Search

Per- and polyfluoroalkyl substances (PFAS) are widespread, persistent environmental contaminants that have been linked to various health issues. Comprehensive PFAS analysis often relies on ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC HRMS) and molecular fragmentation (MS/MS). However, the selection and fragmentation of ions for MS/MS analysis using data-dependent analysis results in only the topmost abundant ions being selected. To overcome these limitations, All Ions fragmentation (AIF) can be used alongside data-dependent analysis. In AIF, ions across the entire m / z range are simultaneously fragmented; hence, precursor-fragment relationships are lost, leading to a high false positive rate. We introduce IonDecon, which filters All Ions data to only those fragments correlating with precursor ions. This software can be used to deconvolute any All Ions files and generates an open source DDA formatted file, which can be used in any downstream nontargeted analysis workflow. In a neat solution, annotation of PFAS standards using IonDecon and All Ions had the exact same false positive rate as when using DDA; this suggests accurate annotation using All Ions and IonDecon. Furthermore, deconvoluted All Ions spectra retained the most abundant peaks also observed in DDA, while filtering out much of the artifact peaks. In complex samples, incorporating AIF and IonDecon into workflows can enhance the MS/MS coverage of PFAS (more than tripling the number of annotations in domestic sewage). Deconvolution in complex samples of All Ions data using IonDecon did retain some false fragments (fragments not observed when using ion selection, which were not isotopes or multimers), and therefore DDA and intelligent acquisition methods should still be acquired when possible alongside All Ions to decrease the false positive rate. Increased coverage of PFAS can inform on the development of regulations to address the entire PFAS problem, including both legacy and newly discovered PFAS.

Meningiomas are among the most common brain tumors that arise from the leptomeningeal cover of the brain and spinal cord and account for around 37% of all central nervous system tumors. According to the World Health Organization, meningiomas are classified into three histological subtypes: benign, atypical, and anaplastic. Sometimes, meningiomas with a histological diagnosis of benign tumors show clinical characteristics and behavior of aggressive tumors. In this study, we examined the metabolomic and lipidomic profiles of meningioma tumors, focusing on comparing low-grade and high-grade tumors and identifying potential markers that can discriminate between benign and malignant tumors. High-resolution mass spectrometry coupled to liquid chromatography was used for untargeted metabolomics and lipidomics analyses of 85 tumor biopsy samples with different meningioma grades. We then applied feature selection and machine learning techniques to find the features with the highest information to aid in the diagnosis of meningioma grades. Three biomarkers were identified to differentiate low- and high-grade meningioma brain tumors. The use of mass-spectrometry-based metabolomics and lipidomics combined with machine learning analyses to prospect and characterize biomarkers associated with meningioma grades may pave the way for elucidating potential therapeutic and prognostic targets.

Bile acids (BAs) are a complex suite of clinically relevant metabolites that include many isomers. Liquid chromatography coupled to mass spectrometry (LC-MS) is an increasingly popular technique due to its high specificity and sensitivity; nonetheless, acquisition times are generally 10-20 min, and isomers are not always resolved. In this study, the application of ion mobility (IM) spectrometry coupled to MS was investigated to separate, characterize, and measure BAs. A subset of 16 BAs was studied, including three groups of isomers belonging to unconjugated, glycine-conjugated, and taurine-conjugated BA classes. A variety of strategies were explored to increase BA isomer separation such as changing the drift gas, measuring different ionic species (i.e., multimers and cationized species), and enhancing the instrumental resolving power. In general, Ar, N 2 , and CO 2 provided the best peak shape, resolving power ( R p ), and separation, especially CO 2 ; He and SF 6 were less preferable. Furthermore, measuring dimers versus monomers improved isomer separation due to enhanced gas-phase structural differences. A variety of cation adducts other than sodium were characterized. Mobility arrival times and isomer separation were affected by the choice of adduct, which was shown to be used to target certain BAs. Finally, a novel workflow that involves high-resolution demultiplexing in combination with dipivaloylmethane ion-neutral clusters was implemented to improve R p dramatically. A maximum R p increase was observed with lower IM field strengths to obtain longer drift times, increasing R p from 52 to 187. A combination of these separation enhancement strategies demonstrates great potential for rapid BA analysis.

