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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: closed (31 July 2023) | Viewed by 18219

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Prof. Dr. Paolo Iadarola

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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
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Special Issue Information

Dear Colleagues,

This Special Issue is the second volume of our previous Special Issue on “Mass Spectrometric Proteomics 2022”. Proteomics is a still-growing field of molecular biology whose 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 the 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

Published Papers (11 papers)

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Editorial

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2 pages, 136 KiB

Open AccessEditorial

Mass Spectrometric Proteomics 2.0

by Paolo Iadarola and Simona Viglio

Int. J. Mol. Sci. 2024, 25(5), 2960; https://doi.org/10.3390/ijms25052960 - 04 Mar 2024

Viewed by 493

Abstract

This Special Issue, “Mass Spectrometric Proteomics 2 [...] Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics 2.0)

Research

Jump to: Editorial

21 pages, 28282 KiB

Open AccessArticle

Comparative Analysis of Different Proteins and Metabolites in the Liver and Ovary of Local Breeds of Chicken and Commercial Chickens in the Later Laying Period

by Yuan Tang, Lingqian Yin, Li Liu, Qian Chen, Zhongzhen Lin, Donghao Zhang, Yan Wang and Yiping Liu

Int. J. Mol. Sci. 2023, 24(18), 14394; https://doi.org/10.3390/ijms241814394 - 21 Sep 2023

Viewed by 1031

Abstract

The liver and ovary perform a vital role in egg production in hens. In the later laying period, the egg-laying capacity of female hens, particularly that of local breeds, declines significantly. Hence, it is essential to study the features and conditions of the ovary and liver during this period. In this research, we characterized the proteins and metabolites in the liver and ovary of 55-week-old Guangyuan gray chickens (Group G) and Hy-Line gray chickens (Group H) by using liquid chromatography chip/electrospray ionization quadruple time-of-flight/mass spectroscopy (LC-MS/MS). In total, 139 differentially expressed proteins (DEPs) and 186 differential metabolites (DMs) were identified in the liver, and 139 DEPs and 36 DMs were identified in the ovary. The upregulated DEPs and DMs in both the liver and ovary of Group G were primarily enriched in pathways involved in amino acid and carbohydrate metabolism. This suggests that energy metabolism was highly active in the Guangyuan gray chickens. In contrast, the upregulated DEPs and DMs in Group H were mainly enriched in pathways associated with lipid metabolism, which may explain the higher egg production and the higher fatty liver rate in Hy-Line gray hens in the later laying period. Additionally, it was found that the unique protein s-(hydroxymethyl) glutathione dehydrogenase (ADH4) in Group G was implicated in functions such as fatty acid degradation, glycolysis, and pyruvate metabolism, whereas the unique proteins, steroid sulfatase (STS), glucosylceramidase (LOC107050229), and phospholipase A2 Group XV (PLA2G15), in Group H were involved in the metabolism of steroid hormones and glycerol phosphate. In conclusion, variations in how carbohydrates, lipids, and amino acids are processed in the liver and ovary of local breeds of chicken and commercial hens towards the end of their laying period could explain the disparities in their egg production abilities. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics 2.0)

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23 pages, 4131 KiB

Open AccessArticle

Less Severe Polymicrobial Sepsis in Conditional mgmt-Deleted Mice Using LysM-Cre System, Impacts of DNA Methylation and MGMT Inhibitor in Sepsis

by Kritsanawan Sae-khow, Pornpimol Phuengmaung, Jiraphorn Issara-Amphorn, Jiradej Makjaroen, Peerapat Visitchanakun, Atsadang Boonmee, Salisa Benjaskulluecha, Tanapat Palaga and Asada Leelahavanichkul

Int. J. Mol. Sci. 2023, 24(12), 10175; https://doi.org/10.3390/ijms241210175 - 15 Jun 2023

