Specific Fragmentation Research Articles

A Multimodal System for Lipid A Structural Analysis from a Single Colony.

Structural elucidation of Gram-negative bacterial lipid A traditionally requires chemical extraction followed by tandem MS data in the negative ion mode. Previously, we reported FLAT and FLATn as methods to rapidly determine the structure of lipid A without chromatographic techniques. In this work, we extend the capability and effectiveness of these techniques to elucidate the chemical structure in a de novo manner by including the use of positive ion mode (FLAT+ and FLATn+) spectral approaches. Advantages of positive mode analysis of lipid A include the generation of more interpretable and informative fragmentation patterns that include the identification of diagnostic fragments, including selective dissociation of a glycosidic bond between two glucosamine units and the selective dissociation at the secondary acyl chain in 2'-N, allowing for the determination of the composition of fatty acids. As a proof of principle, we present here two previously uncharacterized structures of lipid A from Roseomonas mucosa (R. mucosa) and Moraxella canis (M. canis). In R. mucosa, we determined the lipid A structure with a nonconventional backbone of-β-1,6 linked 2,3-dideoxy-2,3-diamno-d-glucopyranose further modified with galacturonic acid in the place of typical 1-phosphate, and in M. canis, we assigned a single discrete structure using the specific fragmentation patterns of terminal phosphate groups present in lipid A. Therefore, FLATn+, in combination with FLAT and FLATn, provides a multimodal structural platform for rapid structure characterization of unusual and complex lipid A structures from a single colony.

Tapping the potential of Calotropis procera hairy roots for cardiac glycosides production and their identification using UHPLC/QTOF-MS.

The present work deals with the establishment of hairy root cultures from different explants of C. procera using Agrobacterium rhizogenes strain A4. A high transformation frequency (95%) was obtained from leaves followed by cotyledons (81.6%) and hypocotyls (38.3%). Genetic transformation of hairy roots was confirmed through PCR by amplifying a 400 bp fragment of the rolB gene. Hairy roots were highly branched, possessed plagiotropic and rapid growth on hormone-free ½ B5 medium. Ten cardiac glycosides, including calotropagenin, calotoxin, frugoside, coroglaucigenin, calotropin, calactin, uzarigenin, asclepin, uscharidin, and uscharin, based on their specific masses and fragmentation properties were identified in ethanolic extracts of hairy roots by ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry UHPLC/QTOF-MS. This protocol could be used as a powerful tool for large-scale in vitro production of highly valued cardiac glycosides and for further transcriptomics or metabolomics studies.

Reliable Detection of Chemical Warfare Agents Using High Kinetic Energy Ion Mobility Spectrometry.

High Kinetic Energy Ion Mobility Spectrometers (HiKE-IMS) ionize and separate ions at reduced pressures of 10-40 mbar and over a wide range of reduced electric field strengths E/N of up to 120 Td. Their reduced operating pressure is distinct from that of conventional drift tube ion mobility spectrometers that operate at ambient pressure for trace compound detection. High E/N can lead to a field-induced fragmentation pattern that provides more specific structural information about the analytes. In addition, operation at high E/N values adds the field dependence of ion mobility as an additional separation dimension to low-field ion mobility, making interfering compounds less likely to cause a false positive alarm. In this work, we study the chemical warfare agents tabun (GA), sarin (GB), soman (GD), cyclosarin (GF) and sulfur mustard (HD) in a HiKE-IMS at variable E/N in both the reaction and the drift region. The results show that varying E/N can lead to specific fragmentation patterns at high E/N values combined with molecular signals at low E/N. Compared to the operation at a single E/N value in the drift region, the variation of E/N in the drift region also provides the analyte-specific field dependence of ion mobility as additional information. The accumulated data establish a unique fingerprint for each analyte that allows for reliable detection of chemical warfare agents even in the presence of interfering compounds with similar low-field ion mobilities, thus reducing false positives.

Soil-derived cellulose-degrading bacteria: screening, identification, the optimization of fermentation conditions, and their whole genome sequencing.

