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Mass Spectrometric Proteomics 3.0
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Mass Spectrometric Proteomics 3.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: 20 January 2025 | Viewed by 8349

Special Issue Editor

Prof. Dr. Paolo Iadarola

E-Mail Website
Guest Editor
Department of Biology and Biotechnology “L. Spallanzani”, Universita degli Studi di Pavia, Pavia, Italy
Interests: purification and characterization of enzymes and structural proteins; investigation of the proteome of different tissues/fluids by using the conventional methods of proteomics/metabolomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the second volume of our previous Special Issue on “Mass Spectrometric Proteomics 2.0”. Proteomics is a still-growing field of molecular biology whose the goal is the systematic identification and quantification of the entire set of proteins (the proteome) expressed at a given time in a biological system (organism, tissue, cell, or biological fluid). Assuming that the variations observed in the proteomes of a system at different times, in response to a specific stimulus, would highlight differences between them, most proteomic (in parallel with metabolomics and genomics) efforts to date have been mainly directed toward biomarker research for a variety of disorders. As proteomics and genomics are complementary techniques, it is questionable what the former adds to the latter. Indeed, the variety of proteins that may be produced both as a result of alternative splicing at the RNA level and after translation (via processes such as phosphorylation, glycosylation, and proteolytic cleavage) makes proteomics more suitable than genomics for a comprehensive understanding of the biochemical processes that govern life. Understanding how proteins function and interact with one another is another goal of proteomics that makes this approach even more intriguing. Because of their ability to handle the complexity of the events mentioned above, mass spectrometry (MS)-based methods have become the primary technology to identify proteins that may be separated by one- and two-dimensional gel electrophoresis (1- and 2-DE) and/or via liquid chromatographic techniques (1- and 2D-LC). Currently, proteomics relies mainly on MS, and the numerous applications thus far described have contributed heavily to providing new insights into the roles played by some proteins in human disorders.

The aim of this Special Issue is to attract contributions on all aspects of MS-based proteomics, with special emphasis on recent/novel technologies that, by pushing the boundaries of MS capabilities, are able to address biological problems that have not yet been resolved.

Prof. Dr. Paolo Iadarola
Guest Editor

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Keywords

  • proteome
  • mass spectrometry
  • biological system
  • genome
  • protein forms
  • biological phenotype
  • expression, localization, interaction and domain structure of proteomics

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Published Papers (6 papers)

