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Keywords = collision-induced dissociation

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18 pages, 2776 KiB  
Article
Furan Dissociation Induced by Collisions with H3+ and C+ Ions
by Tomasz J. Wasowicz
Molecules 2025, 30(12), 2559; https://doi.org/10.3390/molecules30122559 - 12 Jun 2025
Viewed by 408
Abstract
Ion interactions with molecular structures give insights into physicochemical processes in the cosmos, radiation damage, plasma, combustion, and biomass conversion reactions. At the atomic scale, these interactions lead to excitation, ionization, and dissociation of the molecular components of structures found across all these [...] Read more.
Ion interactions with molecular structures give insights into physicochemical processes in the cosmos, radiation damage, plasma, combustion, and biomass conversion reactions. At the atomic scale, these interactions lead to excitation, ionization, and dissociation of the molecular components of structures found across all these environments. Furan, cyclic aromatic ether (C4H4O), serves as a gas-phase deoxyribose analog and is crucial for understanding key pathways in renewable biomass conversion, as its derivatives are versatile molecules from lignocellulosic biomass degradation. Therefore, collisions of H3+ and C+ ions with gas-phase furan molecules were investigated in the 50–1000 eV energy range, exploiting collision-induced emission spectroscopy. High-resolution fragmentation spectra measured at 1000 eV for both cations reveal similar structures, with C+ collisions resulting in more significant furan fragmentation. Relative cross-sections for product formation were measured for H3+ + C4H4O collisions. Possible collisional processes and fragmentation pathways in furan are discussed. These results are compared with those for tetrahydrofuran and pyridine to illustrate how the type and charge of the projectile influence neutral fragmentation in heterocyclic molecules. Full article
(This article belongs to the Section Physical Chemistry)
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12 pages, 1940 KiB  
Article
Post–Column Guanosine Addition as a Screening Tool in the Search for Effective G–Quadruplex Binders—A Case Study of Achyrocline satureioides Phenolic Compounds
by Olga Stężycka, Magdalena Frańska, Damian Nowak, Marcin Hoffmann, Małgorzata Kasperkowiak and Monika Beszterda-Buszczak
Int. J. Mol. Sci. 2025, 26(9), 4312; https://doi.org/10.3390/ijms26094312 - 1 May 2025
Viewed by 382
Abstract
Polyphenols make a numerous and diverse group of plant secondary metabolites exhibiting remarkable anticancer activities, often attributed to their G-quadruplex binding properties. Therefore, there is a need to develop a high–throughput screening assay which would permit the evaluation of polyphenols’ binding properties toward [...] Read more.
Polyphenols make a numerous and diverse group of plant secondary metabolites exhibiting remarkable anticancer activities, often attributed to their G-quadruplex binding properties. Therefore, there is a need to develop a high–throughput screening assay which would permit the evaluation of polyphenols’ binding properties toward G-quadruplex. As deoxyguanosine and guanosine are essential and key building blocks of G-quadruplexes, the stabilities of their adducts with polyphenols may reflect the stabilities of polyphenols–G-quadruplex adducts. In this study, deoxyguanosine/guanosine post-column addition experiments have been performed during HPLC-MS analysis of Achyrocline satureioides extract. The stabilities of the deoxyguanosine/guanosine adducts with 3-O-methylquercetin-7-O-glucoside, 4′-hydroxydehydrokawain-4′-O-glucoside, and 3,5-di-O-caffeoylquinic acid—compounds identified in the Achyrocline satureioides extract—have been tested by using collision-induced dissociation ‘in-source’. The obtained results show that the identified compounds form more stable adducts with deoxyguanosine and guanosine than the standards used for comparison, namely isoquercitrin and rutin. The performed molecular docking provided some insight into the structure of the adducts and revealed that multiple interactions are of key importance for their stabilities. Full article
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22 pages, 4177 KiB  
Article
Global Reaction Route Mapping of C3H2O: Isomerization Pathways, Dissociation Channels, and Bimolecular Reaction with a Water Molecule
by Dapeng Zhang and Naoki Kishimoto
Molecules 2025, 30(8), 1829; https://doi.org/10.3390/molecules30081829 - 18 Apr 2025
Viewed by 406
Abstract
A comprehensive theoretical investigation of the C3H2O potential energy surface (PES) was conducted, revealing 30 equilibrium structures (EQs), 128 transition state structures (TSs), and 35 direct dissociation channels (DCs), establishing a global reaction network comprising 101 isomerization pathways and [...] Read more.
