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Recent Analysis and Applications of Mass Spectrum in Biochemistry 2.0

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

Deadline for manuscript submissions: closed (31 July 2024) | Viewed by 6121

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Lehrstuhl Für Analytische Chemie, Institut Für Umweltforschung, Fakultät Für Chemie Und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Nordrhein-Westfalen, Germany
Interests: analytical chemistry; mass spectrometry; quantitative and structural analyses; theoretical and quantum chemistry
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Special Issue Information

Dear Colleagues,

The analytical mass spectrometry applies irreplaceable approaches to chemical analysis, thus becoming a gold standard of the analytical practice, due to its superior instrumental features and performances. The method shows ultra-high accuracy, reliability, precision, reproducibility, selectivity, sensitivity, and specificity, together with the capability of low- and high-molecular weight analyses as well as very low concentration limits (attomole and fmol) of detection and quantitation of analytes, among other advantages of the mass spectrometric instrumentation. Mass spectrometric methods, among others, contribute crucially in developing clinical precision medicine, due to the requested, compulsory, high-analytical standards of implemented omics protocols. Mass spectrometric application fields include analytical and environmental chemistry, clinical diagnostics, laboratory medicine, petroleum chemistry, biochemistry, medicinal chemistry, pharmaceutical drug design, pharmacy, forensic chemistry and investigations for forensic medico-legal purposes, toxicology, nuclear forensics, food and agricultural science and technology, geology, archaeology, and more. Omics-methods for molecular identification, annotation, and quantification are used in metabolomics, (neuro)-proteomics, lipidomics, food-omics, steroid-omics, glycomics, pesticide analysis and control, genomics, DNA adduct-omics, transcriptomics, lignomics, interactomics, doping control, petrol-omics, isotomics, among others. Clinical trans-omics integrates clinical phenomena with mass spectrometric multi-omics approaches. The ultra-high precision and reliability of omics-protocols determine their implementation into clinical practice. The method performances should be traceable to significantly higher-order analytical standards, defining uncertainty via the criteria of statistics and chemometrics. Mass spectrometry is capable of determining molecular sequences and modifications. It addresses crucial questions on biological processes in vivo as well as provides the knowledge on the relation between molecular structure and biological function, both in vitro and in vivo. Mass spectrometric methods also utilise the techniques of isotope labelling analytes and H/D exchange, thus yielding the complete data on the structural consequences of biomacromolecules and the activation biochemical reactions of enzymes. This knowledge also significantly develops the field of biochemistry. Mass spectrometric tools also involve the imaging technique for mapping biologically active compounds in tissues. This thematic Second Edition of the Special Issue focuses on the field of analytical mass spectrometry, particularly, the field of biochemistry. While describing mass spectrometric ionization approaches, hard-ionization methods should be highlighted, for instance, inductively coupled plasma-mass spectrometry, which has been regarded as a method of choice for simultaneously quantifying the trace amounts of isotope ions of elements in biological fluids. Its protocols have also been routinely implemented in clinical laboratories.

As the former edition of the Special Issue, the Second Edition introduces the reader to the innovations and applications of soft- and hard-ionization mass spectrometric methods to comprehensively understand biochemical transformations in environmental, food, and biological samples.

Dr. Bojidarka Ivanova
Guest Editor

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Keywords

  • soft-ionization mass spectrometry
  • hard-ionization mass spectrometry
  • environmental metabolomics
  • food-omics
  • biological tissue analysis and clinical diagnostics
  • quantitative analysis
  • structural analysis
  • imaging mass spectrometry

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Related Special Issue

Published Papers (4 papers)

