Fentanyl analogs (fentalogs) share many structural and mass spectral similarities that make them difficult to differentiate and accurately identify without chromatographic data. In such situations, the expert algorithm for substance identification (EASI) provides superior classification relative to conventional approaches. Using a database of >57,000 replicate electron-ionization mass spectra of 76 fentalogs from ten laboratories, three challenging sets of isomers were studied in detail. To maximize limits of detection, only the 20 most abundant ions were considered. In each case, 50 % of the data from one laboratory served as the training set. On average, the mean absolute residuals between measured and modeled abundances of known positives were five times smaller using EASI than the consensus approach, which used the means of training sets as the exemplar spectra to which all query spectra were compared. With a conservative threshold of zero false positives, EASI identified isovalerylfentanyl from its two closest isomers with an accuracy of 96.7 %, which was similar to 10 % better than the consensus approach. The associated positive likelihood ratios increased from 366 for the consensus approach to more than 4,200 for EASI. When discriminating isovalerylfentanyl spectra from the other 72 fentalogs, EASI provided errorless results with a positive likelihood ratio exceeding 50,000. For all 9 fentalogs, EASI outperformed the consensus approach and the use of Mahalanobis distance as a metric for identifying outliers. In the absence of retention time information, EASI improves confidence in drug identifications, enables inter-laboratory identifications, and reduces the need for acquiring concomitant spectra of standards.

The clothing of suspected arsonists is often analyzed for the presence of ignitable liquids. Personal care products (PCPs) are ubiquitous in our society and can contaminate clothing, so their potential interference is an important consideration in the interpretation of casework samples. Thirty-two samples of various hygiene products and hand cleaners were analyzed using headspace concentration-gas chromatography/mass spectrometry (GC/MS). Despite occasionally containing one or two hydrocarbon compounds found in ignitable liquids, all the antiperspirants and deodorants were readily distinguished from ignitable liquids because they lacked any of the key diagnostic features of ignitable liquids in their extracted ion profiles (EIPs). Two samples labeled as hand cleaners displayed characteristic patterns of heavy petroleum distillates, which, if found on a suspect's clothing, could cause the misleading assumption that the source of the liquid was flammable. However, the petroleum distillates in these two hand-cleaning products were not flammable, according to both their packaging and safety data sheets, because they were formulated as emulsions with water. This study also includes a casework example of a heavy petroleum distillate in a fire debris sample. However, the co-presence of abundant fatty acid methyl esters increased the probability that the original source was either a biodiesel blend or a non-flammable formulation product and therefore raises reasonable doubt about the flammability of the original product. The results of this work are limited by the GC/MS method, which could not detect volatiles like acetone, propanol, and ethanol eluting before a retention index of 700 nor non-volatile emulsifiers/surfactants.

RationaleCharge transfer dissociation (CTD) is a novel fragmentation technique that demonstrates enhanced structural characterization for a wide variety of molecules compared to standard fragmentation techniques like collision-induced dissociation (CID). Alternative fragmentation techniques, such as electron transfer dissociation, electron capture dissociation, and ultraviolet photodissociation, also overcome many of the shortfalls of CID, but none of them are a silver bullet that can adequately characterize a wide variety of structures and charge states of target compounds. Given the diversity of structural classes and their occasional obstinance towards certain activation techniques, alternative fragmentation techniques are required that rely on novel or alternative modes of activation.MethodsHerein, we present a step-by-step protocol for the installation of CTD on a quadrupole ion trap mass spectrometer and best practices for optimizing the signal-to-noise ratio and acquisition times for CTD mass spectra.ResultsIn addition to two CTD installations in the Jackson laboratory, CTD has also been installed, and is currently in operation, on two 3D ion trap mass spectrometers in France: one in the laboratory of Dr. David Ropartz and Dr. Helene Rogneaux at INRAE in Nantes, and the other in the laboratory of Dr. Jean-Yves Salpin at Universite d'evry Val-d'Essonne, part of the Paris-Saclay University system.ConclusionsHere, we provide a visual protocol to help others accomplish the instrument modification.

