Quadrupole Time-of-flight Instrument Research Articles

Diversity Matters: Optimal Collision Energies for Tandem Mass Spectrometric Analysis of a Large Set of N-Glycopeptides.

Identification and characterization of N-glycopeptides from complex samples are usually based on tandem mass spectrometric measurements. Experimental settings, especially the collision energy selection method, fundamentally influence the obtained fragmentation pattern and hence the confidence of the database search results ("score"). Using standards of naturally occurring glycoproteins, we mapped the Byonic and pGlyco search engine scores of almost 200 individual N-glycopeptides as a function of collision energy settings on a quadrupole time of flight instrument. The resulting unprecedented amount of peptide-level information on such a large and diverse set of N-glycopeptides revealed that the peptide sequence heavily influences the energy for the highest score on top of an expected general linear trend with m/z. Search engine dependence may also be noteworthy. Based on the trends, we designed an experimental method and tested it on HeLa, blood plasma, and monoclonal antibody samples. As compared to the literature, these notably lower collision energies in our workflow led to 10-50% more identified N-glycopeptides, with higher scores. We recommend a simple approach based on a small set of reference N-glycopeptides easily accessible from glycoprotein standards to ease the precise determination of optimal methods on other instruments. Data sets can be accessed via the MassIVE repository (MSV000089657 and MSV000090218).

Fatty Acid Composition by Total Acyl Lipid Collision-Induced Dissociation Time-of-Flight (TAL-CID-TOF) Mass Spectrometry.

Totalacyllipid collision-induced dissociation time-of-flight (TAL-CID-TOF) mass spectrometry uses a quadrupole time-of-flight (QTOF) mass spectrometer to rapidly provide a comprehensive fatty acid composition of a biological lipid extract. Samples are infused into a QTOF instrument, operated in negative mode, and the quadrupole is used to transfer all, or a wide mass range of, precursor ions to the collision cell for fragmentation. Time-of-flight-acquired mass spectra provide mass accuracy and resolution sufficient for chemical formula determination of fatty acids in the complex mixture. Considering the limited number of reasonable CHO variants in fatty acids, one can discern acyl anions with the same nominal mass but different chemical formulas. An online application, LipidomeDB Data Calculation Environment, is employed to process the mass spectral output data and match identified fragments to target fragments at a resolution specified by the user. TAL-CID-TOF methodology is a useful discovery or screening tool to identify and compare fatty acid profiles of biological samples.

Intact protein quantification in biological samples by liquid chromatography – high-resolution mass spectrometry: somatropin in rat plasma

The quantitative determination of intact proteins in biological samples by LC with high-resolution MS detection can be a useful alternative to ligand-binding assays or LC-MS-based quantification of a surrogate peptide after protein digestion. The 22-kDa biopharmaceutical protein somatropin (recombinant human growth hormone) was quantified down to 10 ng/mL (0.45 nM) in 75 μL of rat plasma by the combination of an immunocapture step using an anti-somatropin antibody and LC-MS on a quadrupole-time of flight instrument. Accuracy and precision of the method as well as its selectivity and sensitivity did not depend on the width of the mass extraction window nor on whether only one or a summation of multiple charge states of the protein analyte were used as the detection response. Quantification based on deconvoluted mass spectra showed equally acceptable method performance but with a less favorable lower limit of quantification of 30 ng/mL. Concentrations in plasma after dosing of somatropin to rats correlated well for the deconvolution approach and the quantification based on the summation of the response of the four most intense charge states (14+ to 17+) of somatropin.

Investigation of unknown impurities of paromomycin in a 15% topical cream by liquid chromatography combined with mass spectrometry.

Characterization of unknown impurities in degraded paromomycin 15% topical cream samples by ultra-high-performance liquid chromatography/tandem mass spectrometry (UHPLC/MS/MS) gas-phase fragmentation is described. A volatile reversed-phase high-performance liquid chromatography/charged aerosol detection (RP-HPLC/CAD) method was developed and validated for fast and consistent analysis of the paromomycin potency and impurity values in drug substance and drug product samples. A Veo charged aerosol detector was chosen for routine analysis. The method shows separation of two paromomycin isomers as well as twelve unknown impurity peaks. The identity of the unknown impurities was investigated by LC/MS/MS using a quadrupole time-of-flight (QTOF) mass spectrometer. Six of the HPLC/CAD impurity peaks met the ICH Q3B(R2) threshold for identification and were investigated by coupling the developed LC method with a QTOF instrument. Structures for the impurities were proposed based on gas-phase fragmentation patterns of the paromomycin reference standard. Impurity fragmentation pathways were proposed based on literature of other structurally related aminoglycoside compounds. Nine unknown paromomycin impurities were identified and the observed modifications included acetylation, carbamylation, gain of a hexose, and loss of glucosamine. The most abundant paromomycin modification was carbamylation by urea (a cream excipient) characterized by a 43 Da mass increase.

