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Special Issue "Recent Analysis and Applications of Mass Spectrum on Biochemistry"

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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 August 2023) | Viewed by 6295

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Dr. Bojidarka Ivanova

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Institut für Umweltforschung (INFU) der Fakultät Chemie, Lehrstuhl für Umweltchemie und Analytische Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany
Interests: analytical chemistry; mass spectrometry; quantitative and structural analyses; theoretical and quantum chemistry

Special Issue Information

Dear Colleagues,

The Special Issue is devoted to recent achievements and the application of mass spectrometric methods to the field of biochemistry. The tremendous advances and superior performances of soft-ionization mass spectrometry have risen to a special prominence recently among robust analytical methods, thus making it a gold standard of analytical practice. Mass spectrometry has found irreplaceable applications in analytical science as diverse as environmental biochemistry, foodomics, clinical diagnostics, toxicology, medicine, etc. It completely determines and describes the biological transformations of chemicals. Great progress has been achieved not only by looking at omics methods, but also imaging ones for molecular mapping in biological tissues, thus, gaining crucial new knowledge of local metabolism and an in-depth understanding of biochemical processes, in vivo.

Besides, among hard-ionization approaches, techniques of inductively coupled plasma-mass spectrometry have recently been regarded as methods of choice for simultaneously quantifying trace amounts of isotope ions of elements in biological fluids. Protocols have been applied routinely in clinical laboratories, recently.

Therefore, the major aim of the Special Issue is to introduce the reader to recent advances and applications of soft- and hard-ionization mass spectrometric methods to understand comprehensively biochemical transformations in environmental, food, and biological samples.

Dr. Bojidarka Ivanova
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

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

Published Papers (9 papers)

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Research

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Open AccessArticle

Identification of Antibody-Mediated Hydrolysis Sites of Oligopeptides Corresponding to the SARS-CoV-2 S-Protein by MALDI-TOF Mass Spectrometry

and

Int. J. Mol. Sci. 2023, 24(18), 14342; https://doi.org/10.3390/ijms241814342 - 20 Sep 2023

Viewed by 184

Abstract

Antibodies recognizing RBD and the S-protein have been previously demonstrated to be formed in humans after SARS-CoV-2 infection and vaccination with the Sputnik V adenovirus vaccine. These antibodies were found to be active when hydrolyzing FITC-labeled oligopeptides corresponding to linear epitopes of the S-protein. The thin-layer chromatography method allows the relative accumulation of the reaction product to be estimated but cannot identify hydrolysis sites. This study used the MALDI-TOF MS method to establish oligopeptide hydrolysis sites. Using the MALDI-TOF MS method in combination with the analysis of known hydrolysis sites characteristic of canonical proteases allowed us to establish the unique hydrolysis sites inherent only to catalytically active antibodies. We have discovered two 12-mer oligopeptides to have six hydrolysis sites equally distributed throughout the oligopeptide. The other three oligopeptides were found to have two to three closely spaced hydrolysis sites. In contrast to trypsin and chymotrypsin proteases, the catalytically active antibodies of COVID-19 patients have their peptide bond hydrolyzed mainly after proline, threonine, glycine, or serine residues. Here, we propose a new high-throughput experimental method for analyzing the proteolytic activity of natural antibodies produced in viral pathology. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum on Biochemistry)

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Open AccessArticle

Proteome-Level Investigation of Vitis amurensis Calli Transformed with a Constitutively Active, Ca²⁺-Independent Form of the Arabidopsis AtCPK1 Gene

Galina N. Veremeichik

Dmitry V. Bulgakov

Yuliya A. Konnova

Evgenia V. Brodovskaya

Valeria P. Grigorchuk

and

Victor P. Bulgakov

Int. J. Mol. Sci. 2023, 24(17), 13184; https://doi.org/10.3390/ijms241713184 - 24 Aug 2023

Viewed by 352

Abstract

Calcium-dependent protein kinases (CDPKs) are one of the main Ca²⁺ decoders in plants. Among them, Arabidopsis thaliana AtCPK1 is one of the most studied CDPK genes as a positive regulator of plant responses to biotic and abiotic stress. The mutated form of AtCPK1, in which the autoinhibitory domain is inactivated (AtCPK1-Ca), provides constitutive kinase activity by mimicking a stress-induced increase in the Ca²⁺ flux. In the present study, we performed a proteomic analysis of Vitis amurensis calli overexpressing the AtCPK1-Ca form using untransformed calli as a control. In our previous studies, we have shown that the overexpression of this mutant form leads to the activation of secondary metabolism in plant cell cultures, including an increase in resveratrol biosynthesis in V. amurensis cell cultures. We analyzed upregulated and downregulated proteins in control and transgenic callus cultures using two-dimensional gel electrophoresis, and Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF). In calli transformed with AtCPK1-Ca, an increased amounts of pathogenesis-related proteins were found. A quantitative real-time PCR analysis confirmed this result. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum on Biochemistry)