Novel synthetic anabolic androgenic steroids have been developed not only to dodge current antidoping tests at the professional sports level, but also for consumption by noncompetitive bodybuilders. These novel anabolic steroids are commonly referred to as "designer steroids" and pose a significant risk to users because of the lack of testing for toxicity and safety in animals or humans. Manufacturers of designer steroids dodge regulation by distributing them as nutritional or dietary supplements. Improving the throughput and accuracy of screening tests would help regulators to stay on top of illicit anabolic steroids. High-field asymmetric-waveform ion mobility spectrometry (FAIMS) utilizes an alternating asymmetric electric field to separate ions by their different mobilities at high- and low-fields as they travel through the separation space. When coupled to mass spectrometry (MS), FAIMS enhances the separation of analytes from other interfering compounds with little to no increase in analysis time. Here we investigate the effects of adding various cation species to sample solutions for the separation of structurally similar or isomeric anabolic androgenic steroids. FAIMS-MS spectra for these cation-modified samples show an increased number of compensation field (CF) peaks, some of which are confirmed to be unique for one steroid isomer over another. The CF peaks observed upon addition of cation species correspond to both monomer steroid-cation adduct ions and larger multimer ion complexes. Notably, the number of CF peaks and their CF shifts do not appear to have a straightforward relationship with cation size or electronegativity. Future directions aim at investigating the structures for these analyte-cation adduct ions for building a predictive model for their FAIMS separations.

Opioid addiction is an escalating problem that is compounded by the introduction of synthetic opiate analogues such as fentanyl. Screening methods for these compound classes are challenged by the availability of synthetically manufactured analogues, including isomers of existing substances. High-field asymmetric-waveform ion mobility spectrometry (FAIMS) utilizes an alternating asymmetric electric field to separate ions by their different mobilities at high and low fields as they travel through the separation space. When coupled to mass spectrometry (MS), FAIMS enhances the separation of analytes from other interfering compounds with little to no increase in analysis time. Addition of solvent vapor into the FAIMS carrier gas has been demonstrated to enable and improve the separation of isomers. Here we investigate the effects of several solvents for the separation of four opioids. FAIMS-MS spectra with added solvent vapors show dramatic compensation field (CF) shifts for opioid [M+H] + ions when compared to spectra acquired using dry nitrogen. Addition of vapor from aprotic solvents, such as acetonitrile and acetone, produces significantly improved resolution between the tested opioids, with baseline resolution achieved between certain opioid isomers. For protic solvents, notable CF shift differences were observed in FAIMS separations between addition of water vapor and vapors from small alcohols. Graphical Abstract.

Drift tube ion mobility coupled with mass spectrometry was used to investigate the gas-phase structure of 25-hydroxyvitamin D3 (25OHD3) and D2 (25OHD2) epimers, and to evaluate its potential in rapid separation of these compounds. Experimental results revealed two distinct drift species for the 25OHD3 sodiated monomer, whereas only one of these conformations was observed for its epimer (epi25OHD3). The unique species allowed 25OHD3 to be readily distinguished, and the same pattern was observed for 25OHD2 epimers. Theoretical modeling of 25OHD3 epimers identified energetically stable gas-phase structures, indicating that both compounds may adopt a compact "closed" conformation, but that 25OHD3 may also adopt a slightly less energetically favorable "open" conformation that is not accessible to its epimer. Calculated theoretical collision cross-sections for these structures agreed with experimental results to <2%. Experimentation indicated that additional energy in the ESI source (i.e., increased temperature, spray voltage) affected the ratio of 25OHD3 conformations, with the less energetically favorable "open" conformation increasing in relative intensity. Finally, LC-IM-MS results yielded linear quantitation of 25OHD3, in the presence of the epimer interference, at biologically relevant concentrations. This study demonstrates that ion mobility can be used in tandem with theoretical modeling to determine structural differences that contribute to drift separation. These separation capabilities provide potential for rapid (<60 ms) identification of 25OHD3 and 25OHD2 in mixtures with their epimers. Graphical Abstract ᅟ.