Thisis the second of two manuscripts describing how general linearmodeling (GLM) of a selection of the most abundant normalized fragmention abundances of replicate mass spectra from one laboratory can beused in conjunction with binary classifiers to enable specific andselective identifications with reportable error rates of spectra fromother laboratories. Here, the proof-of-concept uses a training setof 128 replicate cocaine spectra from one crime laboratory as thebasis of GLM modeling. GLM models for the 20 most abundant fragmentsof cocaine were then applied to 175 additional test/validation cocainespectra collected in more than a dozen crime laboratories and 716known negative spectra, which included 10 spectra of three diastereomersof cocaine. Spectral similarity and dissimilarity between the measuredand predicted abundances were assessed using a variety of conventionalmeasures, including the mean absolute residual and NIST's spectralsimilarity score. For each spectral measure, GLM predictions werecompared to the traditional exemplar approach, which used the averageof the cocaine training set as the consensus spectrum for comparisons.In unsupervised models, EASI provided better than a 95% true positiverate for cocaine with a 0% false positive rate. A supervised binarylogistic regression model provided 100% accuracy and no errors usingEASI-predicted abundances of only four peaks at m/z 152, 198, 272, and 303. Regardless of the measureof spectral similarity, error rates for identifications using EASIwere superior to the traditional exemplar/consensus approach. As asupervised binary classifier, EASI was more reliable than using Mahalanobisdistances.

Mass spectrometry has made profound contributions to the criminal justice system by providing an instrumental method of analysis that delivers exquisite analytical figures of merit for a wide variety of samples and analytes. Applications include the characterization of trace metal impurities in hair and glass to the identification of drugs, explosives, polymers, and ignitable liquids. This review describes major historical developments and, where possible, relates the developed capabilities to casework and legal precedents. This review also provides insight into how historical applications have evolved into, and out of, modern consensus standards. Unlike many pattern-based techniques and physical-matching methods, mass spectrometry has strong scientific foundations and a long history of successful applications that have made it one of the most reliable and respected sources of scientific evidence in criminal and civil cases. That said, in several appellate decisions in which mass spectrometric evidence was challenged but admitted, decisions sometimes still went against the mass spectrometric data anyway, which goes to show that mass spectrometric evidence is always just one piece of the larger legal puzzle.

This study aims to resolve one of the longest-standing problems in mass spectrometry, which is how to accurately identify an organic substance from its mass spectrum when a spectrum of the suspected substance has not been analyzed contemporaneously on the same instrument. Part one of this two-part report describes how Rice-Ramsperger-Kassel-Marcus (RRKM) theory predicts that many branching ratios in replicate electron-ionization mass spectra will provide approximately linear correlations when analysis conditions change within or between instruments. Here, proof-of-concept general linear modeling is based on the 20 most abundant fragments in a database of 128 training spectra of cocaine collected over 6 months in an operational crime laboratory. The statistical validity of the approach is confirmed through both analysis of variance (ANOVA) of the regression models and assessment of the distributions of the residuals of the models. General linear modeling models typically explain more than 90% of the variance in normalized abundances. When the linear models from the training set are applied to 175 additional known positive cocaine spectra from more than 20 different laboratories, the linear models enabled ion abundances to be predicted with an accuracy of <2% relative to the base peak, even though the measured abundances vary by more than 30%. The same models were also applied to 716 known negative spectra, including the diastereomers of cocaine: allococaine, pseudococaine, and pseudoallococaine, and the residual errors were larger for the known negatives than for known positives. The second part of the manuscript describes how general linear regression modeling can serve as the basis for binary classification and reliable identification of cocaine from its diastereomers and all other known negatives.

The combination of helium charge transfer dissociation mass spectrometry (He-CTD-MS) with ultrahigh performance liquid chromatography (UHPLC) is presented for the analysis of a complex mixture of acidic and neutral human milk oligosaccharides (HMOs). The research focuses on the identification of the monosaccharide sequence, the branching patterns, the sialylation/fucosylation arrangements, and the differentiation of isomeric oligosaccharides in the mixture. Initial studies first optimized the conditions for the UHPLC separation and the He-CTD-MS conditions. Results demonstrate that He-CTD is compatible with UHPLC timescales and provides unambiguous glycosidic and cross-ring cleavages from both the reducing and the nonreducing ends, which is not typically possible using collision-induced dissociation. He-CTD produces informative fragments, including 0,3An and 0,4An ions, which have been observed with electron transfer dissociation, electron detachment dissociation, and ultraviolet photodissociation (UVPD) and are crucial for differentiating the α-2,3- versus α-2,6-linked sialic acid (Neu5Ac) residues present among sialyllacto-N-tetraose HMOs. In addition to the linkage positions, He-CTD is able to differentiate structural isomers for both sialyllacto-N-tetraoses and lacto-N-fucopentaoses structures by providing unique, unambiguous cross-ring cleavages of types 0,2An, 0,2Xn, and 1,5An while preserving most of the labile Neu5Ac and fucose groups.