Straw cellulose is an abundant renewable resource in nature. In recent years, the conversion of cellulose from waste straw into biofuel by specific microorganisms' fragmentation has attracted extensive attention. Although many bacteria with the ability to degrade cellulose have been identified, comprehensive bioinformatics analyses of these bacteria remain limited, and research exploring optimal fragmentation conditions is scarce. Our study involved the isolation and screening of bacteria from various locations in Yangzhou using carboxymethyl cellulose (CMC) media. Then, the cellulose-degrading bacteria were identified using 16S rRNA and seven candidate bacterial strains with cellulose degrading ability were identified in Yangzhou city for the first time. The cellulase activity was determined by the 3,5-dinitrosalicylic acid (DNS) method in different fragmentation conditions, and finally two bacteria strains with the strongest cellulose degradation ability were selected for whole genome sequencing analysis. Sequencing results revealed that the genome sizes of Rhodococcus wratislaviensis YZ02 and Pseudomonas Xanthosomatis YZ03 were 8.51 Mb and 6.66 Mb, containing 8,466 and 5,745 genes, respectively. A large number of cellulose degradation-related genes were identified and annotated using KEGG, GO and COG analyses. In addition, genomic CAZyme analysis indicated that both R. wratislaviensis YZ02 and P. Xanthosomatis YZ03 harbor a series of glycoside hydrolase family (GH) genes and other genes related to cellulose degradation. Our finding provides new options for the development of cellulose-degrading bacteria and a theoretical basis for improving the cellulose utilization of straw.

EThcD as a Unique Tool for the Top-Down De Novo Sequencing of Intact Natural Ranid Amphibian Peptides.

De novo sequencing of any novel peptide/protein is a difficult task. Full sequence coverage, isomeric amino acid residues, inter- and intramolecular S-S bonds, and numerous other post-translational modifications make the investigators employ various chemical modifications, providing a variety of specific fragmentation MSn patterns. The chemical processes are time-consuming, and their yields never reach 100%, while the subsequent purification often leads to the loss of minor components of the initial peptide mixture. Here, we present the advantages of the EThcD method that enables establishing the full sequence of natural intact peptides of ranid frogs in de novo top-down mode without any chemical modifications. The method provides complete sequence coverage, including the cyclic disulfide section, and reliable identification of isomeric leucine/isoleucine residues. The proposed approach demonstrated its efficiency in the analysis of peptidomes of ranid frogs from several populations of Rana arvalis, Rana temporaria, and Pelophylax esculentus complexes.

Experimentally Determined Diagnostic Ions for Identification of Peptide Glycotopes.

The analysis of the structures of glycans present on glycoproteins is an essential component for determining glycoprotein function; however, detailed glycan structural assignment on glycopeptides from proteomics mass spectrometric data remains challenging. Glycoproteomic analysis by mass spectrometry currently can provide significant, yet incomplete, information about the glycans present, including the glycan monosaccharide composition and in some circumstances the site(s) of glycosylation. Advancements in mass spectrometric resolution, using high-mass accuracy instrumentation and tailored MS/MS fragmentation parameters, coupled with a dedicated definition of diagnostic fragmentation ions have enabled the determination of some glycan structural features, or glycotopes, expressed on glycopeptides. Here we present a collation of diagnostic glycan fragments produced by traditional positive-ion-mode reversed-phase LC-ESI MS/MS proteomic workflows and describe the specific fragmentation energy settings required to identify specific glycotopes presented on N- or O-linked glycopeptides in a typical proteomics MS/MS experiment.

Relaxation of the 2a1 ionized water dimer: An interplay of intermolecular Coulombic decay (ICD) and proton transfer processes.

This article investigates the relaxation dynamics of the ionized 2a1 state of a water molecule within a water dimer. The study was motivated by findings from two previous pieces of research that focused on the relaxation behaviors of the inner-valence ionized water dimer. The present study discloses an observation indicating that water dimers display specific fragmentation patterns following inner-valence ionization, depending on the position of the vacancy. Vacancies were created in the 2a1 state of the proton-donating water molecule (PDWM) and proton-accepting water molecule (PAWM). Utilizing Born-Oppenheimer molecular dynamics simulations, the propagation of the 2a1 ionized state was carried out for both scenarios. The results revealed proton transfer occurred when the vacancy resided in the PDWM, accompanied by the closing of decay channels for O-H bond distance (RO-H) > 1.187Å (matching Richter et al.'s findings). Conversely, when vacancy was on PAWM, we observed no closing of decay channels (aligning with Jahnke et al.'s findings). This difference translates to distinct fragmentation pathways. In PDWM cases, 2a1 state ionization leads to H3O+ -OH• formation. In contrast, PAWM vacancies result in decay pathways leading to H2O+-H2O+ products.