Untargeted omics analyses aim to comprehensively characterize biomolecules within a biological system. Changes in the presence or quantity of these biomolecules can indicate important biological perturbations, such as those caused by disease. With current technological advancements, the entire genome can now be sequenced; however, in the burgeoning fields of lipidomics, only a subset of lipids can be identified. The recent emergence of high resolution tandem mass spectrometry (HR-MS/MS), in combination with ultra-high performance liquid chromatography, has resulted in an increased coverage of the lipidome. Nevertheless, identifications from MS/MS are generally limited by the number of precursors that can be selected for fragmentation during chromatographic elution. Therefore, we developed the software IE-Omics to automate iterative exclusion (IE), where selected precursors using data-dependent topN analyses are excluded in sequential injections. In each sequential injection, unique precursors are fragmented until HR-MS/MS spectra of all ions above a user-defined intensity threshold are acquired. IE-Omics was applied to lipidomic analyses in Red Cross plasma and substantia nigra tissue. Coverage of the lipidome was drastically improved using IE. When applying IE-Omics to Red Cross plasma and substantia nigra lipid extracts in positive ion mode, 69% and 40% more molecular identifications were obtained, respectively. In addition, applying IE-Omics to a lipidomics workflow increased the coverage of trace species, including odd-chained and short-chained diacylglycerides and oxidized lipid species. By increasing the coverage of the lipidome, applying IE to a lipidomics workflow increases the probability of finding biomarkers and provides additional information for determining etiology of disease. Graphical Abstract ᅟ.

Ion mobility-mass spectrometry (IM-MS) has recently seen increased use in the analysis of small molecules, especially in the field of metabolomics, for increased breadth of information and improved separation of isomers. In this study, steroid epimers androsterone and trans-androsterone were analyzed with IM-MS to investigate differences in their relative mobilities. Although sodiated monomers exhibited very similar collision cross-sections (CCS), baseline separation was observed for the sodiated dimer species (R S = 1.81), with measured CCS of 242.6 and 256.3 Å 2 , respectively. Theoretical modeling was performed to determine the most energetically stable structures of solution-phase and gas-phase monomer and dimer structures. It was revealed that these epimers differ in their preferred dimer binding mode in solution phase: androsterone adopts a R=O - Na + - OH-R' configuration, whereas trans-androsterone adopts a R=O - Na + - O=R' configuration. This difference contributes to a significant structural variation, and subsequent CCS calculations based on these structures relaxed in the gas phase were in agreement with experimentally measured values (ΔCCS ~ 5%). Additionally, these calculations accurately predicted the relative difference in mobility between the epimers. This study illustrates the power of combining experimental and theoretical results to better elucidate gas-phase structures. Graphical Abstract ᅟ.

Skeletal muscles are composed of heterogeneous muscle fibers that have different physiological, morphological, biochemical, and histological characteristics. In this work, skeletal muscles extensor digitorum longus, soleus, and whole gastrocnemius were analyzed by matrix-assisted laser desorption/ionization mass spectrometry to characterize small molecule metabolites of oxidative and glycolytic muscle fiber types as well as to visualize biomarker localization. Multivariate data analysis such as principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were performed to extract significant features. Different metabolic fingerprints were observed from oxidative and glycolytic fibers. Higher abundances of biomolecules such as antioxidant anserine as well as acylcarnitines were observed in the glycolytic fibers, whereas taurine and some nucleotides were found to be localized in the oxidative fibers.

Our long-time association with Jim Morrison and the work that came from it is the result of a series of fortunate coincidences. We are pleased to be able to share recollections here of our interactions with Jim and how his life and work have influenced us and the field of mass spectrometry.

Detection of drugs in tissue typically requires extensive sample preparation in which the tissue is first homogenized, followed by drug extraction, before the extracts are finally analyzed by LC/MS. Directly analyzing drugs in intact tissue would eliminate any complications introduced by sample pretreatment. A matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS(n)) method as been developed for the quantification of cocaine present in postmortem brain tissue of a chronic human cocaine user. It is shown that tandem mass spectrometry (MS(2) and MS(3) increase selectivity, which is critical for differentiating analyte ions from background ions such as matrix clusters and endogenous compounds found in brain tissue. It is also shown that the use of internal standards corrects for signal variability during quantitative MALDI, which can be caused by inhomogeneous crystal formation, inconsistent sample preparation, and laser shot-to-shot variability. The MALDI-MS(n) method developed allows for a single MS(3) experiment that uses a wide isolation window to isolate both analyte and internal standard target ions. This method is shown to provide improved precision [approximately 10-20 times reduction in percent relative standard deviation (%RSD)] for quantitative analysis compared to using two alternating MS(3) experiments that separately isolate the target analyte and internal standard ions., (2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved.)