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Research

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14 pages, 4109 KiB  
Article
Proteomic Analysis Reveals Physiological Activities of Aβ Peptide for Alzheimer’s Disease
by Xiaorui Ai, Zeyu Cao, Zhaoru Ma, Qinghuan Liu, Wei Huang, Taolei Sun, Jing Li and Chenxi Yang
Int. J. Mol. Sci. 2024, 25(15), 8336; https://doi.org/10.3390/ijms25158336 - 30 Jul 2024
Cited by 1 | Viewed by 1201
Abstract
With the rapid progress in deciphering the pathogenesis of Alzheimer’s disease (AD), it has been widely accepted that the accumulation of misfolded amyloid β (Aβ) in the brain could cause the neurodegeneration in AD. Although much evidence demonstrates the neurotoxicity of Aβ, the [...] Read more.
With the rapid progress in deciphering the pathogenesis of Alzheimer’s disease (AD), it has been widely accepted that the accumulation of misfolded amyloid β (Aβ) in the brain could cause the neurodegeneration in AD. Although much evidence demonstrates the neurotoxicity of Aβ, the role of Aβ in the nervous system are complex. However, more comprehensive studies are needed to understand the physiological effect of Aβ40 monomers in depth. To explore the physiological mechanism of Aβ, we employed mass spectrometry to investigate the altered proteomic events induced by a lower submicromolar concentration of Aβ. Human neuroblastoma SH-SY5Y cells were exposed to five different concentrations of Aβ1-40 monomers and collected at four time points. The proteomic analysis revealed the time–course behavior of proteins involved in biological processes, such as RNA splicing, nuclear transport and protein localization. Further biological studies indicated that Aβ40 monomers may activate PI3K/AKT signaling to regulate p-Tau, Ezrin and MAP2. These three proteins are associated with dendritic morphogenesis, neuronal polarity, synaptogenesis, axon establishment and axon elongation. Moreover, Aβ40 monomers may regulate their physiological forms by inhibiting the expression of BACE1 and APP via activation of the ERK1/2 pathway. A comprehensive exploration of pathological and physiological mechanisms of Aβ is beneficial for exploring novel treatment. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics 3.0)
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19 pages, 2319 KiB  
Article
Proteomic Characterization of a 3D HER2+ Breast Cancer Model Reveals the Role of Mitochondrial Complex I in Acquired Resistance to Trastuzumab
by Ivana J. Tapia, Davide Perico, Virginia J. Wolos, Marcela S. Villaverde, Marianela Abrigo, Dario Di Silvestre, Pierluigi Mauri, Antonella De Palma and Gabriel L. Fiszman
Int. J. Mol. Sci. 2024, 25(13), 7397; https://doi.org/10.3390/ijms25137397 - 5 Jul 2024
Viewed by 1103
Abstract
HER2-targeted therapies, such as Trastuzumab (Tz), have significantly improved the clinical outcomes for patients with HER2+ breast cancer (BC). However, treatment resistance remains a major obstacle. To elucidate functional and metabolic changes associated with acquired resistance, we characterized protein profiles of BC Tz-responder [...] Read more.
HER2-targeted therapies, such as Trastuzumab (Tz), have significantly improved the clinical outcomes for patients with HER2+ breast cancer (BC). However, treatment resistance remains a major obstacle. To elucidate functional and metabolic changes associated with acquired resistance, we characterized protein profiles of BC Tz-responder spheroids (RSs) and non-responder spheroids (nRSs) by a proteomic approach. Three-dimensional cultures were generated from the HER2+ human mammary adenocarcinoma cell line BT-474 and a derived resistant cell line. Before and after a 15-day Tz treatment, samples of each condition were collected and analyzed by liquid chromatography–mass spectrometry. The analysis of differentially expressed proteins exhibited the deregulation of energetic metabolism and mitochondrial pathways. A down-regulation of carbohydrate metabolism and up-regulation of mitochondria organization proteins, the tricarboxylic acid cycle, and oxidative phosphorylation, were observed in nRSs. Of note, Complex I-related proteins were increased in this condition and the inhibition by metformin highlighted that their activity is necessary for nRS survival. Furthermore, a correlation analysis showed that overexpression of Complex I proteins NDUFA10 and NDUFS2 was associated with high clinical risk and worse survival for HER2+ BC patients. In conclusion, the non-responder phenotype identified here provides a signature of proteins and related pathways that could lead to therapeutic biomarker investigation. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics 3.0)
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18 pages, 7133 KiB  
Article
Proteomics Analyses of Small Extracellular Vesicles of Aqueous Humor: Identification and Validation of GAS6 and SPP1 as Glaucoma Markers
by Raquel Rejas-González, Ana Montero-Calle, Alejandro Valverde, Natalia Pastora Salvador, María José Crespo Carballés, Emma Ausín-González, Juan Sánchez-Naves, Susana Campuzano, Rodrigo Barderas and Ana Guzman-Aranguez
Int. J. Mol. Sci. 2024, 25(13), 6995; https://doi.org/10.3390/ijms25136995 - 26 Jun 2024
Cited by 1 | Viewed by 1412
Abstract
Cataracts and glaucoma account for a high percentage of vision loss and blindness worldwide. Small extracellular vesicles (sEVs) are released into different body fluids, including the eye’s aqueous humor. Information about their proteome content and characterization in ocular pathologies is not yet well [...] Read more.
Cataracts and glaucoma account for a high percentage of vision loss and blindness worldwide. Small extracellular vesicles (sEVs) are released into different body fluids, including the eye’s aqueous humor. Information about their proteome content and characterization in ocular pathologies is not yet well established. In this study, aqueous humor sEVs from healthy individuals, cataracts, and glaucoma patients were studied, and their specific protein profiles were characterized. Moreover, the potential of identified proteins as diagnostic glaucoma biomarkers was evaluated. The protein content of sEVs from patients’ aqueous humor with cataracts and glaucoma compared to healthy individuals was analyzed by quantitative proteomics. Validation was performed by western blot (WB) and ELISA. A total of 828 peptides and 192 proteins were identified and quantified. After data analysis with the R program, 8 significantly dysregulated proteins from aqueous humor sEVs in cataracts and 16 in glaucoma showed an expression ratio ≥ 1.5. By WB and ELISA using directly aqueous humor samples, the dysregulation of 9 proteins was mostly confirmed. Importantly, GAS6 and SPP1 showed high diagnostic ability of glaucoma, which in combination allowed for discriminating glaucoma patients from control individuals with an area under the curve of 76.1% and a sensitivity of 65.6% and a specificity of 87.7%. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics 3.0)
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16 pages, 1491 KiB  
Article
Prefrontal Cortex Cytosolic Proteome and Machine Learning-Based Predictors of Resilience toward Chronic Social Isolation in Rats
by Dragana Filipović, Božidar Novak, Jinqiu Xiao, Predrag Tadić and Christoph W. Turck
Int. J. Mol. Sci. 2024, 25(5), 3026; https://doi.org/10.3390/ijms25053026 - 6 Mar 2024
Cited by 2 | Viewed by 1448
Abstract
Chronic social isolation (CSIS) generates two stress-related phenotypes: resilience and susceptibility. However, the molecular mechanisms underlying CSIS resilience remain unclear. We identified altered proteome components and biochemical pathways and processes in the prefrontal cortex cytosolic fraction in CSIS-resilient rats compared to CSIS-susceptible and [...] Read more.
Chronic social isolation (CSIS) generates two stress-related phenotypes: resilience and susceptibility. However, the molecular mechanisms underlying CSIS resilience remain unclear. We identified altered proteome components and biochemical pathways and processes in the prefrontal cortex cytosolic fraction in CSIS-resilient rats compared to CSIS-susceptible and control rats using liquid chromatography coupled with tandem mass spectrometry followed by label-free quantification and STRING bioinformatics. A sucrose preference test was performed to distinguish rat phenotypes. Potential predictive proteins discriminating between the CSIS-resilient and CSIS-susceptible groups were identified using machine learning (ML) algorithms: support vector machine-based sequential feature selection and random forest-based feature importance scores. Predominantly, decreased levels of some glycolytic enzymes, G protein-coupled receptor proteins, the Ras subfamily of GTPases proteins, and antioxidant proteins were found in the CSIS-resilient vs. CSIS-susceptible groups. Altered levels of Gapdh, microtubular, cytoskeletal, and calcium-binding proteins were identified between the two phenotypes. Increased levels of proteins involved in GABA synthesis, the proteasome system, nitrogen metabolism, and chaperone-mediated protein folding were identified. Predictive proteins make CSIS-resilient vs. CSIS-susceptible groups linearly separable, whereby a 100% validation accuracy was achieved by ML models. The overall ratio of significantly up- and downregulated cytosolic proteins suggests adaptive cellular alterations as part of the stress-coping process specific for the CSIS-resilient phenotype. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics 3.0)
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14 pages, 5559 KiB  
Article
Flexible Quality Control for Protein Turnover Rates Using d2ome
by Henock M. Deberneh and Rovshan G. Sadygov
Int. J. Mol. Sci. 2023, 24(21), 15553; https://doi.org/10.3390/ijms242115553 - 25 Oct 2023
Cited by 1 | Viewed by 1153
Abstract
Bioinformatics tools are used to estimate in vivo protein turnover rates from the LC-MS data of heavy water labeled samples in high throughput. The quantification includes peak detection and integration in the LC-MS domain of complex input data of the mammalian proteome, which [...] Read more.
Bioinformatics tools are used to estimate in vivo protein turnover rates from the LC-MS data of heavy water labeled samples in high throughput. The quantification includes peak detection and integration in the LC-MS domain of complex input data of the mammalian proteome, which requires the integration of results from different experiments. The existing software tools for the estimation of turnover rate use predefined, built-in, stringent filtering criteria to select well-fitted peptides and determine turnover rates for proteins. The flexible control of filtering and quality measures will help to reduce the effects of fluctuations and interferences to the signals from target peptides while retaining an adequate number of peptides. This work describes an approach for flexible error control and filtering measures implemented in the computational tool d2ome for automating protein turnover rates. The error control measures (based on spectral properties and signal features) reduced the standard deviation and tightened the confidence intervals of the estimated turnover rates. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics 3.0)
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Review