Searching for optimal solutions in a landscape fragmentation assessment: A case study from Poland – Identification of spatial data and methods

There is no single correct or optimal scale for describing spatial landscape heterogeneity. However, since landscape patterns are scale-dependent, using different scales in the analysis may result in different outcomes, which can affect landscape management options. The main goal of our research was to identify the most adequate GIS solution for converting vector data to raster data while keeping the spatial continuity of most linear features and input land cover data as detailed as possible. In addition, to compare our database with the CORINE Land Cover data approach, we used 3 different rasterization methods and raster data with 100- and 50-m pixel sizes, first, to match the geometric accuracy of the CORINE Land Cover data and second, to compare the calculation results acquired with the higher-resolution rasterized BDOT10k data. We found that it was possible to compare these methods and assess how much data resolution and selection of rasterization methods affected the calculations of the landscape metrics. The calculation results of specific fragmentation metrics differed tremendously when higher data resolutions and rasterization methods were used, especially when using the custom priority rasterization method.

Two-Dimensional Projected-Momentum Covariance Mapping for Coulomb Explosion Imaging.

We introduce projected-momentum covariance mapping, an extension of recoil-frame covariance mapping for 2D ion imaging studies. By considering the two-dimensional projection of the ion momenta as recorded by the detector, one opens the door to a complex suite of analysis tools adapted from three-dimensional momentum imaging studies. This includes the use of different frames of reference to unravel the dynamics of fragmentation and the application of fragment momentum constraints to isolate specific fragmentation channels. The technique is demonstrated on data from a two-dimensional ion imaging study of the Coulomb explosion of the cis and trans isomers of 1,2-dichloroethene, following strong-field ionization by an intense near-infrared femtosecond laser pulse. Classical simulations are used to guide the interpretation of projected-momentum covariance maps. The results offer a detailed insight into the distinct Coulomb explosion dynamics for this pair of isomers and lay the groundwork for future time-resolved studies of photoisomerization dynamics in this molecular system.

Abstract 7019: Identifying cell free DNA methylation signatures in cerebrospinal fluids for the early detection of brain metastasis in non-small cell lung cancer

Abstract Brain metastasis (BM) is major complication for adult cancer patients. Up to 2% of all cancer patients develop BM. Non-small cell lung cancer (NSCLC) contributes up to 55% of all BM. Approximately 15-20% of NSCLC patients show metastases at diagnosis, and approximately half will develop BM during their clinical course. Even after treatments like surgery, radiation and immunotherapy, the prognosis is dismal with median overall survival less than 13 months. No standard screening or early diagnostic testing exists for BM now. There is an urgent need to identify genomic features that predispose towards brain metastasis - these biomarkers could be used for early detection and disease monitoring. The cfDNA methylation and fragmentation patterns provide potential epigenetic biomarkers for detecting cancer. These patterns are specific to cell/tissue origin and cancer types. DNA methylation refers to a chemical modification of a specific carbon with an added methyl group in the cytosine. Hypomethylation in the gene body and hypermethylation in the promoter region lead to cancer development. We hypothesize that there are specific cfDNA methylation and fragmentation signatures in CSF that reflect the epigenetic states of BMs, and cancer predisposition for brain metastasis. We applied a novel single molecule sequencing approach to study CSF cfDNA methylation of BM from NSCLC. Our cohort consisted of ten patients with NSCLC-BM (samples N=14) and eleven healthy controls (N=11). Briefly, extracted cfDNA was obtained from CSF samples. Multiplexed sequencing libraries were prepared following an optimized protocol, and sequenced on PromethION flow cell for 72hr by Oxford nanopore technologies. Data were processed with the onboard base and methylation calling, followed by our bioinformatic pipelines for cfDNA size and methylation analysis. Distinct methylation patterns were found on significant CpG sites (fdr-corrected p<0.01) between cancer patients and controls, in both gene-body and promoter region. Biological pathway analysis showed enrichment in essential functions involving PI3K, ERBB2, TNF-α signaling (p<0.03), all of which play a role in NSCLC. Enriched mono-nucleosome levels (p = 1.07e-03) and differentiated mono-/tri- nucleosome ratios (p = 1.34e-03) were found in cancer vs. controls. Overall, our results suggest that a combination of cfDNA methylation and fragmentation can detect NSCLC-BM. This study will benefit BM patients with early detection and better prognosis, and extend our understanding in brain metastases in NSCLC. Citation Format: Tianqi (Kiki) Chen, Billy T. Lau, Xiangqi Bai, Melanie Hayden Gephart, Hanlee P. Ji. Identifying cell free DNA methylation signatures in cerebrospinal fluids for the early detection of brain metastasis in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7019.