Viewed by 1306

Abstract

The O6-methylguanine-DNA methyltransferase (MGMT) is a DNA suicide repair enzyme that might be important during sepsis but has never been explored. Then, the proteomic analysis of lipopolysaccharide (LPS)-stimulated wild-type (WT) macrophages increased proteasome proteins and reduced oxidative phosphorylation proteins compared with control, possibly related to cell injury. With LPS stimulation, mgmt null (mgmt^flox/flox; LysM-Cre^cre/-) macrophages demonstrated less profound inflammation; supernatant cytokines (TNF-α, IL-6, and IL-10) and pro-inflammatory genes (iNOS and IL-1β), with higher DNA break (phosphohistone H2AX) and cell-free DNA, but not malondialdehyde (the oxidative stress), compared with the littermate control (mgmt^flox/flox; LysM-Cre^-/-). In parallel, mgmt null mice (MGMT loss only in the myeloid cells) demonstrated less severe sepsis in the cecal ligation and puncture (CLP) model (with antibiotics), as indicated by survival and other parameters compared with sepsis in the littermate control. The mgmt null protective effect was lost in CLP mice without antibiotics, highlighting the importance of microbial control during sepsis immune modulation. However, an MGMT inhibitor in CLP with antibiotics in WT mice attenuated serum cytokines but not mortality, requiring further studies. In conclusion, an absence of mgmt in macrophages resulted in less severe CLP sepsis, implying a possible influence of guanine DNA methylation and repair in macrophages during sepsis. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics 2.0)

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24 pages, 4343 KiB

Open AccessArticle

Less Severe Sepsis in Cecal Ligation and Puncture Models with and without Lipopolysaccharide in Mice with Conditional Ezh2-Deleted Macrophages (LysM-Cre System)

by Pornpimol Phuengmaung, Phuriwat Khiewkamrop, Jiradej Makjaroen, Jiraphorn Issara-Amphorn, Atsadang Boonmee, Salisa Benjaskulluecha, Patcharee Ritprajak, Aleksandra Nita-Lazar, Tanapat Palaga, Nattiya Hirankarn and Asada Leelahavanichkul

Int. J. Mol. Sci. 2023, 24(10), 8517; https://doi.org/10.3390/ijms24108517 - 10 May 2023

Cited by 1 | Viewed by 1961

Abstract

Despite a previous report on less inflammatory responses in mice with an absence of the enhancer of zeste homologue 2 (Ezh2), a histone lysine methyltransferase of epigenetic regulation, using a lipopolysaccharide (LPS) injection model, proteomic analysis and cecal ligation and puncture (CLP), a sepsis model that more resembles human conditions was devised. As such, analysis of cellular and secreted protein (proteome and secretome) after a single LPS activation and LPS tolerance in macrophages from Ezh2 null (Ezh2^flox/flox; LysM-Cre^cre/−) mice (Ezh2 null) and the littermate control mice (Ezh2^fl/fl; LysM-Cre^−/−) (Ezh2 control) compared with the unstimulated cells from each group indicated fewer activities in Ezh2 null macrophages, especially by the volcano plot analysis. Indeed, supernatant IL-1β and expression of genes in pro-inflammatory M1 macrophage polarization (IL-1β and iNOS), TNF-α, and NF-κB (a transcription factor) were lower in Ezh2 null macrophages compared with the control. In LPS tolerance, downregulated NF-κB compared with the control was also demonstrated in Ezh2 null cells. In CLP sepsis mice, those with CLP alone and CLP at 2 days after twice receiving LPS injection, representing sepsis and sepsis after endotoxemia, respectively, symptoms were less severe in Ezh2 null mice, as indicated by survival analysis and other biomarkers. However, the Ezh2 inhibitor improved survival only in CLP, but not LPS with CLP. In conclusion, an absence of Ezh2 in macrophages resulted in less severe sepsis, and the use of an Ezh2 inhibitor might be beneficial in sepsis. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics 2.0)

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11 pages, 1006 KiB

Open AccessCommunication

Proteomic Profiling of Mouse Brain Pyruvate Kinase Binding Proteins: A Hint for Moonlighting Functions of PKM1?

by Olga Buneeva, Arthur Kopylov, Oksana Gnedenko, Marina Medvedeva, Alexander Veselovsky, Alexis Ivanov, Victor Zgoda and Alexei Medvedev

Int. J. Mol. Sci. 2023, 24(8), 7634; https://doi.org/10.3390/ijms24087634 - 21 Apr 2023