Propofol (2,6-diisopropyl phenol) is a widely used intravenous anesthetic. To define its pharmacokinetics and pharmacodynamics, methods for its quantitation in biological matrixes have been developed, but its pattern of mass spectral fragmentation is unknown. We found that fragmentation of the [M - H](-) ion (m/z 177) of propofol in both APCI MS/MS and ESI MS/MS involves the stepwise loss of a methyl radical and a hydrogen radical from one isopropyl side chain to give the most intense product ion, [M -H - CH(4)](-), at m/z 161. This two-step process is also the preferred mode of fragmentation for similar branched alkyl substituted phenols. This mode of fragmentation of the [M - H](-) ion is supported by three independent lines of evidence: (1) the presence of the intermediary [M - H - CH(3)](-) radical ion under conditions of reduced collision energy, (2) the determination of the mass of the predominant [M - H - CH(4)](-) product ion by high resolution mass spectrometry, and (3) the pattern of product ions resulting from further fragmentation of the [M - H - CH(4)](-) product ion. Phenols with a single straight chain alkyl substituent, in contrast, undergo beta elimination of the alkyl radical irrespective of the length of the alkyl chain, yielding the most intense product ion at m/z 106. This product ion represents a special case of a stable intermediary radical for the two-step process described for branched side chains, because further elimination of a hydrogen radical from the beta carbon is not possible.

The efficiency of the collision-induced dissociation (CID) process as a function of the internal energy deposited into the ion during the ionization event was evaluated. (M + H)+ ions of pyrrole, pyrrolidine, pyridine and piperidine (five and six-membered ring heterocyclics) were generated by chemical ionization (CI). The internal energy of the ions was varied by using different reagent gases. Both high-energy (keV) and low-energy (eV) CID were performed on these ions. The experiments showed that the (M + H)+ ions of the five-membered ring compounds, pyrrole and pyrrolidine, have higher fragmentation efficiencies than the six-membered ring compounds, pyridine and piperidine. Fragmentation efficiencies in high-energy CID clearly correlate with the internal energy deposited by the ionization technique. Experiments showed that the low-energy CID process is more sensitive than high-energy CID to changes in internal energy.

A pulsed valve positioned just outside the ion trap electrodes (within the vacuum chamber) has been characterized. The observed gas pulse widths and the maximum ion intensities were found to decrease as the distance between the pulsed valve and the ion trap electrodes increased. An explanation is presented within. The pulsed valve was found to impart temporal separation in ion-molecule reactions by permitting the removal of interfering neutrals. Other factors that affect the degree of temporal separation also are presented.

The design of a novel multipass optical arrangement for use with infrared multiple photon dissociation (IRMPD) in the quadrupole ion trap is presented. This design circumvents previous problems of limited IR laser power, small IR absorption cross sections for many molecules, and the limited ion statistics of trapping and detection of ions for IRMPD in the quadrupole ion trap. In contrast to previous designs that utilized the quadrupole ion store, the quadrupole ion trap was operated in the mass selective instability mode with concurrent resonance ejection. The instrumental design consisted of a modified ring electrode with three spherical concave mirrors mounted on the inner surface of the ring. This modified design allowed for eight laser passes across the radial plane of the ring electrode. IRMPD of protonated bis(2-methoxyethyl)ether (diglyme) was used to characterize the performance of the multipass ring electrode. Two consecutive reactions for the IRMPD of protonated diglyme were observed with a lower energy channel predominant at less than 0.6 J (irradiation times from 1 to 30 ms) and a second channel predominant at energies greater than 0.6 J (irradiation times > 30 ms). Other studies presented include a discussion of the dissociation kinetics of protonated diglyme, the use of a pulsed valve for increased trapping efficiency of parent ion populations, and the effects of laser wavelength and of ion residence time in the radial plane of the ring electrode on photodissociation efficiency.

The effects of applied voltages and reaction times on negative ion chemical ionization in the quadrupole ion trap are investigated. Mass-selected ejection of undesired reagent ions and selective mass storage of only negative ions are required for practical negative ion chemical ionization. This is achieved by application of rf and dc voltages to the ring electrode to control the mass-to-charge ratios one polarity) of ions stored, as well as by application of a supplemental rf voltage applied across the endcap electrodes to selectively eject ions of a particular mass-to-charge ratio. Even with careful control of these parameters, negative chemical ionization is not as sensitive as electron ionization and positive chemical ionization because of the lack of thermal electrons in the ion trap. Mass selection of the hydroxide anion as a reagent ion and exclusion of all positive ions provide [M - H](-) ions with little or no fragmentation for a wide variety of compounds.

