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Label-Free Proteome Profiling
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Label-Free Proteome Profiling

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 9897

Special Issue Editors

Dr. Marianna Caterino

E-Mail Website
Guest Editor
Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
Interests: molecular mechanism involved in inborn error of metabolism; label-free quantitative proteomics; PPI, protein–protein interaction; metabolomics; lipidomics
Special Issues, Collections and Topics in MDPI journals
Dr. Alessio Soggiu

E-Mail Website
Guest Editor
Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
Interests: proteomics of host-pathogen interaction; immunoproteomics; metaproteomics; metagenomics; zoonotic and infectious diseases; bacterial competition
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The accurate determination of quantitative changes, describing the biological systems, has attracted a considerable amount of interest in the scientific community. Biological processes are regulated through the abundance of proteins. In addition, the relative abundance of each protein in a complex system may influence the modulation of its activity and its function. Over the past decade, mass spectrometry-based proteomics has become an indispensable tool in deciphering the exact abundance of each protein in composite mixtures. Indeed, the fast development of mass spectrometry-based proteomic technologies and the accessibility of powerful data analysis tools have increasingly boosted the transition of proteomic analysis from qualitative to quantitative, with a strong impact on the biological interpretation of protein functions. The described technological improvement, such as the advent of new high-resolution instruments, has allowed us to overcome classical, label-based quantitative approaches and use proteomics to move toward label-free techniques.

This Special Issue invites original and interesting contributions on quantitative proteomic studies and aims to describe the translational applicability of label-free proteomic profiling in a wide range of scientific fields. However, the Special Issue is also open to discussions about the methodological progress linked to quantitative proteomics in order to facilitate the sharing of experimental and technical details in terms of methodological conditions and bioinformatic analysis.

Dr. Marianna Caterino
Dr. Alessio Soggiu
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. Molecules is an international peer-reviewed open access semimonthly 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 2700 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

  • Label-free quantitation
  • Mass spectrometry-based quantitative analysis
  • Biofluids and tissue quantitative proteomics
  • Proteome dynamics
  • Protein-protein interactions in macromolecular complexes

Published Papers (4 papers)