Cited by 2 | Viewed by 1128

Abstract

Affinity-based proteomic profiling is widely used for the identification of proteins involved in the formation of various interactomes. Since protein–protein interactions (PPIs) reflect the role of particular proteins in the cell, identification of interaction partners for a protein of interest can reveal its function. The latter is especially important for the characterization of multifunctional proteins, which can play different roles in the cell. Pyruvate kinase (PK), a classical glycolytic enzyme catalyzing the last step of glycolysis, exists in four isoforms: PKM1, PKM2, PKL, and PKR. The enzyme isoform expressed in actively dividing cells, PKM2, exhibits many moonlighting (noncanonical) functions. In contrast to PKM2, PKM1, predominantly expressed in adult differentiated tissues, lacks well-documented moonlighting functions. However, certain evidence exists that it can also perform some functions unrelated to glycolysis. In order to evaluate protein partners, bound to PKM1, in this study we have combined affinity-based separation of mouse brain proteins with mass spectrometry identification. The highly purified PKM1 and a 32-mer synthetic peptide (PK peptide), sharing high sequence homology with the interface contact region of all PK isoforms, were used as the affinity ligands. This proteomic profiling resulted in the identification of specific and common proteins bound to both affinity ligands. Quantitative affinity binding to the affinity ligands of selected identified proteins was validated using a surface plasmon resonance (SPR) biosensor. Bioinformatic analysis has shown that the identified proteins, bound to both full-length PKM1 and the PK peptide, form a protein network (interactome). Some of these interactions are relevant for the moonlighting functions of PKM1. The proteomic dataset is available via ProteomeXchange with the identifier PXD041321. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics 2.0)

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31 pages, 2602 KiB

Open AccessArticle

Deciphering the Kidney Matrisome: Identification and Quantification of Renal Extracellular Matrix Proteins in Healthy Mice

by Umut Rende, Seong Beom Ahn, Subash Adhikari, Edward S. X. Moh, Carol A. Pollock, Sonia Saad and Anna Guller

Int. J. Mol. Sci. 2023, 24(3), 2827; https://doi.org/10.3390/ijms24032827 - 01 Feb 2023

Cited by 3 | Viewed by 2177

Abstract

Precise characterization of a tissue’s extracellular matrix (ECM) protein composition (matrisome) is essential for biomedicine. However, ECM protein extraction that requires organ-specific optimization is still a major limiting factor in matrisome studies. In particular, the matrisome of mouse kidneys is still understudied, despite mouse models being crucial for renal research. Here, we comprehensively characterized the matrisome of kidneys in healthy C57BL/6 mice using two ECM extraction methods in combination with liquid chromatography tandem mass spectrometry (LC-MS/MS), protein identification, and label-free quantification (LFQ) using MaxQuant. We identified 113 matrisome proteins, including 22 proteins that have not been previously listed in the Matrisome Database. Depending on the extraction approach, the core matrisome (structural proteins) comprised 45% or 73% of kidney ECM proteins, and was dominated by glycoproteins, followed by collagens and proteoglycans. Among matrisome-associated proteins, ECM regulators had the highest LFQ intensities, followed by ECM-affiliated proteins and secreted factors. The identified kidney ECM proteins were primarily involved in cellular, developmental and metabolic processes, as well as in molecular binding and regulation of catalytic and structural molecules’ activity. We also performed in silico comparative analysis of the kidney matrisome composition in humans and mice based on publicly available data. These results contribute to the first reference database for the mouse renal matrisome. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics 2.0)

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30 pages, 4073 KiB

Open AccessArticle

Modeling SILAC Data to Assess Protein Turnover in a Cellular Model of Diabetic Nephropathy

by Barbara Di Camillo, Lucia Puricelli, Elisabetta Iori, Gianna Maria Toffolo, Paolo Tessari and Giorgio Arrigoni

Int. J. Mol. Sci. 2023, 24(3), 2811; https://doi.org/10.3390/ijms24032811 - 01 Feb 2023