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16 pages, 1968 KiB  
Article
DNA-Binding Proteins and Passenger Proteins in Plasma DNA–Protein Complexes: Imprint of Parental Cells or Key Mediators of Carcinogenesis Processes?
by Oleg Tutanov, Aleksei Shefer, Evgenii Shefer, Pavel Ruzankin, Yuri Tsentalovich and Svetlana Tamkovich
Int. J. Mol. Sci. 2024, 25(10), 5165; https://doi.org/10.3390/ijms25105165 - 9 May 2024
Viewed by 1448
Abstract
Knowledge of the composition of proteins that interact with plasma DNA will provide a better understanding of the homeostasis of circulating nucleic acids and the various modes of interaction with target cells, which may be useful in the development of gene targeted therapy [...] Read more.
Knowledge of the composition of proteins that interact with plasma DNA will provide a better understanding of the homeostasis of circulating nucleic acids and the various modes of interaction with target cells, which may be useful in the development of gene targeted therapy approaches. The goal of the present study is to shed light on the composition and architecture of histone-containing nucleoprotein complexes (NPCs) from the blood plasma of healthy females (HFs) and breast cancer patients (BCPs) and to explore the relationship of proteins with crucial steps of tumor progression: epithelial–mesenchymal transition (EMT), cell proliferation, invasion, cell migration, stimulation of angiogenesis, and immune response. MALDI-TOF mass spectrometric analysis of NPCs isolated from blood samples using affine chromatography was performed. Bioinformatics analysis showed that the shares of DNA-binding proteins in the compositions of NPCs in normal and cancer patients are comparable and amount to 40% and 33%, respectively; in total, we identified 38 types of DNA-binding motifs. Functional enrichment analysis using FunRich 3.13 showed that, in BCP blood, the share of DNA-binding proteins involved in nucleic acid metabolism increased, while the proportion of proteins involved in intercellular communication and signal transduction decreased. The representation of NPC passenger proteins in breast cancer also changes: the proportion of proteins involved in transport increases and the share of proteins involved in energy biological pathways decreases. Moreover, in the HF blood, proteins involved in the processes of apoptosis were more represented in the composition of NPCs and in the BCP blood—in the processes of active secretion. For the first time, bioinformatics approaches were used to visualize the architecture of circulating NPCs in the blood and to show that breast cancer has an increased representation of passenger proteins involved in EMT, cell proliferation, invasion, cell migration, and immune response. Using breast cancer protein data from the Human Protein Atlas (HPA) and DEPC, we found that 86% of NPC proteins in the blood of BCPs were not previously annotated in these databases. The obtained data may indirectly indicate directed protein sorting in NPCs, which, along with extracellular vesicles, can not only be diagnostically significant molecules for liquid biopsy, but can also carry out the directed transfer of genetic material from donor cells to recipient cells. Full article
(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum in Biochemistry 2.0)
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13 pages, 3906 KiB  
Article
Evaluation of PAC and FASP Performance: DIA-Based Quantitative Proteomic Analysis
by Maria Stella Murfuni, Licia E. Prestagiacomo, Annarita Giuliano, Caterina Gabriele, Sara Signoretti, Giovanni Cuda and Marco Gaspari
Int. J. Mol. Sci. 2024, 25(10), 5141; https://doi.org/10.3390/ijms25105141 - 9 May 2024
Cited by 1 | Viewed by 1692
Abstract
The aim of this study was to compare filter-aided sample preparation (FASP) and protein aggregation capture (PAC) starting from a three-species protein mix (Human, Soybean and Pisum sativum) and two different starting amounts (1 and 10 µg). Peptide mixtures were [...] Read more.
The aim of this study was to compare filter-aided sample preparation (FASP) and protein aggregation capture (PAC) starting from a three-species protein mix (Human, Soybean and Pisum sativum) and two different starting amounts (1 and 10 µg). Peptide mixtures were analyzed by data-independent acquisition (DIA) and raw files were processed by three commonly used software: Spectronaut, MaxDIA and DIA-NN. Overall, the highest number of proteins (mean value of 5491) were identified by PAC (10 µg), while the lowest number (4855) was identified by FASP (1 µg). The latter experiment displayed the worst performance in terms of both specificity (0.73) and precision (0.24). Other tested conditions showed better diagnostic accuracy, with specificity values of 0.95–0.99 and precision values between 0.61 and 0.86. In order to provide guidance on the data analysis pipeline, the accuracy diagnostic of three software was investigated: (i) the highest sensitivity was obtained with Spectronaut (median of 0.67) highlighting the ability of Spectronaut to quantify low-abundance proteins, (ii) the best precision value was obtained by MaxDIA (median of 0.84), but with a reduced number of identifications compared to Spectronaut and DIA-NN data, and (iii) the specificity values were similar (between 0.93 and 0.99). The data are available on ProteomeXchange with the identifier PXD044349. Full article