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Research

20 pages, 2780 KiB  
Article
Changes in Whey Proteome between Mediterranean and Murrah Buffalo Colostrum and Mature Milk Reflect Their Pharmaceutical and Medicinal Value
by Mahmoud Abdel-Hamid, Pan Yang, Islam Mostafa, Ali Osman, Ehab Romeih, Yongxin Yang, Zizhen Huang, Awad A. Awad and Ling Li
Molecules 2022, 27(5), 1575; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27051575 - 27 Feb 2022
Cited by 7 | Viewed by 2009
Abstract
Milk represents an integrated meal for newborns; its whey protein is rich in many health beneficial components and proteins. The current study aimed to investigate the differences between colostrum and mature milk from Mediterranean and Murrah buffaloes using labeled proteomics and bioinformatics tools. [...] Read more.
Milk represents an integrated meal for newborns; its whey protein is rich in many health beneficial components and proteins. The current study aimed to investigate the differences between colostrum and mature milk from Mediterranean and Murrah buffaloes using labeled proteomics and bioinformatics tools. In the current work, LC-MS/MS analysis led to identification of 780 proteins from which 638 were shared among three independent TMT experiments. The significantly changed proteins between the studied types were analyzed using gene ontology enrichment and KEGG pathways, and their interactions were generated using STRING database. Results indicated that immunological, muscular development and function, blood coagulation, heme related, neuronal, translation, metabolic process, and binding proteins were the main terms. Overall, colostrum showed higher levels of immunoglobulins, myosins, actin, neurofascin, syntaxins, thyroglobulins, and RNA-binding proteins, reflecting its importance in the development and activity of immunological, muscular, cardiac, neuronal, and thyroid systems, while lactoferrin and ferritin were increased in mature milk, highlighting its role in iron storage and hemoglobin formation. Full article
(This article belongs to the Special Issue Label-Free Proteome Profiling)
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13 pages, 17737 KiB  
Article
Exploring the Bile Stress Response of Lactobacillus mucosae LM1 through Exoproteome Analysis
by Bernadette B. Bagon, Ju Kyoung Oh, Valerie Diane V. Valeriano, Edward Alain B. Pajarillo and Dae-Kyung Kang
Molecules 2021, 26(18), 5695; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26185695 - 20 Sep 2021
Cited by 5 | Viewed by 2049
Abstract
Lactobacillus sp. have long been studied for their great potential in probiotic applications. Recently, proteomics analysis has become a useful tool for studies on potential lactobacilli probiotics. Specifically, proteomics has helped determine and describe the physiological changes that lactic acid bacteria undergo in [...] Read more.
Lactobacillus sp. have long been studied for their great potential in probiotic applications. Recently, proteomics analysis has become a useful tool for studies on potential lactobacilli probiotics. Specifically, proteomics has helped determine and describe the physiological changes that lactic acid bacteria undergo in specific conditions, especially in the host gut. In particular, the extracellular proteome, or exoproteome, of lactobacilli contains proteins specific to host– or environment–microbe interactions. Using gel-free, label-free ultra-high performance liquid chromatography tandem mass spectrometry, we explored the exoproteome of the probiotic candidate Lactobacillus mucosae LM1 subjected to bile treatment, to determine the proteins it may use against bile stress in the gut. Bile stress increased the size of the LM1 exoproteome, secreting ribosomal proteins (50S ribosomal protein L27 and L16) and metabolic proteins (lactate dehydrogenase, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate dehydrogenases, among others) that might have moonlighting functions in the LM1 bile stress response. Interestingly, membrane-associated proteins (transporters, peptidase, ligase and cell division protein ftsH) were among the key proteins whose secretion were induced by the LM1 bile stress response. These specific proteins from LM1 exoproteome will be useful in observing the proposed bile response mechanisms via in vitro experiments. Our data also reveal the possible beneficial effects of LM1 to the host gut. Full article
(This article belongs to the Special Issue Label-Free Proteome Profiling)
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8 pages, 1181 KiB  
Communication
Proteomics Analysis Reveals Altered Nutrients in the Whey Proteins of Dairy Cow Milk with Different Thermal Treatments
by Yangdong Zhang, Li Min, Sheng Zhang, Nan Zheng, Dagang Li, Zhihua Sun and Jiaqi Wang
Molecules 2021, 26(15), 4628; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26154628 - 30 Jul 2021
Cited by 2 | Viewed by 2259
Abstract
Thermal treatments of milk induce changes in the properties of milk whey proteins. The aim of this study was to investigate the specific changes related to nutrients in the whey proteins of dairy cow milk after pasteurization at 85 °C for 15 s [...] Read more.
Thermal treatments of milk induce changes in the properties of milk whey proteins. The aim of this study was to investigate the specific changes related to nutrients in the whey proteins of dairy cow milk after pasteurization at 85 °C for 15 s or ultra-high temperature (UHT) at 135 °C for 15 s. A total of 223 whey proteins were confidently identified and quantified by TMT-based global discovery proteomics in this study. We found that UHT thermal treatment resulted in an increased abundance of 17 proteins, which appeared to show heat insensitivity. In contrast, 15 heat-sensitive proteins were decreased in abundance after UHT thermal treatment. Some of the heat-sensitive proteins were connected with the biological immune functionality, suggesting that UHT thermal treatment results in a partial loss of immune function in the whey proteins of dairy cow milk. The information reported here will considerably expand our knowledge about the degree of heat sensitivity in the whey proteins of dairy cow milk in response to different thermal treatments and offer a knowledge-based reference to aid in choosing dairy products. It is worth noting that the whey proteins (lactoperoxidase and lactoperoxidase) in milk that were significantly decreased by high heat treatment in a previous study (142 °C) showed no significant difference in the present study (135 °C). These results may imply that an appropriately reduced heating intensity of UHT retains the immunoactive proteins to the maximum extent possible. Full article
(This article belongs to the Special Issue Label-Free Proteome Profiling)
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16 pages, 3937 KiB  
Article
Proteomic and Bioinformatic Investigation of Altered Pathways in Neuroglobin-Deficient Breast Cancer Cells
by Michele Costanzo, Marco Fiocchetti, Paolo Ascenzi, Maria Marino, Marianna Caterino and Margherita Ruoppolo
Molecules 2021, 26(8), 2397; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26082397 - 20 Apr 2021
Cited by 19 | Viewed by 2477
Abstract
Neuroglobin (NGB) is a myoglobin-like monomeric globin that is involved in several processes, displaying a pivotal redox-dependent protective role in neuronal and extra-neuronal cells. NGB remarkably exerts its function upon upregulation by NGB inducers, such as 17β-estradiol (E2) and H2O2 [...] Read more.
Neuroglobin (NGB) is a myoglobin-like monomeric globin that is involved in several processes, displaying a pivotal redox-dependent protective role in neuronal and extra-neuronal cells. NGB remarkably exerts its function upon upregulation by NGB inducers, such as 17β-estradiol (E2) and H2O2. However, the molecular bases of NGB’s functions remain undefined, mainly in non-neuronal cancer cells. Human MCF-7 breast cancer cells with a knocked-out (KO) NGB gene obtained using CRISPR/Cas9 technology were analyzed using shotgun label-free quantitative proteomics in comparison with control cells. The differential proteomics experiments were also performed after treatment with E2, H2O2, and E2 + H2O2. All the runs acquired using liquid chromatography–tandem mass spectrometry were elaborated within the same MaxQuant analysis, leading to the quantification of 1872 proteins in the global proteomic dataset. Then, a differentially regulated protein dataset was obtained for each specific treatment. After the proteomic study, multiple bioinformatics analyses were performed to highlight unbalanced pathways and processes. Here, we report the proteomic and bioinformatic investigations concerning the effects on cellular processes of NGB deficiency and cell treatments. Globally, the main processes that were affected were related to the response to stress, cytoskeleton dynamics, apoptosis, and mitochondria-driven pathways. Full article
(This article belongs to the Special Issue Label-Free Proteome Profiling)
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