A comprehensive theoretical investigation of the C3H2O potential energy surface (PES) was conducted, revealing 30 equilibrium structures (EQs), 128 transition state structures (TSs), and 35 direct dissociation channels (DCs), establishing a global reaction network comprising 101 isomerization pathways and dissociation channels. Particular focus was placed on the five most stable isomers, H2CCCO (EQ3), OC(H)CCH (EQ7), H-c-CC(O)C-H (EQ0), HCC(H)CO (EQ1), and HO-c-CCC-H (EQ12), and their reactions with water molecules. Multicomponent artificial force-induced reaction (MC-AFIR) calculations were employed to study bimolecular collisions between H2O and these stable isomers. The product distributions revealed isomer-specific reactivity patterns: EQ3 and EQ7 predominantly formed neutral species at high collision energies, EQ0 produced both ionic and neutral species, while EQ1 and EQ12 exhibited more accessible reaction pathways at lower collision energies with a propensity for spontaneous isomerization. Born–Oppenheimer Molecular Dynamics (BOMD) simulations complemented these findings, suggesting several viable products emerge from reactions with water molecules, including HCCC(OH)2H (EQ7 + H2O), OCCHCH2OH (EQ1 + H2O), and HO-c-CC(H)C(OH)-H (EQ12 + H2O). This investigation elucidates the intrinsic relationships between isomers and their potential products, formed through biomolecular collisions with water molecules, establishing a fundamental framework for future conformational and reactivity studies of the C3H2O family. Full article
(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)
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14 pages, 1531 KiB  
Article
Conjugation of Short-Chain Fatty Acids to Bicyclic-Amines for Analysis by Liquid Chromatography Tandem Mass Spectroscopy
by Daniel N. Darlington
Molecules 2025, 30(2), 341; https://doi.org/10.3390/molecules30020341 - 16 Jan 2025
Cited by 2 | Viewed by 903
Abstract
Conjugation of short-chain fatty acids (SDFAs) to amines containing ring structures allows for better measurement by liquid chromatography tandem mass spectroscopy (LC-MS/MS). However, collision-induced dissociation (CID) results in breaking the conjugate back to the original SCFA and amine. We therefore set out to [...] Read more.
Conjugation of short-chain fatty acids (SDFAs) to amines containing ring structures allows for better measurement by liquid chromatography tandem mass spectroscopy (LC-MS/MS). However, collision-induced dissociation (CID) results in breaking the conjugate back to the original SCFA and amine. We therefore set out to find an amine that would remain on the SCFA after CID and create a unique daughter for selectivity of measurement. Of twenty-seven amines with ring structures, we found four that contain bicycle-type structures (two rings connected by a carbon) with nitrogen in the second ring. CID removes the second ring at the nitrogen, leaving the first ring on the daughter. Of the four amines, 4-(pyrrolidine-1-ylmethyl) benzylamine (4PyBA) showed the strongest conjugation. Conjugation of 4PyBA to SCFA (C3–C6), their isomers and their phenylated versions (and isomers) resulted in good chromatographic peaks and separation. CID resulted in unique daughters that allowed for selectivity of measurement. Using this method, standard curves were generated that show good linearity (r2 > 0.99) in the nM and μM range with lower limits of detection between 40 and 229 nM for a 10 μL sample. Finally, we used this method to measure SCFA in plasma, liver, platelets, and red blood cells, demonstrating its use in biological systems. Because SCFAs are an index of microbiome diversity in the gastrointestinal track, this method will allow us to study changes in SCFAs and the microbiome in pathologic conditions including trauma, hemorrhage, and sepsis. Full article
(This article belongs to the Topic Advances in Chromatographic Separation)
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19 pages, 3022 KiB  
Article
Protein Identification Improvement in Complex Samples Using Higher Frequency MS Acquisition and PEAKS Software
by Arman Kulyyassov, Saya Makhsatova and Aruzhan Kurmanbay
Appl. Sci. 2025, 15(2), 666; https://doi.org/10.3390/app15020666 - 11 Jan 2025
Viewed by 1866
Abstract
Protein identification in complex biological samples using the shotgun mode of LC-MS/MS is typically enhanced by employing longer LC columns and extended gradient times. However, improved identification rates can also be achieved by optimizing MS acquisition frequencies and employing advanced software, without increasing [...] Read more.