Cited by 1 | Viewed by 1683

Abstract

Protein turnover rate is finely regulated through intracellular mechanisms and signals that are still incompletely understood but that are essential for the correct function of cellular processes. Indeed, a dysfunctional proteostasis often impacts the cell’s ability to remove unfolded, misfolded, degraded, non-functional, or damaged proteins. Thus, altered cellular mechanisms controlling protein turnover impinge on the pathophysiology of many diseases, making the study of protein synthesis and degradation rates an important step for a more comprehensive understanding of these pathologies. In this manuscript, we describe the application of a dynamic-SILAC approach to study the turnover rate and the abundance of proteins in a cellular model of diabetic nephropathy. We estimated protein half-lives and relative abundance for thousands of proteins, several of which are characterized by either an altered turnover rate or altered abundance between diabetic nephropathic subjects and diabetic controls. Many of these proteins were previously shown to be related to diabetic complications and represent therefore, possible biomarkers or therapeutic targets. Beside the aspects strictly related to the pathological condition, our data also represent a consistent compendium of protein half-lives in human fibroblasts and a rich source of important information related to basic cell biology. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics 2.0)

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15 pages, 3172 KiB

Open AccessArticle

Estimating Total Quantitative Protein Content in Escherichia coli, Saccharomyces cerevisiae, and HeLa Cells

by Georgii V. Dolgalev, Taras A. Safonov, Viktoriia A. Arzumanian, Olga I. Kiseleva and Ekaterina V. Poverennaya

Int. J. Mol. Sci. 2023, 24(3), 2081; https://doi.org/10.3390/ijms24032081 - 20 Jan 2023

Cited by 4 | Viewed by 2278

Abstract

The continuous improvement of proteomic techniques, most notably mass spectrometry, has generated quantified proteomes of many organisms with unprecedented depth and accuracy. However, there is still a significant discrepancy in the reported numbers of total protein molecules per specific cell type. In this article, we explore the results of proteomic studies of Escherichia coli, Saccharomyces cerevisiae, and HeLa cells in terms of total protein copy numbers per cell. We observe up to a ten-fold difference between reported values. Investigating possible reasons for this discrepancy, we conclude that neither an unmeasured fraction of the proteome nor biases in the quantification of individual proteins can explain the observed discrepancy. We normalize protein copy numbers in each study using a total protein amount per cell as reported in the literature and create integrated proteome maps of the selected model organisms. Our results indicate that cells contain from one to three million protein molecules per µm³ and that protein copy density decreases with increasing organism complexity. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics 2.0)

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12 pages, 2777 KiB

Open AccessArticle

Software Tool for Visualization and Validation of Protein Turnover Rates Using Heavy Water Metabolic Labeling and LC-MS

by Henock M. Deberneh and Rovshan G. Sadygov

Int. J. Mol. Sci. 2022, 23(23), 14620; https://doi.org/10.3390/ijms232314620 - 23 Nov 2022

Cited by 4 | Viewed by 1353

Abstract

Metabolic stable isotope labeling followed by liquid chromatography coupled with mass spectrometry (LC-MS) is a powerful tool for in vivo protein turnover studies of individual proteins on a large scale and with high throughput. Turnover rates of thousands of proteins from dozens of time course experiments are determined by data processing tools, which are essential components of the workflows for automated extraction of turnover rates. The development of sophisticated algorithms for estimating protein turnover has been emphasized. However, the visualization and annotation of the time series data are no less important. The visualization tools help to validate the quality of the model fits, their goodness-of-fit characteristics, mass spectral features of peptides, and consistency of peptide identifications, among others. Here, we describe a graphical user interface (GUI) to visualize the results from the protein turnover analysis tool, d2ome, which determines protein turnover rates from metabolic D₂O labeling followed by LC-MS. We emphasize the specific features of the time series data and their visualization in the GUI. The time series data visualized by the GUI can be saved in JPEG format for storage and further dissemination. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics 2.0)

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19 pages, 3179 KiB

Open AccessArticle

Proteomics Unveils Post-Mortem Changes in Beef Muscle Proteins and Provides Insight into Variations in Meat Quality Traits of Crossbred Young Steers and Heifers Raised in Feedlot

by Mariane Severino, Mohammed Gagaoua, Welder Baldassini, Richard Ribeiro, Juliana Torrecilhas, Guilherme Pereira, Rogério Curi, Luis Artur Chardulo, Pedro Padilha and Otávio Machado Neto