Microseparation techniques coupled to mass spectrometry for a sensitive and unequivocal identification of glycopeptides

Capillary electrophoresis (CE) and low-flow liquid chromatography (i.e., micro, capillary, and nanoLC) both coupled to mass spectrometry (MS) are nowadays widely accepted for glycopeptide analysis. However, there are still analytical challenges related to the separation of glycopeptide glycoforms and their unequivocal identification. In the present study, CE-MS and capillary LC-MS (capLC-MS) were evaluated for a robust and high-throughput analysis of glycopeptides. Recombinant human erythropoietin (rhEPO) was selected as model glycoprotein due to its relevance as a biopharmaceutical and its high glycopeptide microheterogeneity. The CE-MS method provided adequate glycopeptide separation for those glycoforms differing in the number of sialic acids. However, the separation of glycoforms with the same sialic acid content but different glycan branching (number of antennas) was not achieved. In contrast, capLC-MS with an appropriate reversed phase C18 column enabled to improve their separation. Furthermore, the analysis of rhEPO glycopeptides with the established microseparation methods coupled to tandem mass spectrometry (CE-MS/MS and capLC-MS/MS) provided specific fragmentation patterns and a more reliable glycoform identification. The capLC-MS/MS method was the most promising as, it was able to detect and unequivocally identify a greater number of glycopeptide glycoforms compared to the CE-MS/MS method, including those with glycolylneuraminic acid, which are necessary to differentiate between endogenous and recombinant hEPO.Data are available via ProteomeXchange with identifier PXD047106.

Investigating the proteases responsible for specific SNAP-25 fragmentation during bacterial production

Investigating the proteases responsible for specific SNAP-25 fragmentation during bacterial production

Circulating DNA reveals a specific and higher fragmentation of the Y chromosome.

Chromosome stability is a key point in genome evolution, particularly that of the Y chromosome. The Y chromosome loss in blood and tumor cells is well established. Through processes that are common to other chromosomes too, the Y chromosome undergoes degradation and fragmentation in the blood stream before elimination. This process gives rise to circulating DNA (cirDNA) fragments, whose examination may provide potential insight into the role of DNA fragmentation in blood for the Y chromosome elimination. In this study, we employed shallow whole genome sequencing (sWGS) to comprehensively assess the total cirDNA and the individual chromosome fragment size profiles in the plasma of healthy male individuals. Here, we show that (i) the fragment size profiles of total circulating DNA (cirDNA) and DNA fragments originating from autosomes and the X chromosome in blood plasma are homogeneous, and have a remarkably low variability (mean CV = 7%) among healthy individuals, (ii) the Y chromosome has a distinct fragment size profile with the accumulation of the fragment < 145 bp and depletion of the dinucleosome-associated fragments (290-390 bp), and its fragment fraction in blood decreases with age. These results indicate a higher fragmentation of the Y chromosome compared to other chromosomes and this in turn might be due to its increased susceptibility to degradation. Our findings pave the way for an elucidation of the impact of chromosomal origin on DNA degradation and the Y chromosome biology.

A validated LC-MS/MS method for quantitative determination of L-dopa in Fagioli di Sarconi beans (Phaseolus vulgaris L.).