Protein identification in complex biological samples using the shotgun mode of LC-MS/MS is typically enhanced by employing longer LC columns and extended gradient times. However, improved identification rates can also be achieved by optimizing MS acquisition frequencies and employing advanced software, without increasing analysis time, thus maintaining the throughput of the method. To date, we found only one study in the literature examining the influence of MS acquisition frequency on protein identification, specifically using two ion trap mass spectrometer models. This study aims to address the gap by analyzing the impact of MS acquisition tuning of the QTOF instrument on the analysis of complex samples. Our findings indicate that increasing acquisition frequency generally improves protein identification, although the extent of improvement depends on the sample type. For CHO cell lysates, protein identifications increased by over 10%, while E. coli and albumin-depleted plasma samples demonstrated gains of 3.6% and 2.6%, respectively. Higher contributions to protein identification were also achieved with extended LC gradients, resulting in improvements of 21.6% for CHO, 18.2% for E. coli, and 10.3% for plasma. Moreover, enabling PEAKS’ deep learning feature significantly boosted identifications, with increases of 22.9% for CHO, 23.2% for E. coli, and 9.2% for plasma. Full article
(This article belongs to the Special Issue Recent Applications of Artificial Intelligence for Bioinformatics)
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11 pages, 1793 KiB  
Article
Installation of an Indole on the BRCA1 Disordered Domain Using Triazine Chemistry
by Liam E. Claton, Chrissy Baker, Hayes Martin, Sergei V. Dzyuba, Khadiza Zaman, Laszlo Prokai, Mikaela D. Stewart and Eric E. Simanek
Biomolecules 2024, 14(12), 1625; https://doi.org/10.3390/biom14121625 - 18 Dec 2024
Viewed by 1070
Abstract
The functionalization of protein sidechains with highly water-soluble chlorotriazines (or derivatives thereof) using nucleophilic aromatic substitution reactions has been commonly employed to install various functional groups, including poly(ethylene glycol) tags or fluorogenic labels. Here, a poorly soluble dichlorotriazine with an appended indole is [...] Read more.
The functionalization of protein sidechains with highly water-soluble chlorotriazines (or derivatives thereof) using nucleophilic aromatic substitution reactions has been commonly employed to install various functional groups, including poly(ethylene glycol) tags or fluorogenic labels. Here, a poorly soluble dichlorotriazine with an appended indole is shown to react with a construct containing the disordered domain of BRCA1. Subsequently, this construct can undergo proteolytic cleavage to remove the SUMO-tag: the N-terminal poly(His) tag is still effective for purification. Steady-state fluorescence, circular dichroism spectroscopy, and isothermal titration calorimetry with the binding partner of BRCA1, PALB2, are used to characterize the indole-labeled BRCA1. Neither the reaction conditions nor the indole-tag appreciably alter the structure of the BRCA1. Mass spectrometry confirms that the target is modified once, although the location of modification cannot be determined by tandem mass spectrometry with collision-induced dissociation due to disadvantageous fragmentation patterns. Full article
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14 pages, 2796 KiB  
Article
Energy-Resolved Mass Spectrometry and Mid-Infrared Spectroscopy for Purity Assessment of a Synthetic Peptide Cyclised by Intramolecular Huisgen Click Chemistry
by Alicia Maroto, Ricard Boqué, Dany Jeanne Dit Fouque and Antony Memboeuf
Methods Protoc. 2024, 7(6), 97; https://doi.org/10.3390/mps7060097 - 2 Dec 2024
Cited by 2 | Viewed by 1198
Abstract
Cyclic peptides have higher stability and better properties as therapeutic agents than their linear peptide analogues. Consequently, intramolecular click chemistry is becoming an increasingly popular method for the synthesis of cyclic peptides from their isomeric linear peptides. However, assessing the purity of these [...] Read more.