Trends in Analysis of Cortisol and Its Derivatives.

Determination of concentration of cortisol in various biological fluids can provide extensive information about a person's health. Historically, cortisol and its derivatives were (and still are) determined using immunoaffinity-based methods such as colorimetric ELISA assay, chemiluminescent immunoassay, fluorescence assays, radioimmunoassay, electrochemiluminescence immunoassay, immunochromatographic test, or sensors and immunosensors. Recently, mass spectrometry (MS)-based methods started to be used in determination of cortisol and its derivatives. These MS methods are net superior to immunoaffinity-based assays, but are not easily applicable and are also time-consuming and price prohibitive. Furthermore the standard MS instruments used are triple quadrupole instruments. Here we review the literature on the MS and non-MS based methods for determination of cortisol and its derivatives and also explore the use of a less used quadrupole-time of flight instrument in determination of these compounds.

A novel antibody-based enrichment and mass spectrometry approach for the detection of species-specific blood peptides in feed matrices

Blood is an important animal by-product and an attractive source for animal feed production. However, the outspread of bovine spongiform encephalopathy led to strict regulations on the usage of animal by-products in animal feed. Although, the ban on certain processed animal proteins has been partially abolished in recent years, it is still challenging to distinguish legal from illegal protein additives in complex feed products using analytical methods. To overcome these gaps, this study aimed to develop a tissue-specific and sensitive immuno-based enrichment and mass spectrometry-based detection method to identify haemoglobin peptides of ruminant or porcine origin when mixed in a background of vegetal feed, fish meal, aquaculture feed, blood compounds, or milk powder. Here we report the first analytical method able to species-specifically detect adulterations of as little as 0.05%–1% (w/w) ruminant blood meal in various matrices on a quadrupole-time of flight instrument.

Optimisation of Milk Protein Top-Down Sequencing Using In-Source Collision-Induced Dissociation in the Maxis Quadrupole Time-of-Flight Mass Spectrometer

Top-down sequencing in proteomics has come of age owing to continuous progress in LC-MS. With their high resolution and broad mass range, Quadrupole Time-of-Flight (Q-ToF) hybrid mass spectrometers equipped with electrospray ionisation source and tandem MS capability by collision-induced dissociation (CID) can be employed to analyse intact proteins and retrieve primary sequence information. To our knowledge, top-down proteomics methods with Q-ToF have only been evaluated using samples of relatively low complexity. Furthermore, the in-source CID (IS-CID) capability of Q-ToF instruments has been under-utilised. This study aimed at optimising top-down sequencing of intact milk proteins to achieve the greatest sequence coverage possible from samples of increasing complexity, assessed using nine known proteins. Eleven MS/MS methods varying in their IS-CID and conventional CID parameters were tested on individual and mixed protein standards as well as raw milk samples. Top-down sequencing results from the nine most abundant proteoforms of caseins, alpha-lactalbumin and beta-lactoglubulins were compared. Nine MS/MS methods achieved more than 70% sequence coverage overall to distinguish between allelic proteoforms, varying only by one or two amino acids. The optimal methods utilised IS-CID at low energy. This experiment demonstrates the utility of Q-ToF systems for top-down proteomics and that IS-CID could be more frequently employed.

Non-volatile extractable analysis of prefilled syringes for parenteral administration of drug products

The determination of extractable profiles for single-use technologies represents an important aspect of pharmaceutical production to minimize any possible compromise in drug product quality or potential risk to patients by identifying substances that may potentially leach from such devices. An approach for the extractable assessment of prefilled syringes, a promising alternative for parenteral administration of pharmaceutical products, is described herein. Four extraction solvents were selected: a mixture 2-propanol:water (1:1), was intended to represent aggressive conditions to extract a broad spectrum of extractables, including organic additives and substances which are poorly water-soluble. Extractions with buffers at three different working pH values spanning a range standardly used in pharmaceutical formulations were also evaluated to identify substances that require specific conditions for their extraction due to their individual chemical properties. Syringes from two different brands were analysed along with their corresponding plunger stoppers. Syringes were extracted at 40°C for 4days, the plunger stoppers were extracted with 2-propanol at 70°C for 24h according to ISO 10993-12:2012. Extractables were identified by UHPLC–MS on a quadrupole time of flight instrument using a non-targeted discovery strategy. A total of 25 compounds were identified, mostly polymer additives and their degradation products. The presented methodology represents a reference point for further studies focused on the characterisation of extractables and leachables from prefilled syringes.

Surface-Induced Dissociation of Protein Complexes in a Hybrid Fourier Transform Ion Cyclotron Resonance Mass Spectrometer.