Research in natural products (NPs) has gained interest as drug developers turn to nature to combat problems with drug resistance, drug delivery, and emerging diseases. Whereas NPs offer a tantalizing source of new pharmacologically active compounds, their structural complexity presents a challenge for analytical characterization and organic synthesis. Of particular concern is the characterization of cyclic-, polycyclic-, or macrocyclic compounds. One example of endogenous compounds as inspiration for NP development are cobalamins, like vitamin B12. An example of exogenous NPs is the class of macrolides that includes erythromycin. Both classes of macrocycles feature analogues with a range of modifications on their macrocyclic cores, but because of their cyclic nature, they are generally resistant to fragmentation by collision-induced dissociation (CID). In the present work, charge-transfer dissociation (CTD) was employed, with or without supplemental collisional activation, to produce radical-driven, high-energy fragmentation products of different macrocyclic precursors. With the assistance of collisional activation of CTnoD products, CTD frequently cleaved two covalent bonds within the macrocycle cores to reveal rich, informative spectra that helped identify sites of modification and resolve structural analogues. In a third example of macrocycle fragmentation, CTD enabled an impurity in a biological sample to be characterized as a cyclic polymer of nylon-6,6. In each example, CTD spectra are starkly different from CID and are highly reminiscent of other highenergy fragmentation techniques like extreme ultraviolet dissociative photoionization (XUV-DPI) and electron ionization-induced dissociation (EID). The results indicate that CTD-MS is a useful tool for the characterization of natural and synthetic macrocycles.

The ability to understand the function of a protein often relies on knowledge about its detailed structure. Sometimes, seemingly insignificant changes in the primary structure of a protein, like an amino acid substitution, can completely disrupt a protein's function. Long-lived proteins (LLPs), which can be found in critical areas of the human body, like the brain and eye, are especially susceptible to primary sequence alterations in the form of isomerization and epimerization. Because long-lived proteins do not have the corrective regeneration capabilities of most other proteins, points of isomerism and epimerization that accumulate within the proteins can severely hamper their functions and can lead to serious diseases like Alzheimer's disease, cancer and cataracts. Whereas tandem mass spectrometry (MS/MS) in the form of collision-induced dissociation (CID) generally excels at peptide characterization, MS/MS often struggles to pinpoint modifications within LLPs, especially when the differences are only isomeric or epimeric in nature. One of the most prevalent and difficult-to-identify modifications is that of aspartic acid between its four isomeric forms: L-Asp, L-isoAsp, D-Asp, and D-isoAsp. In this study, peptides containing isomers of Asp were analyzed by charge transfer dissociation (CTD) mass spectrometry to identify spectral features that could discriminate between the different isomers. For the four isomers of Asp in three model peptides, CTD produced diagnostic ions of the form cn+57 on the N-terminal side of iso-Asp residues, but not on the N-terminal side of Asp residues. Using CTD, the L- and D forms of Asp and isoAsp could also be differentiated based on the relative abundance of y- and z ions on the C-terminal side of Asp residues. Differentiation was accomplished through a chiral discrimination factor, R, which compares an ion ratio in a spectrum of one epimer or isomer to the same ion ratio in the spectrum of a different epimer or isomer. The R values obtained using CTD are as robust and statistically significant as other fragmentation techniques, like radical directed dissociation (RDD). In summary, the extent of backbone and side-chain fragments produced by CTD enabled the differentiation of isomers and epimers of Asp in a variety of peptides.