Cyclic peptides have higher stability and better properties as therapeutic agents than their linear peptide analogues. Consequently, intramolecular click chemistry is becoming an increasingly popular method for the synthesis of cyclic peptides from their isomeric linear peptides. However, assessing the purity of these cyclic peptides by mass spectrometry is a significant challenge, as the linear and cyclic peptides have identical masses. In this paper, we have evaluated the analytical capabilities of energy-resolved mass spectrometry (ER MS) and mid-infrared microscopy (IR) to address this challenge. On the one hand, mixtures of both peptides were subjected to collision-induced dissociation tandem mass spectrometry (CID MS/MS) experiments in an ion trap mass spectrometer at several excitation energies. Two different calibration models were used: a univariate model (at a single excitation voltage) and a multivariate model (using multiple excitation voltages). The multivariate model demonstrated slightly enhanced analytical performance, which can be attributed to more effective signal averaging when multiple excitation voltages are considered. On the other hand, IR microscopy was used for the quantification of the relative amount of linear peptide. This was achieved through univariate calibration, based on the absorbance of an alkyne band specific to the linear peptide, and through Partial Least Squares (PLS) multivariate calibration. The PLS calibration model demonstrated superior performance in comparison to univariate calibration, indicating that consideration of the full IR spectrum is preferable to focusing on the specific peak of the linear peptide. The advantage of IR microscopy is that it is linear across the entire working interval, from linear peptide molar ratios of 0 (equivalent to pure cyclic peptide) up to 1 (pure linear peptide). In contrast, the ER MS calibration models exhibited linearity only up to 0.3 linear peptide molar ratio. However, ER MS showed better performances in terms of the limit of detection, intermediate precision and the root-mean-square-error of calibration. Therefore, ER MS is the optimal choice for the detection and quantification of the lowest relative amounts of linear peptides. Full article
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16 pages, 19868 KiB  
Article
Kinetic Features of Degradation of R-Loops by RNase H1 from Escherichia coli
by Aleksandra A. Kuznetsova, Iurii A. Kosarev, Nadezhda A. Timofeyeva, Darya S. Novopashina and Nikita A. Kuznetsov
Int. J. Mol. Sci. 2024, 25(22), 12263; https://doi.org/10.3390/ijms252212263 - 15 Nov 2024
Cited by 1 | Viewed by 1286
Abstract
R-loops can act as replication fork barriers, creating transcription–replication collisions and inducing replication stress by arresting DNA synthesis, thereby possibly causing aberrant processing and the formation of DNA strand breaks. RNase H1 (RH1) is one of the enzymes that participates in R-loop degradation [...] Read more.
R-loops can act as replication fork barriers, creating transcription–replication collisions and inducing replication stress by arresting DNA synthesis, thereby possibly causing aberrant processing and the formation of DNA strand breaks. RNase H1 (RH1) is one of the enzymes that participates in R-loop degradation by cleaving the RNA strand within a hybrid RNA–DNA duplex. In this study, the kinetic features of the interaction of RH1 from Escherichia coli with R-loops of various structures were investigated. It was found that the values of the dissociation constants Kd were minimal for complexes of RH1 with model R-loops containing a 10–11-nt RNA–DNA hybrid part, indicating effective binding. Analysis of the kinetics of RNA degradation in the R-loops by RH1 revealed that the rate-limiting step of the process was catalytic-complex formation. In the presence of RNA polymerase, the R-loops containing a ≤16-nt RNA–DNA hybrid part were efficiently protected from cleavage by RH1. In contrast, R-loops containing longer RNA–DNA hybrid parts, as a model of an abnormal transcription process, were not protected by RNA polymerase and were effectively digested by RH1. Full article
(This article belongs to the Special Issue Role of RNA Decay in Bacterial Gene Regulation)
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16 pages, 2250 KiB  
Article
MS2Lipid: A Lipid Subclass Prediction Program Using Machine Learning and Curated Tandem Mass Spectral Data
by Nami Sakamoto, Takaki Oka, Yuki Matsuzawa, Kozo Nishida, Jayashankar Jayaprakash, Aya Hori, Makoto Arita and Hiroshi Tsugawa
Metabolites 2024, 14(11), 602; https://doi.org/10.3390/metabo14110602 - 7 Nov 2024
Cited by 2 | Viewed by 1722
Abstract
Background: Untargeted lipidomics using collision-induced dissociation-based tandem mass spectrometry (CID-MS/MS) is essential for biological and clinical applications. However, annotation confidence still relies on manual curation by analytical chemists, despite the development of various software tools for automatic spectral processing based on rule-based [...] Read more.