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Open AccessArticle

Chemical, Aroma and Pro-Health Characteristics of Kaffir Lime Juice—The Approach Using Optimized HS-SPME-GC-TOFMS, MP-OES, 3D-FL and Physiochemical Analysis

Martyna Lubinska-Szczygeł

Żaneta Polkowska

Małgorzata Rutkowska

and

Shela Gorinstein

Int. J. Mol. Sci. 2023, 24(15), 12410; https://doi.org/10.3390/ijms241512410 - 03 Aug 2023

Viewed by 593

Abstract

The study aimed to provide the chemical, aroma and prohealth characteristics of the kaffir lime juice. A procedure using solid-phase microextraction with gas chromatography (SPME-GC-TOFMS) was optimized and validated for the determination of terpenes of kaffir lime. Main physicochemical parameters: pH, vitamin C, citric acid and °Brix were evaluated. Micro- and macro elements were determined using microwave plasma optic emission spectrometry (MP-OES). The binding of kaffir lime terpenes to human serum albumin (HSA) was investigated by fluorescence spectroscopy (3D-FL). β-Pinene and Limonene were selected as the most abundant terpenes with the concentration of 1225 ± 35 and 545 ± 16 µg/g, respectively. The values of citric acid, vitamin C, °Brix and pH were 74.74 ± 0.50 g/kg, 22.31 ± 0.53 mg/100 mL, 10.35 ± 0.70 and 2.406 ± 0.086 for, respectively. Iron, with a concentration of 16.578 ± 0.029 mg/kg, was the most abundant microelement. Among the macroelements, potassium (8121 ± 52 mg/kg) was dominant. Kaffir lime binding to HSA was higher than β-Pinene, which may indicate the therapeutic effect of the juice. Kaffir lime juice is a source of terpenes with good aromatic and bioactive properties. Fluorescence measurements confirmed its therapeutic effect. Kaffir lime juice is also a good source of citric acid with potential industrial application. The high content of minerals compared to other citruses increases its prohealth value. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum on Biochemistry)

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Open AccessArticle

Optimization of Mass Spectrometry Imaging for Drug Metabolism and Distribution Studies in the Zebrafish Larvae Model: A Case Study with the Opioid Antagonist Naloxone

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Int. J. Mol. Sci. 2023, 24(12), 10076; https://doi.org/10.3390/ijms241210076 - 13 Jun 2023

Viewed by 749

Abstract

Zebrafish (ZF; Danio rerio) larvae have emerged as a promising in vivo model in drug metabolism studies. Here, we set out to ready this model for integrated mass spectrometry imaging (MSI) to comprehensively study the spatial distribution of drugs and their metabolites inside ZF larvae. In our pilot study with the overall goal to improve MSI protocols for ZF larvae, we investigated the metabolism of the opioid antagonist naloxone. We confirmed that the metabolic modification of naloxone is in high accordance with metabolites detected in HepaRG cells, human biosamples, and other in vivo models. In particular, all three major human metabolites were detected at high abundance in the ZF larvae model. Next, the in vivo distribution of naloxone was investigated in three body sections of ZF larvae using LC-HRMS/MS showing that the opioid antagonist is mainly present in the head and body sections, as suspected from published human pharmacological data. Having optimized sample preparation procedures for MSI (i.e., embedding layer composition, cryosectioning, and matrix composition and spraying), we were able to record MS images of naloxone and its metabolites in ZF larvae, providing highly informative distributional images. In conclusion, we demonstrate that all major ADMET (absorption, distribution, metabolism, excretion, and toxicity) parameters, as part of in vivo pharmacokinetic studies, can be assessed in a simple and cost-effective ZF larvae model. Our established protocols for ZF larvae using naloxone are broadly applicable, particularly for MSI sample preparation, to various types of compounds, and they will help to predict and understand human metabolism and pharmacokinetics. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum on Biochemistry)