The ability to understand the function of a protein often relies on knowledge about its detailed structure. Sometimes, seemingly insignificant changes in the primary structure of a protein, like an amino acid substitution, can completely disrupt a protein’s function. Long-lived proteins (LLPs), which can be found in critical areas of the human body, like the brain and eye, are especially susceptible to primary sequence alterations in the form of isomerization and epimerization. Because long-lived proteins do not have the corrective regeneration capabilities of most other proteins, points of isomerism and epimerization that accumulate within the proteins can severely hamper their functions and can lead to serious diseases like Alzheimer’s disease, cancer and cataracts. Whereas tandem mass spectrometry (MS/MS) in the form of collision-induced dissociation (CID) generally excels at peptide characterization, MS/MS often struggles to pinpoint modifications within LLPs, especially when the differences are only isomeric or epimeric in nature. One of the most prevalent and difficult-to-identify modifications is that of aspartic acid between its four isomeric forms: L-Asp, L-isoAsp, D-Asp, and D-isoAsp. In this study, peptides containing isomers of Asp were analyzed by charge transfer dissociation (CTD) mass spectrometry to identify spectral features that could discriminate between the different isomers. For the four isomers of Asp in three model peptides, CTD produced diagnostic ions of the form cn+57 on the N-terminal side of iso-Asp residues, but not on the N-terminal side of Asp residues. Using CTD, the Land D forms of Asp and isoAsp could also be differentiated based on the relative abundance of yand z ions on the C-terminal side of Asp residues. Differentiation was accomplished through a chiral discrimination factor, R, which compares an ion ratio in a spectrum of one epimer or isomer to the same ion ratio in the spectrum of a different epimer or isomer. The R values obtained using CTD are as robust and statistically significant as other fragmentation techniques, like radical directed dissociation (RDD). In summary, the extent of backbone and side-chain fragments produced by CTD enabled the differentiation of isomers and epimers of Asp in a variety of peptides.

Charge transfer dissociation mass spectrometry (CTD-MS) has been shown to induce high energy fragmentation of biological ions in the gas phase and provide fragmentation spectra similar to extreme ultraviolet photodissociation (XUVPD). To date, CTD has typically employed helium cations with kinetic energies between 4-10 keV to initiate radical-directed fragmentation of analytes. However, as a reagent, helium has recently been listed as a critical mineral that is becoming scarcer and more expensive, so this study explored the potential for using cheaper and more readily available reagent gases. A model peptide, bradykinin, and a model oligosaccharide, κ-carrageenan with a degree of polymerization of 4, were fragmented using a variety of CTD reagent gases, which included helium, hydrogen, oxygen, nitrogen, argon and lab air. The CTD results were also contrasted with low-energy collision-induced dissociation (LE-CID), which were collected on the same 3D ion trap. Using constant reagent ion fluxes and kinetic energies, all five alterative reagent gases generated remarkably consistent sequence coverage and fragmentation efficiencies relative to He-CTD, which suggests that the ionization energy of the reagent gas has a negligible effect on the activation of the biological ions. The CTD efficiencies of all the gases ranged from 11-13% for bradykinin and 7-8% for κ-carrageenan. Within these tight ranges, the abundance of the CTnoD peak of bradykinin and the efficiency of CTD fragmentation of bradykinin both correlated with the ionization energy of the CTD reagent gas, which suggests that resonant charge transfer plays a small role in the activation of this peptide. The majority of the excitation energy for bradykinin and for κ-carrageenan comes from an electron stopping mechanism, which is described by long-range interactions between the reagent cations and electrons in the highest occupied molecular orbitals (HOMOs) of the biological ions. The CTD spectra do not provide any evidence for covalently bound products between the biological ions and the more-reactive gases like hydrogen, oxygen and nitrogen, which implies that the high kinetic energies of the reagent ions make them unavailable for covalent reactions. This work demonstrates that any of the substitute reagent gases tested are viable options for future CTD-MS experiments.

RATIONALE The binding affinity of an antibody can be substantially altered by the replacement of Leu with Ile, and vice versa, so the ability to identify the correct isomer using mass spectrometric tools helps resolve important biological questions. Tandem mass spectrometry approaches for Xle discrimination have been developed, but they all have certain limitations. METHODS Four model peptides and two wild-type peptide sequences containing either leucine (Leu) or isoleucine (Ile) residues were subjected to charge transfer dissociation (CTD) mass spectrometry on a modified 3D ion trap. The peptides were analyzed in both the 1+ and 2+ charge states, and the results were compared to conventional CID spectra of the same peptides on the same instrument. RESULTS CTD resulted in 100% sequence coverage for each of the studied peptides and provided a variety of side-chain cleavages, including d-, w-, and v ions. Using CTD, reliable d- and w ions of Xle residues were observed more than 80% of the time. When present, d ions are typically greater than 10% the abundance of the corresponding a ions from which they derived, and w ions are typically more abundant than the z ions from which they derive. CONCLUSIONS CTD has the benefit of being applicable to both 1+ and 2+ precursor ions, and the overall performance is comparable with other high-energy activation techniques like HECD and UVPD. CTD does not require chemical modifications of the precursor peptides, nor does it require additional levels of isolation and fragmentation.