Background: Untargeted lipidomics using collision-induced dissociation-based tandem mass spectrometry (CID-MS/MS) is essential for biological and clinical applications. However, annotation confidence still relies on manual curation by analytical chemists, despite the development of various software tools for automatic spectral processing based on rule-based fragment annotations. Methods: In this study, we present a novel machine learning model, MS2Lipid, for the prediction of known lipid subclasses from MS/MS queries, providing an orthogonal approach to existing lipidomics software programs in determining the lipid subclass of ion features. We designed a new descriptor, MCH (mode of carbon and hydrogen), to increase the specificity of lipid subclass prediction in nominal mass resolution MS data. Results: The model, trained with 6760 and 6862 manually curated MS/MS spectra for the positive and negative ion modes, respectively, classified queries into one or several of 97 lipid subclasses, achieving an accuracy of 97.4% in the test set. The program was further validated using various datasets from different instruments and curators, with the average accuracy exceeding 87.2%. Using an integrated approach with molecular spectral networking, we demonstrated the utility of MS2Lipid by annotating microbiota-derived esterified bile acids, whose abundance was significantly increased in fecal samples of obese patients in a human cohort study. This suggests that the machine learning model provides an independent criterion for lipid subclass classification, enhancing the annotation of lipid metabolites within known lipid classes. Conclusions: MS2Lipid is a highly accurate machine learning model that enhances lipid subclass annotation from MS/MS data and provides an independent criterion. Full article
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18 pages, 2104 KiB  
Article
Integrating Epoxidation, High-Resolution Mass Spectrometry and Ultraviolet Spectroscopy to Unravel the Complex Profile of Boswellic Acids and Related Compounds in the Boswellia serrata Gum Resin Extract
by Andrea Castellaneta, Ilario Losito, Stefania Cometa, Francesco Busto, Elvira De Giglio and Tommaso R. I. Cataldi
Molecules 2024, 29(20), 4967; https://doi.org/10.3390/molecules29204967 - 21 Oct 2024
Viewed by 1235
Abstract
The chemical characterization of natural products is often a complex task that demands powerful analytical techniques. Liquid chromatography with high-resolution tandem mass spectrometry (HRMS/MS) is often employed, yet it can face hard challenges when isomeric species are present, and reference standards are lacking. [...] Read more.
The chemical characterization of natural products is often a complex task that demands powerful analytical techniques. Liquid chromatography with high-resolution tandem mass spectrometry (HRMS/MS) is often employed, yet it can face hard challenges when isomeric species are present, and reference standards are lacking. In such cases, the confidence level in compound identification can be significantly improved by the collection of orthogonal information on target analytes. In this work, 23 key compounds in Boswellia serrata extract (BSE), 12 of which correspond to boswellic acids (BAs) and 11 to triterpenoidic acid isomers, were identified by combining RPLC followed by serial UV and ESI(-)-FTMS and FTMS/MS detections with the evaluation of the reactivity towards C=C bond epoxidation with meta-chloroperoxybenzoic acid (m-CPBA), proposed as a fast chemical tool to gather information about C=C bond steric hindrance, a key structural feature of BAs and related compounds. The interpretation of UV spectra acquired after chromatographic separation corroborated the identification of the substitution patterns of enonic and dienic residues in ketoboswellic and dehydroboswellic acids. Moreover, MS/MS based on higher-energy collision-induced dissociation (HCD) unveiled new fragmentation pathways, providing important structural details on target analytes. The integrated approach developed during this study might pave the way for a deeper understanding of the BSE bioactive properties. Moreover, it can be considered an example of a more general strategy for the analysis of complex mixtures of natural compounds including also isomeric species. Full article
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16 pages, 8494 KiB  
Article
Identification of a Chimera Mass Spectrum of Isomeric Lipid A Species Using Negative Ion Tandem Mass Spectrometry
by Ágnes Dörnyei, Anikó Kilár and Viktor Sándor
Toxins 2024, 16(7), 322; https://doi.org/10.3390/toxins16070322 - 18 Jul 2024
Cited by 1 | Viewed by 1777
Abstract
The toxic nature of bacterial endotoxins is affected by the structural details of lipid A, including the variety and position of acyl chains and phosphate group(s) on its diglucosamine backbone. Negative-ion mode tandem mass spectrometry is a primary method for the structure elucidation [...] Read more.