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19 pages, 882 KiB  
Review
The Impact of Serum/Plasma Proteomics on SARS-CoV-2 Diagnosis and Prognosis
by Maura D’Amato, Maria Antonietta Grignano, Paolo Iadarola, Teresa Rampino, Marilena Gregorini and Simona Viglio
Int. J. Mol. Sci. 2024, 25(16), 8633; https://doi.org/10.3390/ijms25168633 - 8 Aug 2024
Viewed by 1115
Abstract
While COVID-19’s urgency has diminished since its emergence in late 2019, it remains a significant public health challenge. Recent research reveals that the molecular intricacies of this virus are far more complex than initially understood, with numerous post-translational modifications leading to diverse proteoforms [...] Read more.
While COVID-19’s urgency has diminished since its emergence in late 2019, it remains a significant public health challenge. Recent research reveals that the molecular intricacies of this virus are far more complex than initially understood, with numerous post-translational modifications leading to diverse proteoforms and viral particle heterogeneity. Mass spectrometry-based proteomics of patient serum/plasma emerges as a promising complementary approach to traditional diagnostic methods, offering insights into SARS-CoV-2 protein dynamics and enhancing understanding of the disease and its long-term consequences. This article highlights key findings from three years of pandemic-era proteomics research. It delves into biomarker discovery, diagnostic advancements, and drug development efforts aimed at monitoring COVID-19 onset and progression and exploring treatment options. Additionally, it examines global protein abundance and post-translational modification profiling to elucidate signaling pathway alterations and protein-protein interactions during infection. Finally, it explores the potential of emerging multi-omics analytic strategies in combatting SARS-CoV-2. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics 3.0)
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