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Open AccessArticle

Serum Vitamin D Metabolites by HPLC-MS/MS Combined with Differential Ion Mobility Spectrometry: Aspects of Sample Preparation without Derivatization

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Int. J. Mol. Sci. 2023, 24(9), 8111; https://doi.org/10.3390/ijms24098111 - 30 Apr 2023

Viewed by 920

Abstract

In current clinical practice, a thorough understanding of vitamin D metabolism is in high demand both for patients with various diseases and for healthy individuals. Analytical techniques that provide simultaneous measurement of multiple metabolites are preferred. Herein, the development of an HPLC-DMS-MS/MS method for the quantitation of vitamin D compounds (25(OH)D₃, 25(OH)D₂, 1,25(OH)₂D₃, 3-epi-25(OH)D₃, 24,25(OH)₂D₃, and D₃) in serum is described. The selected sample preparation procedure based on the combination of liquid–liquid and solid-phase extraction, which excluded a lengthy derivatization step, was compared with other common approaches. Sensitivity was increased through the implementation of differential ion mobility separation. The proposed assay allowed us to determine the low abundant 1,25(OH)₂D₃ with the detection limit of 10 pg/mL. The validation study showed good linearity (r² > 0.99), a wide analytical range (2.5–75 ng/mL for 25(OH)D₃), and acceptable precision (<7%) for all metabolites. The recovery ranged from 71% to 93% and the matrix effect from 0.80 to 0.95 depending on the metabolite; accuracy determination was performed using DEQAS controls. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum on Biochemistry)

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Open AccessCommunication

New Perspectives of Multiplex Mass Spectrometry Blood Protein Quantification on Microsamples in Biological Monitoring of Elderly Patients

Aleksandra Maleska Maceski

and

Int. J. Mol. Sci. 2023, 24(8), 6989; https://doi.org/10.3390/ijms24086989 - 10 Apr 2023

Viewed by 808

Abstract

Blood microsampling combined with large panels of clinically relevant tests are of major interest for the development of home sampling and predictive medicine. The aim of the study was to demonstrate the practicality and medical utility of microsamples quantification using mass spectrometry (MS) in a clinical setting by comparing two types of microsamples for multiplex MS protein detection. In a clinical trial based on elderly population, we compared 2 µL of plasma to dried blood spot (DBS) with a clinical quantitative multiplex MS approach. The analysis of the microsamples allowed the quantification of 62 proteins with satisfactory analytical performances. A total of 48 proteins were significantly correlated between microsampling plasma and DBS (p < 0.0001). The quantification of 62 blood proteins allowed us to stratify patients according to their pathophysiological status. Apolipoproteins D and E were the best biomarker link to IADL (instrumental activities of daily living) score in microsampling plasma as well as in DBS. It is, thus, possible to detect multiple blood proteins from micro-samples in compliance with clinical requirements and this allows, for example, to monitor the nutritional or inflammatory status of patients. The implementation of this type of analysis opens new perspectives in the field of diagnosis, monitoring and risk assessment for personalized medicine approaches. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum on Biochemistry)

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Open AccessArticle

Stochastic Dynamic Mass Spectrometric Quantitative and Structural Analyses of Pharmaceutics and Biocides in Biota and Sewage Sludge

Bojidarka Ivanova

Int. J. Mol. Sci. 2023, 24(7), 6306; https://doi.org/10.3390/ijms24076306 - 27 Mar 2023

Cited by 1 | Viewed by 923

Abstract

Mass spectrometric innovations in analytical instrumentation tend to be accompanied by the development of a data-processing methodology, expecting to gain molecular-level insights into real-life objects. Qualitative and semi-quantitative methods have been replaced routinely by precise, accurate, selective, and sensitive quantitative ones. Currently, mass spectrometric 3D molecular structural methods are attractive. As an attempt to establish a reliable link between quantitative and 3D structural analyses, there has been developed an innovative formula [

D_{S D}^{″, t o t} = \sum_{i}^{n} D_{S D}^{″, i} = \sum_{i}^{n} {2.6388.10}^{- 17} \times \bar{I_{i}^{2}} - {(\bar{I_{i}})}^{2}