The toxic nature of bacterial endotoxins is affected by the structural details of lipid A, including the variety and position of acyl chains and phosphate group(s) on its diglucosamine backbone. Negative-ion mode tandem mass spectrometry is a primary method for the structure elucidation of lipid A, used independently or in combination with separation techniques. However, it is challenging to accurately characterize constitutional isomers of lipid A extracts by direct mass spectrometry, as the elemental composition and molecular mass of these molecules are identical. Thus, their simultaneous fragmentation leads to a composite, so-called chimera mass spectrum. The present study focuses on the phosphopositional isomers of the classical monophosphorylated, hexaacylated Escherichia coli-type lipid A. Collision-induced dissociation (CID) was performed in an HPLC-ESI-QTOF system. Energy-resolved mass spectrometry (ERMS) was applied to uncover the distinct fragmentation profiles of the phosphorylation isomers. A fragmentation strategy applying multi-levels of collision energy has been proposed and applied to reveal sample complexity, whether it contains only a 4′-phosphorylated species or a mixture of 1- and 4′-phosphorylated variants. This comparative fragmentation study of isomeric lipid A species demonstrates the high potential of ERMS-derived information for the successful discrimination of co-ionized phosphorylation isomers of hexaacylated lipid A. Full article
(This article belongs to the Topic Application of Analytical Technology in Metabolomics)
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10 pages, 4712 KiB  
Communication
Cyanoacetohydrazide as a Novel Derivatization Agent for the Determination of UHPLC-HRMS Steroids in Urine
by Azamat Temerdashev, Maria Zorina, Yu-Qi Feng, Elina Gashimova, Victor V. Dotsenko, Vitalij Ioutsi and Sanka N. Atapattu
Molecules 2024, 29(11), 2433; https://doi.org/10.3390/molecules29112433 - 22 May 2024
Viewed by 1344
Abstract
The possibility of cyanoacetohydrazide usage as a novel derivatizing agent is demonstrated in the presented article, and a comparison with hydroxylamine as the most commonly used reagent is provided. Optimal conditions for steroid derivatization with cyanoacetohydrazide are provided. According to the collected data, [...] Read more.
The possibility of cyanoacetohydrazide usage as a novel derivatizing agent is demonstrated in the presented article, and a comparison with hydroxylamine as the most commonly used reagent is provided. Optimal conditions for steroid derivatization with cyanoacetohydrazide are provided. According to the collected data, the maximum yield of derivatives was observed at pH 2.8 within 70 min at 40 °C with 5 ng/mL limit of detection for all investigated analytes. It was shown that cyanoacetohydrazide derivatives produces both syn- and anti-forms as well as hydroxylamine, and their ratios were evaluated and shown in presented work. An efficiency enchantment from two to up to five times was achieved with a novel derivatization reagent. Its applicability for qualitative analysis of steroids in urine was presented at real samples. Additionally, the reproducible fragmentation of the derivatizing agent in collision-induced dissociation offers opportunities for simplified non-targeted steroidomic screening. Furthermore, cyanoacetohydrazide increases ionization efficiency in positive mode, which can eliminate the need for redundant high-resolution instrument runs required for both positive and negative mode analyses. Full article
(This article belongs to the Section Analytical Chemistry)
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20 pages, 6224 KiB  
Article
Proteins in Scalp Hair of Preschool Children
by Cynthia R. Rovnaghi, Kratika Singhal, Ryan D. Leib, Maria Xenochristou, Nima Aghaeepour, Allis S. Chien, Deendayal Dinakarpandian and Kanwaljeet J. S. Anand
Psych 2024, 6(1), 143-162; https://doi.org/10.3390/psych6010009 - 29 Jan 2024
Viewed by 2673
Abstract
Background. Early childhood experiences have long-lasting effects on subsequent mental and physical health, education, and employment. The measurement of these effects relies on insensitive behavioral signs, subjective assessments by adult observers, neuroimaging or neurophysiological studies, or retrospective epidemiologic outcomes. Despite intensive research, the [...] Read more.