Contributions of higher-order fields to the quadrupolar storage field produce nonlinear resonances in the quadrupole ion trap. Storing ions with secular frequencies corresponding to these nonlinear resonances allows absorption of power from the higher-order fields. This results in increased axial and radial amplitudes which can cause ion ejection and collision-induced dissociation (CID). Experiments employing long storage times and/or high ion populations, such as chemical ionization, ion-molecule reaction studies, and resonance excitation CID, can be particularly susceptible to nonlinear resonance effects. The effects of higher-order fields on stored ions are presented and the influence of instrumental parameters such as radiofrequency and direct current voltage (qZ and az values), ion population, and storage time are discussed.

We present a detailed study of the energies of the ions stored in a quadrupole ion trap mass spectrometer (QITMS). Previous studies have shown that the rate constant, k, for the charge exchange reaction Ar(+) N(+) 2 →, N(+) 2+Ar increases with increasing ion-molecule center-of-mass kinetic energy (K.E.cm). Thus, we have determined k for this chemical "thermometer" reaction at a variety of Ar and N2 pressures and have assigned K.E.cm values as a function of the q2 of the Ar(+) ion both with and without He buffer gas present in the trap. The K.E.cm energies are found to lie within the range 0.11-0.34 eV over the variety of experimental conditions investigated. Quantitative "cooling" effects due to the presence of He buffer gas are reported, as are increases in K.E.cm due to an increase in the q2 of the Ar(+) ion. "Effective" temperatures of the Ar(+) ions in He buffer are determined based on a Maxwell-Boltzmann distribution of ion energies. The resulting temperatures are found to lie within the range ≈ 1700-3300 K. We have also examined the K.E.cm, values arising from the chemical thermometer reaction of O(+) 2 with CH4, as previous assignments of effective ion temperatures based on this reaction have been called into question.

A new ion trap scan function for gas chromatography/mass spectrometry (GC/MS) quantitation is described that employs alternating mass-selective storage (rf/dc isolation) of ions from an analyte and its coeluting isotopically labeled internal standard. This scan includes two separate ionization/isolation/mass analysis sequences within the same scan function, each optimized for either the analyte or the internal standard. This results in alternating between analyzing the analyte and the internal standard during their coelution. The method is conceptually similar to using two different scan functions to analyze either the analyte or the internal standard in alternating scans; however, it is much faster because it eliminates the slow procedure of continuously downloading alternating scan functions from disk. This allows more data points to be obtained over a GC peak, resulting in more reproducible GC peak profiles as well as better sensitivity and precision. Results of calibration curves spanning four orders of magnitude (0.5 pg to 5 pg injected on column) obtained by using this method give excellent linear correlations (r (2) > 0.9990) and precision (relative standard deviations of triplicate injections < 10%).

Some intriguing discoveries were made concerning the collision-activated dissociation behavior of the derivatized carboxylate anions of PGE2 and PGF2α. The carboxylate anion [MPFB](-) formed from electron-capture negative chemical ionization of the pentafluorobenzyl ester-trimethylsilyl derivative of PGF2α showed little fragmentation under typical collision gas pressures and energies (<2.0 mtorr N2 and <20 eV). In contrast, the daughter spectra of the carboxylate anion of the methoxime-pentafluorobenzyl ester-trimethylsilyl derivative of PGE2 produced many intense fragments under the same conditions.

The ability to produce and detect products of model DNA/carcinogen ion-molecule reactions is demonstrated in the ion source and the collision cell of a triple quadrupole tandem mass spectrometer. Reaction between adenine and benzoyl chloride in the ion source is shown to produce the DNA adduct benzoyl adenine. The daughter ion mass spectrum of the reaction product is compared to that of the synthesized standard. Mass chromatograms of the reaction between mass-selected pyridine ions and various analytes eluting from a GC column into the collision cell are demonstrated and illustrate the ability to detect only the GC eluates that react with pyridine. This technique could provide a rapid and sensitive method for screening complex environmental samples for carcinogens, as well as for estimating the relative mutagenic/carcinogenic potential of environmental contaminants.