Various samples of the Eastern oyster, Crassostrea virginica, were collected from five harvest bay areas in the Gulf of Mexico coastal waters of Florida (FL), Louisiana (LA) and Texas (TX). Cadmium and lead concentrations from the extracted whole-body soft tissues were analyzed by inductively coupled plasma-mass spectrometry (ICP-MS), and bulk δ13C and δ15N isotope ratios and amino-acid-specific δ13C values were analyzed via isotope ratio mass-spectrometry (IRMS). The combined data was subjected to multivariate statistical analysis to assess whether oysters could be linked to their harvest area. Results indicate that discriminant analysis using the δ13C values of five amino acids-serine, glycine, valine, lysine and phenylalanine-could discriminate oysters from two adjacent harvesting in Florida with 90% success rate, using leave-one-out cross validation. The combination of trace elements and isotope ratios could also predict geographic provenance of oysters with a success rate superior to the isolated use of each technique. The combinatory approach proposed in this study is a proof-of-concept that compound specific stable isotope analysis is a potential tool for oyster fisheries managers, wildlife, and food safety enforcement officers, as well as to forensics and ecology research areas, although significantly more work would need to be completed to fully validate the approach and achieve more reliable statistical results.

Pectins are natural polysaccharides made from galacturonic acid residues, and they are widely used as an excipient in food and pharmaceutical industries. The degree of methyl-esterification, the monomeric composition, and the linkage pattern are all important factors that influence the physical and chemical properties of pectins, such as the solubility. This work focuses on the successful online coupling of charge transfer dissociation-mass spectrometry (CTD-MS) with ultrahigh-performance liquid chromatography (UHPLC) to differentiate isomers of oligogalacturonans derived from citrus pectins. This work employed CTD fragmentation of the pectin mixtures in data-dependent acquisition mode. Compared to the UHPLC with collision-induced dissociation mass spectrometry (UHPLC-CID-MS), UHPLC-CTD-MS yielded fewer ambiguous ions and more structurally informative results. The developed UHPLC-CTD-MS method resulted in abundant cross-ring cleavages-and especially 1,4Xn, 1,5Xn, and 2,4Xn ions-which helped to identify most of the isomers. The Gal A isomers differed only in the methyl group position along the galacturonic acid backbone. The combination of CTD in real time with UHPLC provides a new tool for the structural characterization of complex mixtures of oligogalacturonans and potentially other classes of oligosaccharides.

Alkali and alkaline earth metal adducts of a branched glycan, XXXG, were analyzed with helium charge transfer dissociation (He-CTD) and low-energy collision-induced dissociation (LE-CID) to investigate if metalation would impact the type of fragments generated and the structural characterization of the analyte. The studied adducts included 1+ and 2+ precursors involving one or more of the cations: H+, Na+, K+, Ca2+, and Mg2+. Regardless of the metal adduct, He-CTD generated abundant and numerous glycosidic and cross-ring cleavages that were structurally informative and able to identify the 1,4-linkage and 1,6-branching patterns. In contrast, the LE-CID spectra mainly contained glycosidic cleavages, consecutive fragments, and numerous neutral losses, which complicated spectral interpretation. LE-CID of [M + K + H](2+) and [M + Na](+) precursors generated a few cross-ring cleavages, but they were not sufficient to identify the 1,4-linkage and 1,6-branching pattern of the XXXG xyloglucan. He-CTD predominantly generated 1+ fragments from 1+ precursors and 2+ product ions from 2+ precursors, although both LE-CID and He-CTD were able to generate 1+ product ions from 2+ adducts of magnesium and calcium. The singly charged fragments derive from the loss of H+ from the metalated product ions and the formation of a protonated complementary product ion; such observations are similar to previous reports for magnesium and calcium salts undergoing electron capture dissociation (ECD) activation. However, during He-CTD, the [M + Mg](2+) precursor generated more singly charged product ions than [M + Ca](2+), either because Mg has a higher second ionization potential than Ca or because of conformational differences and the locations of the charging adducts during fragmentation. He-CTD of the [M + 2Na](2+) and the [M + 2 K](2+) precursors generated singly charged product ions from the loss of a sodium ion and potassium ion, respectively. In summary, although the metal ions influence the mass and charge state of the observed product ions, the metal ions had a negligible effect on the types of cross-ring cleavages observed.