Background. Early childhood experiences have long-lasting effects on subsequent mental and physical health, education, and employment. The measurement of these effects relies on insensitive behavioral signs, subjective assessments by adult observers, neuroimaging or neurophysiological studies, or retrospective epidemiologic outcomes. Despite intensive research, the underlying mechanisms of these long-term changes in development and health status remain unknown. Methods. We analyzed scalp hair from healthy children and their mothers using an unbiased proteomics platform combining tandem mass spectrometry, ultra-performance liquid chromatography, and collision-induced dissociation to reveal commonly observed hair proteins with a spectral count of 3 or higher. Results. We observed 1368 non-structural hair proteins in children and 1438 non-structural hair proteins in mothers, with 1288 proteins showing individual variability. Mothers showed higher numbers of peptide spectral matches and hair proteins compared to children, with important age-related differences between mothers and children. Age-related differences were also observed in children, with differential protein expression patterns between younger (2 years and below) and older children (3–5 years). We observed greater similarity in hair protein patterns between mothers and their biological children compared with mothers and unrelated children. The top 5% of proteins driving population variability represented biological pathways associated with brain development, immune signaling, and stress response regulation. Conclusions. Non-structural proteins observed in scalp hair include promising biomarkers to investigate the long-term developmental changes and health status associated with early childhood experiences. Full article
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22 pages, 5525 KiB  
Article
Self-Assembly of a Novel Pentapeptide into Hydrogelated Dendritic Architecture: Synthesis, Properties, Molecular Docking and Prospective Applications
by Stefania-Claudia Jitaru, Andra-Cristina Enache, Corneliu Cojocaru, Gabi Drochioiu, Brindusa-Alina Petre and Vasile-Robert Gradinaru
Gels 2024, 10(2), 86; https://doi.org/10.3390/gels10020086 - 23 Jan 2024
Cited by 5 | Viewed by 2794
Abstract
Currently, ultrashort oligopeptides consisting of fewer than eight amino acids represent a cutting-edge frontier in materials science, particularly in the realm of hydrogel formation. By employing solid-phase synthesis with the Fmoc/tBu approach, a novel pentapeptide, FEYNF-NH2, was designed, inspired by a [...] Read more.
Currently, ultrashort oligopeptides consisting of fewer than eight amino acids represent a cutting-edge frontier in materials science, particularly in the realm of hydrogel formation. By employing solid-phase synthesis with the Fmoc/tBu approach, a novel pentapeptide, FEYNF-NH2, was designed, inspired by a previously studied sequence chosen from hen egg-white lysozyme (FESNF-NH2). Qualitative peptide analysis was based on reverse-phase high performance liquid chromatography (RP-HPLC), while further purification was accomplished using solid-phase extraction (SPE). Exact molecular ion confirmation was achieved by matrix-assisted laser desorption–ionization mass spectrometry (MALDI-ToF MS) using two different matrices (HCCA and DHB). Additionally, the molecular ion of interest was subjected to tandem mass spectrometry (MS/MS) employing collision-induced dissociation (CID) to confirm the synthesized peptide structure. A combination of research techniques, including Fourier-transform infrared spectroscopy (FTIR), fluorescence analysis, transmission electron microscopy, polarized light microscopy, and Congo red staining assay, were carefully employed to glean valuable insights into the self-assembly phenomena and gelation process of the modified FEYNF-NH2 peptide. Furthermore, molecular docking simulations were conducted to deepen our understanding of the mechanisms underlying the pentapeptide’s supramolecular assembly formation and intermolecular interactions. Our study provides potential insights into amyloid research and proposes a novel peptide for advancements in materials science. In this regard, in silico studies were performed to explore the FEYNF peptide’s ability to form polyplexes. Full article
(This article belongs to the Special Issue Hydrogelated Matrices: Structural, Functional and Applicative Aspects)
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11 pages, 1596 KiB  
Article
Very Low-Pressure CID Experiments: High Energy Transfer and Fragmentation Pattern at the Single Collision Regime
by Dániel Szabó, Ágnes Gömöry, Krisztina Ludányi, Károly Vékey and László Drahos
Molecules 2024, 29(1), 211; https://doi.org/10.3390/molecules29010211 - 30 Dec 2023
Viewed by 1861
Abstract
We have performed CID experiments on a triple quadrupole instrument, lowering the collision gas pressure by 50 times compared to its conventional value. The results show that at very low-collision gas pressure, single collisions dominate the spectra. Indirectly, these results suggest that under [...] Read more.
We have performed CID experiments on a triple quadrupole instrument, lowering the collision gas pressure by 50 times compared to its conventional value. The results show that at very low-collision gas pressure, single collisions dominate the spectra. Indirectly, these results suggest that under conventional conditions, 20–50 collisions may be typical in CID experiments. The results show a marked difference between low- and high-pressure CID spectra, the latter being characterized in terms of ‘slow heating’ and predominance of consecutive reactions. The results indicate that under single collision conditions, the collisional energy transfer efficiency is very high: nearly 100% of the center of mass kinetic energy is converted to internal energy. Full article
(This article belongs to the Section Analytical Chemistry)
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