] capable of the exact determination of the analyte amount and its 3D structure. It processed, herein, ultra-high resolution mass spectrometric variables of paracetamol, atenolol, propranolol, and benzalkonium chlorides in biota, using mussel tissue and sewage sludge. Quantum chemistry and chemometrics were also used. Results: Data on mixtures of antibiotics and surfactants in biota and the linear dynamic range of concentrations 2–80 ng.(mL)⁻¹ and collision energy CE = 5–60 V are provided. Quantitative analysis of surfactants in biota via calibration equation ln[D″_SD] = f(conc.) yields the exact parameter |r| = 0.9999₁, examining the peaks of BAC-C12 at m/z 212.209 ± 0.1 and 211.75 ± 0.15 for tautomers of fragmentation ions. Exact parameter |r| = 1 has been obtained, correlating the theory and experiments in determining the 3D molecular structures of ions of paracetamol at m/z 152, 158, 174, 301, and 325 in biota. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum on Biochemistry)

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Review

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Open AccessReview

Quantitative Mass Spectrometry Characterizes Client Spectra of Components for Targeting of Membrane Proteins to and Their Insertion into the Membrane of the Human ER

Martin Jung

and

Richard Zimmermann

Int. J. Mol. Sci. 2023, 24(18), 14166; https://doi.org/10.3390/ijms241814166 - 15 Sep 2023

Viewed by 307

Abstract

To elucidate the redundancy in the components for the targeting of membrane proteins to the endoplasmic reticulum (ER) and/or their insertion into the ER membrane under physiological conditions, we previously analyzed different human cells by label-free quantitative mass spectrometry. The HeLa and HEK293 cells had been depleted of a certain component by siRNA or CRISPR/Cas9 treatment or were deficient patient fibroblasts and compared to the respective control cells by differential protein abundance analysis. In addition to clients of the SRP and Sec61 complex, we identified membrane protein clients of components of the TRC/GET, SND, and PEX3 pathways for ER targeting, and Sec62, Sec63, TRAM1, and TRAP as putative auxiliary components of the Sec61 complex. Here, a comprehensive evaluation of these previously described differential protein abundance analyses, as well as similar analyses on the Sec61-co-operating EMC and the characteristics of the topogenic sequences of the various membrane protein clients, i.e., the client spectra of the components, are reported. As expected, the analysis characterized membrane protein precursors with cleavable amino-terminal signal peptides or amino-terminal transmembrane helices as predominant clients of SRP, as well as the Sec61 complex, while precursors with more central or even carboxy-terminal ones were found to dominate the client spectra of the SND and TRC/GET pathways for membrane targeting. For membrane protein insertion, the auxiliary Sec61 channel components indeed share the client spectra of the Sec61 complex to a large extent. However, we also detected some unexpected differences, particularly related to EMC, TRAP, and TRAM1. The possible mechanistic implications for membrane protein biogenesis at the human ER are discussed and can be expected to eventually advance our understanding of the mechanisms that are involved in the so-called Sec61-channelopathies, resulting from deficient ER protein import. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum on Biochemistry)

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Open AccessReview

NanoLC-EI-MS: Perspectives in Biochemical Analysis

Natalia Gabrielly Pereira dos Santos

Edvaldo Vasconcelos Soares Maciel

Deyber Arley Vargas Medina

and

Fernando Mauro Lanças

Int. J. Mol. Sci. 2023, 24(14), 11746; https://doi.org/10.3390/ijms241411746 - 21 Jul 2023

Viewed by 376

Abstract

Although LC-MS with atmospheric pressure ionization (API) sources is the primary technique used in modern bioanalytical studies, electron ionization mass spectrometry (EI-MS) can provide some substantial advantages over it. EI-MS is a matrix effect-free technique that provides reproducible and comparable mass spectra, serving as a compound fingerprint for easy identification through automated comparison with spectral libraries. Leveraging EI-MS in biochemical studies can yield critical analytical benefits for targeted and untargeted analyses. However, to fully utilize EI-MS for heavy and non-volatile molecules, a new technology that enables the coupling of liquid chromatography with EI-MS is needed. Recent advancements in nanoLC have addressed the compatibility issues between LC and EI-MS, and innovative interfacing strategies such as Direct-EI, liquid electron ionization (LEI), and Cold-EI have extended the application of EI-MS beyond the determination of volatile organic molecules. This review provides an overview of the latest developments in nanoLC-EI-MS interfacing technologies, discussing their scope and limitations. Additionally, selected examples of nanoLC-EI-MS applications in the field of biochemical analysis are presented, highlighting the potential prospects and benefits that the establishment of this technique can bring to this field. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Mass Spectrum on Biochemistry)

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