Int. J. Mol. Sci. 2022, 23(20), 12259; https://doi.org/10.3390/ijms232012259 - 14 Oct 2022

Cited by 7 | Viewed by 2160

Abstract

Proteomics has been widely used to study muscle biology and meat quality traits from different species including beef. Beef proteomics studies allow a better understanding of the biological processes related to meat quality trait determination. This study aimed to decipher by means of two-dimensional electrophoresis (2D-PAGE), mass spectrometry and bioinformatics the changes in post-mortem muscle with a focus on proteins differentially expressed in the Longissimus thoracis (LT) muscle of immunocastrated young heifers and steers. Carcass traits, chemical composition, pH, instrumental color (L*, a*, b*), cooking loss and Warner-Bratzler shear force (WBSF) of meat from F1 Montana-Nellore cattle were also evaluated. Backfat thickness (BFT) and intramuscular fat content (IMF) were 46.8% and 63.6% higher in heifers (p < 0.05), respectively, while evaporation losses (EL) were 10.22% lower compared to steers. No differences (p > 0.05) were observed for tenderness evaluated by WBSF (3, 10, and 17 days post-mortem), pH, and color traits (L*, a* and b*) between the experimental groups. The study revealed several proteins to be differentially expressed proteins in heifers compared steers (p < 0.05). In heifers, proteins involved in nutrient transport (TF, ALB, and MB), energy metabolism (ALDOA, GAPDH, and PKM), and oxidative stress and response to stress (HSPA8 and CA3) were associated with a greater BFT and IMF deposition. The higher expression of these proteins indicated greater oxidative capacity and lower glycolytic activity in the LT muscle of heifers. In steers, there was greater abundance of protein expression related to muscle contraction and proteins of structure (ACTA1, TPM2 and TNNT3), energy metabolism (ENO1, ENO3, PYGM, PGM1 and TPI1) and ATP metabolism (ATP5F1B, PEBP1 and AK1), indicating greater glycogenolysis in LT muscle, suggesting a shift in the glycolytic/oxidative fibers of steers. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics 2.0)

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17 pages, 3219 KiB

Open AccessArticle

Revealing the Hidden Diagnostic Clues of Male Infertility from Human Seminal Plasma by Dispersive Solid Phase Extraction and MALDI-TOF MS

by Serena Correnti, Mariaimmacolata Preianò, Pierpaolo Murfone, Annalisa Fregola, Massimo Bitonti, Rocco Savino and Rosa Terracciano

Int. J. Mol. Sci. 2022, 23(18), 10786; https://doi.org/10.3390/ijms231810786 - 15 Sep 2022

Cited by 3 | Viewed by 1694

Abstract

Seminal plasma (SP) mirrors the local pathophysiology of the male reproductive system and represents a non-invasive fluid for the study of infertility. Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) provides a high-throughput platform to rapidly extrapolate the diagnostic profiles of information-rich patterns. In this study, dispersive solid phase extraction (d-SPE) combined with MALDI-TOF-MS was applied for the first time to the human SP, with the aim of revealing a diagnostic signature for male infertility. Commercially available octadecyl (C₁₈)-, octyl (C₈)-bonded silica sorbents and hexagonal mesoporous silica (HMS) were tested and the robustness of MALDI-TOF peptide profiling was evaluated. Best performances were obtained for C₁₈-bonded silica with the highest detection of peaks and the lowest variation of spectral features. To assess the diagnostic potential of the method, C₁₈-bonded silica d-SPE and MALDI-TOF-MS were used to generate enriched endogenous peptide profiles of SP from 15 fertile and 15 non-fertile donors. Principal component analysis (PCA) successfully separated fertile from non-fertile men into two different clusters. An array of seven semenogelin-derived peptides was found to distinguish the two groups, with high statistical significance. These findings, while providing a rapid and convenient route to selectively enrich native components of SP peptidome, strongly reinforce the prominent role of semenogelins in male infertility. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics 2.0)

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