This work focuses on the application of charge transfer dissociation (CTD) to a mannuronic acid oligomer with different extents of Na/H exchange. The goals were to determine if CTD could effectively characterize the oligomer and to investigate how Na/H exchanges impact the CTD fragmentation pathways of even a simple oligomer like mannuronic acid. CTD provided unique and unambiguous fragments that helped determine the 1-4-linkage pattern between core mannuronic acid residues. CTD of precursors with no Na/H exchange mainly had unambiguous product ions. However, CTD of precursor ions containing two or more Na/H exchanges increased the number of possible product ion identities and yielded many isobaric product ions and, hence, more ambiguity in spectral assignments. The use of 18O labelling on the reducing terminus helped resolve some isobaric interferences between A/X, and C/Z ions but created some nominal overlap with fragment ions containing Na/H exchanges. CTD spectra demonstrated that when three or more Na/H exchanges are present in the precursor, there are at least two main structures of Na/H exchange sites: the first structure contains three Na/H exchanges on adjacent sugars closest to the non-reducing terminus and a second structure contains two adjacent Na/H exchanges on the reducing terminus. When four or five Na/H exchanges are present, the positions of the fourth and fifth sodium ions could not be confirmed, presumably because the isolated precursors contain a distribution of structures with Na/H exchanges in different positions. In the absence of Na/H exchanges, He-CTD spectra provided rich structural information and very few ambiguous product ions. Therefore, until CTD is coupled to high-resolution mass spectrometers—which could readily resolve the ambiguity in most of the peak identities—precursors that contain the fewest possible number of Na/H exchanges will provide the most confident peak assignments and structural characterization.

Rationale The function of a protein or the binding affinity of an antibody can be substantially altered by the replacement of leucine (Leu) with isoleucine (Ile), and vice versa, so the ability to identify the correct isomer using mass spectrometry can help resolve important biological questions. Tandem mass spectrometry approaches for Leu/Ile (Xle) discrimination have been developed, but they all have certain limitations. Methods Four model peptides and two wild-type peptide sequences containing either Leu or Ile residues were subjected to charge transfer dissociation (CTD) mass spectrometry on a modified three-dimensional ion trap. The peptides were analyzed in both the 1+ and 2+ charge states, and the results were compared to conventional collision-induced dissociation spectra of the same peptides obtained using the same instrument. Results CTD resulted in 100% sequence coverage for each of the studied peptides and provided a variety of side-chain cleavages, including d, w and v ions. Using CTD, reliable d and w ions of Xle residues were observed more than 80% of the time. When present, d ions are typically greater than 10% of the abundance of the corresponding a ions from which they derive, and w ions are typically more abundant than the z ions from which they derive. Conclusions CTD has the benefit of being applicable to both 1+ and 2+ precursor ions, and the overall performance is comparable to that of other high-energy activation techniques like hot electron capture dissociation and UV photodissociation. CTD does not require chemical modifications of the precursor peptides, nor does it require additional levels of isolation and fragmentation.

Ultra-high-performance liquid chromatography (UHPLC) with charge transfer dissociation mass spectrometry (CTD-MS) is presented for the analysis of a mixture of complex sulfated oligosaccharides. The mixture contained kappa (κ), iota (ι), and lambda (λ) carrageenans that contain anhydro bridges, different degrees of sulfation ranging from one to three per dimer, different positioning of the sulfate groups along the backbone, and varying degrees of polymerization (DP) between 4 and 12. Optimization studies using standard mixtures of carrageenans helped establish the optimal conditions for online UHPLC-CTD-MS/MS analysis. Optimization included (1) UHPLC conditions; (2) ion source conditions, such as the capillary voltage, drying gas and nebulizing gas temperature, and flow rate; and (3) CTD-MS conditions, including data-dependent CTD-MS. The UHPLC-CTD results were contrasted with UHPLC-CID results of the same mixture on the same instrument. Whereas CID tends to produce B/Y and C/Z ions with many neutral losses, CTD produced more abundant A/X ions and less abundant neutral losses, which enabled more confident structural detail. The results demonstrate that He-CTD is compatible with the timescale of UHPLC and provides more structural information about carrageenans compared to state-of-the-art methods like UHPLC-CID analysis.