(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum in Biochemistry 2.0)
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21 pages, 5411 KiB  
Article
Influence of Cold Stress on Physiological and Phytochemical Characteristics and Secondary Metabolite Accumulation in Microclones of Juglans regia L.
by Nina V. Terletskaya, Elvira A. Shadenova, Yuliya A. Litvinenko, Kazhybek Ashimuly, Malika Erbay, Aigerim Mamirova, Irada Nazarova, Nataliya D. Meduntseva, Nataliya O. Kudrina, Nazym K. Korbozova and Erika D. Djangalina
Int. J. Mol. Sci. 2024, 25(9), 4991; https://doi.org/10.3390/ijms25094991 - 3 May 2024
Cited by 2 | Viewed by 1529
Abstract
The current study investigated the impact of cold stress on the morphological, physiological, and phytochemical properties of Juglans regia L. (J. regia) using in vitro microclone cultures. The study revealed significant stress-induced changes in the production of secondary antioxidant metabolites. According [...] Read more.
The current study investigated the impact of cold stress on the morphological, physiological, and phytochemical properties of Juglans regia L. (J. regia) using in vitro microclone cultures. The study revealed significant stress-induced changes in the production of secondary antioxidant metabolites. According to gas chromatography–mass spectrometry (GC–MS) analyses, the stress conditions profoundly altered the metabolism of J. regia microclones. Although the overall spectrum of metabolites was reduced, the production of key secondary antioxidant metabolites significantly increased. Notably, there was a sevenfold (7×) increase in juglone concentration. These findings are crucial for advancing walnut metabolomics and enhancing our understanding of plant responses to abiotic stress factors. Additionally, study results aid in identifying the role of individual metabolites in these processes, which is essential for developing strategies to improve plant resilience and tolerance to adverse conditions. Full article
(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum in Biochemistry 2.0)
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15 pages, 2569 KiB  
Article
Discrimination of Etiologically Different Cholestasis by Modeling Proteomics Datasets
by Laura Guerrero, Jorge Vindel-Alfageme, Loreto Hierro, Luiz Stark, David Vicent, Carlos Óscar S. Sorzano and Fernando J. Corrales
Int. J. Mol. Sci. 2024, 25(7), 3684; https://doi.org/10.3390/ijms25073684 - 26 Mar 2024
Cited by 1 | Viewed by 900
Abstract
Cholestasis is characterized by disrupted bile flow from the liver to the small intestine. Although etiologically different cholestasis displays similar symptoms, diverse factors can contribute to the progression of the disease and determine the appropriate therapeutic option. Therefore, stratifying cholestatic patients is essential [...] Read more.
Cholestasis is characterized by disrupted bile flow from the liver to the small intestine. Although etiologically different cholestasis displays similar symptoms, diverse factors can contribute to the progression of the disease and determine the appropriate therapeutic option. Therefore, stratifying cholestatic patients is essential for the development of tailor-made treatment strategies. Here, we have analyzed the liver proteome from cholestatic patients of different etiology. In total, 7161 proteins were identified and quantified, of which 263 were differentially expressed between control and cholestasis groups. These differential proteins point to deregulated cellular processes that explain part of the molecular framework of cholestasis progression. However, the clustering of different cholestasis types was limited. Therefore, a machine learning pipeline was designed to identify a panel of 20 differential proteins that segregate different cholestasis groups with high accuracy and sensitivity. In summary, proteomics combined with machine learning algorithms provides valuable insights into the molecular mechanisms of cholestasis progression and a panel of proteins to discriminate across different types of cholestasis. This strategy may prove useful in developing precision medicine approaches for patient care. Full article
(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum in Biochemistry 2.0)
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