An analytical method based on ultrasound assisted extraction (UAE) and liquid chromatography coupled to electrospray tandem mass spectrometry (LC-ESI/MS/MS) was validated and applied for determining L-dopa in four ecotypes of Fagioli di Sarconi beans (Phaseolus vulgaris L.), marked with the European label PGI (Protected Geographical Indication). The selectivity of the proposed method was ensured by the specific fragmentation of the analyte. Simple isocratic chromatographic conditions and mass spectrometric detection in multiple reaction monitoring (MRM) acquisition mode were used for sensitive quantification. The LC-ESI/MS/MS method was validated within a linear range of 0.001-5.000 μg/mL. Values of 0.4 and 1.1ng/mL were obtained for the limits of detection and quantification, respectively. The repeatability, inter-day precision, and recovery values ranges were 0.6%-4.5%, 5.4%-9.9%, and 83%-93%, respectively. Fresh and dried beans, as well as pods, cultivated exclusively with organic methods avoiding any synthetic fertilizers and pesticides were analyzed showing an L-dopa content ranging from 0.020 ± 0.005 to 2.34 ± 0.05 μg/g dry weight.

Argentination: A Silver Bullet for Cannabinoid Separation by Differential Mobility Spectrometry.

As the legality of cannabis continues to evolve globally, there is a growing demand for methods that can accurately quantitate cannabinoids found in commercial products. However, the isobaric nature of many cannabinoids, along with variations in extraction methods and product formulations, makes cannabinoid quantitation by mass spectrometry (MS) challenging. Here, we demonstrate that differential mobility spectrometry (DMS) and tandem-MS can distinguish a set of seven cannabinoids, five of which are isobaric: Δ9-tetrahydrocannabinol (Δ9-THC), Δ8-THC, exo-THC, cannabidiol, cannabichromene, cannabinol, and cannabigerol. Analytes were detected as argentinated species ([M + Ag]+), which, when subjected to collision-induced dissociation, led to the unexpected discovery that argentination promotes distinct fragmentation patterns for each cannabinoid. The unique fragment ions formed were rationalized by discerning fragmentation mechanisms that follow each cannabinoid's MS3 behavior. The differing fragmentation behaviors between species suggest that argentination can distinguish cannabinoids by tandem-MS, although not quantitatively as some cannabinoids produce small amounts of a fragment ion that is isobaric with the major fragment generated by another cannabinoid. By adding DMS to the tandem-MS workflow, it becomes possible to resolve each cannabinoid in a pure N2 environment by deconvoluting the contribution of each cannabinoid to a specific fragmentation channel. To this end, we used DMS in conjunction with a multiple reaction monitoring workflow to assess cannabinoid levels in two cannabis extracts. Our methodology exhibited excellent accuracy, limits of detection (10-20 ppb depending on the cannabinoid), and linearity during quantitation by standard addition (R2 > 0.99).

Drag Coefficient Parameterization under Hurricane Wind Conditions

The influence of small-scale processes at the ocean–atmosphere boundary layer such as spray and foam on the surface waves prediction is studied. Estimates of the effect of including the exact number of specific fragmentation “parachute” type in the spray on the resulting drag coefficient is shown. For the estimates, the numerical simulations within WAVEWATCH III wave model are performed. The parameterizations of wind input are tested within WAVEWATCH III wave model: default ST4 and ST6 parameterizations and the ST1 and ST6 parameterizations used together with the implemented drag coefficient parameterization. The proposed parameterization takes into account the presence of foam and spay. The obtained results are compared with the NDBC buoys data. The importance of small-scale processes for waves at hurricane winds prediction and the prospects for their inclusion in modern numerical wave models is shown.

