characterize the midgut proteome of R. prolixus, we describe a set of functional groups of proteins, as well as the biological processes in which they are involved. This is the first proteomic analysis showing an elaborated hematophagy machinery involved in the digestion of blood, among which, several families of proteases have been characterized. The evaluation of the activity of cathepsin D proteases in the anterior part of the digestive tract of the insect suggested the existence of a proteolytic activity within this compartment, suggesting that digestion occurs early in this compartment. Moreover, several heat shock proteins, blood clotting inhibitors, and a powerful antioxidant enzyme machinery against reactive oxygen species (ROS) and cell detoxification have been identified. Highlighting the complexity and importance of the digestive physiology of insects could be a starting point for the selection of new targets for innovative control strategies of Chagas disease. Full article
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15 pages, 2600 KiB  
Technical Note
Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform
by Subina Mehta, Caleb W. Easterly, Ray Sajulga, Robert J. Millikin, Andrea Argentini, Ignacio Eguinoa, Lennart Martens, Michael R. Shortreed, Lloyd M. Smith, Thomas McGowan, Praveen Kumar, James E. Johnson, Timothy J. Griffin and Pratik D. Jagtap
Proteomes 2020, 8(3), 15; https://doi.org/10.3390/proteomes8030015 - 8 Jul 2020
Cited by 9 | Viewed by 4606
Abstract
For mass spectrometry-based peptide and protein quantification, label-free quantification (LFQ) based on precursor mass peak (MS1) intensities is considered reliable due to its dynamic range, reproducibility, and accuracy. LFQ enables peptide-level quantitation, which is useful in proteomics (analyzing peptides carrying post-translational modifications) and [...] Read more.
For mass spectrometry-based peptide and protein quantification, label-free quantification (LFQ) based on precursor mass peak (MS1) intensities is considered reliable due to its dynamic range, reproducibility, and accuracy. LFQ enables peptide-level quantitation, which is useful in proteomics (analyzing peptides carrying post-translational modifications) and multi-omics studies such as metaproteomics (analyzing taxon-specific microbial peptides) and proteogenomics (analyzing non-canonical sequences). Bioinformatics workflows accessible via the Galaxy platform have proven useful for analysis of such complex multi-omic studies. However, workflows within the Galaxy platform have lacked well-tested LFQ tools. In this study, we have evaluated moFF and FlashLFQ, two open-source LFQ tools, and implemented them within the Galaxy platform to offer access and use via established workflows. Through rigorous testing and communication with the tool developers, we have optimized the performance of each tool. Software features evaluated include: (a) match-between-runs (MBR); (b) using multiple file-formats as input for improved quantification; (c) use of containers and/or conda packages; (d) parameters needed for analyzing large datasets; and (e) optimization and validation of software performance. This work establishes a process for software implementation, optimization, and validation, and offers access to two robust software tools for LFQ-based analysis within the Galaxy platform. Full article
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25 pages, 1086 KiB  
Review
A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field
by Emmalyn J. Dupree, Madhuri Jayathirtha, Hannah Yorkey, Marius Mihasan, Brindusa Alina Petre and Costel C. Darie
Proteomes 2020, 8(3), 14; https://doi.org/10.3390/proteomes8030014 - 6 Jul 2020
Cited by 158 | Viewed by 27392
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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