Discrimination of raffinose and planteose based on porous graphitic carbon chromatography in combination with mass spectrometry

Raffinose and planteose are non-reducing, isomeric trisaccharides present in many higher plants. Structurally, they differ in the linkage of α-D-galactopyranosyl to either glucose C(6) or to C (6′) of fructose, respectively and thus differentiating each other is very challenging. The negative ion mode mass spectrometric analysis is shown to distinguish planteose and raffinose. However, to facilitate the robust identification of planteose in complex mixtures, herein, we have demonstrated the use of porous graphitic carbon (PGC) chromatography combined with QTOF-MS2 analysis. The separation of planteose and raffinose was achieved on PGC, wherein both have recorded different retention time. Detection through MS2 analysis revealed the specific fragmentation patterns for planteose and raffinose that are distinctive to each other. The applicability of this method on oligosaccharides pool extracted from different seeds showed clear separation of planteose that allowed unambiguous identification from complex mixtures. Therefore, we propose PGC-LC-MS/MS can be employed for sensitive, throughput screening of planteose from wider plant sources.

Development of Sequence‐Controlled, Degradable, and Cytocompatible Oligomers with Explicit Fragmentation Pathways

Back Cover: In Article 2200788, Feiyue Xing, Yingshan Zhou, Pu Xiao, and co-workers demonstrate the preparation of novel sequence-controlled pentamers by single unit monomer insertion. The oligomers are degradable due to the ester bonds of 5,6-benzo-2-methylene-1,3-dioxepane undergoing radical ring-opening polymerization. The well-defined structures of the degraded products are fully confirmed by specific fragmentation pathways and show no cytotoxicity for the potential biomedical applications.

Hypochlorous Acid and Chloramines Induce Specific Fragmentation and Cross-Linking of the G1-IGD-G2 Domains of Recombinant Human Aggrecan, and Inhibit ADAMTS1 Activity

Atherosclerosis is a chronic inflammatory disease and a leading cause of mortality. It is characterized by arterial wall plaques that contain high levels of cholesterol and other lipids and activated leukocytes covered by a fibrous cap of extracellular matrix (ECM). The ECM undergoes remodelling during atherogenesis, with increased expression of aggrecan, a proteoglycan that binds low-density-lipoproteins (LDL). Aggrecan levels are regulated by proteases, including a disintegrin and metalloproteinase with thrombospondin motifs 1 (ADAMTS1). Activated leukocytes release myeloperoxidase (MPO) extracellularly, where it binds to proteins and proteoglycans. Aggrecan may therefore mediate colocalization of MPO and LDL. MPO generates hypochlorous acid (HOCl) and chloramines (RNHCl species, from reaction of HOCl with amines on amino acids and proteins) that damage LDL and proteins, but effects on aggrecan have not been examined. The present study demonstrates that HOCl cleaves truncated (G1-IGD-G2) recombinant human aggrecan at specific sites within the IGD domain, with these being different from those induced by ADAMTS1 which also cleaves within this region. Irreversible protein cross-links are also formed dose-dependently. These effects are limited by the HOCl scavenger methionine. Chloramines including those formed on amino acids, proteins, and ECM materials induce similar damage. HOCl and taurine chloramines inactivate ADAMTS1 consistent with a switch from proteolytic to oxidative aggrecan fragmentation. Evidence is also presented for colocalization of aggrecan and HOCl-generated epitopes in advanced human atherosclerotic plaques. Overall, these data show that HOCl and chloramines can induce specific modifications on aggrecan, and that these effects are distinct from those of ADAMTS1.

Photofragmentation specificity of photoionized cyclic amino acids (diketopiperazines) as precursors of peptide building blocks.

The photoionisation and photofragmentation of the two cyclic dipetides cyclo(alanyl-glycine) cGA and cyclo(glycyl-glycine) cGG, have been studied combining experiments and simulations. State selected fragments from the ionized molecules are detected using photo-electron photo-ion coincidence (PEPICO) measurements and specific fragmentation paths are identified and characterized via the use of ion-neutral coincidence maps. The simulations, performed using Quantum Chemistry methods, allow us to infer the fragmentation mechanisms of the ionized and excited molecules. We show that ring opening is followed by emission of the neutral fragments CO and HNCO. In the case of cGG the emission of neutral CO leads to a metastable structure that breaks producing small cationic fragments. The studied cyclic dipeptides evolve under ionizing radiation generating different small aziridin moieties and oxazolidinones. These two species are key reactants to elongate producing peptide chains. The corresponding mechanisms have been computed and show that the reaction requires very low energy and may occur in the presence of ionizing radiation.