Mass spectrometry continues to develop as a valuable tool in the analysis of proteins and protein complexes. In protein complex mass spectrometry studies, surface-induced dissociation (SID) has been successfully applied in quadrupole time-of-flight (Q-TOF) instruments. SID provides structural information on noncovalent protein complexes that is complementary to other techniques. However, the mass resolution of Q-TOF instruments can limit the information that can be obtained for protein complexes by SID. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provides ultrahigh resolution and ultrahigh mass accuracy measurements. In this study, an SID device was designed and successfully installed in a hybrid FT-ICR instrument in place of the standard gas collision cell. The SID-FT-ICR platform has been tested with several protein complex systems (homooligomers, a heterooligomer, and a protein-ligand complex, ranging from 53 to 85 kDa), and the results are consistent with data previously acquired on Q-TOF platforms, matching predictions from known protein interface information. SID fragments with the same m/z but different charge states are well-resolved based on distinct spacing between adjacent isotope peaks, and the addition of metal cations and ligands can also be isotopically resolved with the ultrahigh mass resolution available in FT-ICR.

TEMPO-Assisted Free Radical-Initiated Peptide Sequencing Mass Spectrometry (FRIPS MS) in Q-TOF and Orbitrap Mass Spectrometers: Single-Step Peptide Backbone Dissociations in Positive Ion Mode

The present study demonstrates that one-step peptide backbone fragmentations can be achieved using the TEMPO [2-(2,2,6,6-tetramethyl piperidine-1-oxyl)]-assisted free radical-initiated peptide sequencing (FRIPS) mass spectrometry in a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer and a Q-Exactive Orbitrap instrument in positive ion mode, in contrast to two-step peptide fragmentation in an ion-trap mass spectrometer (reference Anal. Chem. 85, 7044-7051 (30)). In the hybrid Q-TOF and Q-Exactive instruments, higher collisional energies can be applied to the target peptides, compared with the low collisional energies applied by the ion-trap instrument. The higher energy deposition and the additional multiple collisions in the collision cell in both instruments appear to result in one-step peptide backbone dissociations in positive ion mode. This new finding clearly demonstrates that the TEMPO-assisted FRIPS approach is a very useful tool in peptide mass spectrometry research. Graphical Abstract ᅟ.

Efficient forensic toxicological screening and quantitation workflow using QTOF LC–MS/MS system

Quadrupole time-of-flight (QTOF) mass spectrometry is becoming the desired technology for sensitive and selective screening workflows in a forensic toxicological setting. The technology overcomes many challenges faced when using traditional techniques and more significantly captures all information about the sample in one injection to allow for retrospectively mining the data. Here we describe a new benchtop QTOF system with revolutionary N-optic designed flight path and new, intuitive software for easy adoption of accurate mass technology to forensic testing. Blank human urine was spiked with more than 50 common drugs found in forensics setting at different concentration levels. HPLC separation was performed using the SCIEX ExionLC AC system on a reverse-phase column. Data was collected on a SCIEX X500R QTOF mass spectrometer with SCIEX OS software: TOF – MS survey scan with Information Dependent Acquisition (IDA) – triggering of up to 16 product ion scans; or SWATH® acquisition. For SWATH® acquisition, the precursor isolation window width was varied for each MS/MS experiment. Data processing was also performed in SCIEX OS software with simultaneous identification and quantification being accomplished in single software. Screening: multiple confidence criteria including mass accuracy, retention time, isotope, and most importantly, library matching were used. The availability of MS/MS information for identification was required in this study through library searching the acquired spectra against a SCIEX high resolution forensic library containing MS/MS spectra of 1700 compounds. Excellent true positive rates were accomplished for both acquisition modes (89% with IDA and 98% with SWATH® acquisition). This result is consistent with the expectation that the IDA-MS/MS data acquisition has the risk of occasionally missing acquiring MS/MS. The acquisition of MS/MS data in the screening approach allowed the confident identification of structural isomers that have similar retention times through unique fragment ions and their ratios. Simultaneous Quantification Linearity on the new QTOF system for the majority of compounds tested was four orders linear dynamic range covering 0.1 to 1000 ng/mL. SWATH® acquisition ensures that all data, including MS/MS, is acquired at all times. Due to the fast scanning speed (up to 100 Hz at 35 K resolution) in MS/MS mode, a fast cycletime (0.5 sec) was used for the 6.5-min LC method that allowed for one TOF-MS scan and 16 MS/MS scans that covered 120 to 500 m/z range. A sensitive and selective workflow was developed for toxicological compound screening in a forensic setting using the new X500R QTOF system. The newly designed software that accompanies the new benchtop QTOF instrument allows for simultaneous compound identification and quantification in one step all in one place. SCIEX OS software allows the easy adoption of accurate mass technology for routine forensic workflows.

The Art of Destruction: Optimizing Collision Energies in Quadrupole-Time of Flight (Q-TOF) Instruments for Glycopeptide-Based Glycoproteomics.

In-depth site-specific investigations of protein glycosylation are the basis for understanding the biological function of glycoproteins. Mass spectrometry-based N- and O-glycopeptide analyses enable determination of the glycosylation site, site occupancy, as well as glycan varieties present on a particular site. However, the depth of information is highly dependent on the applied analytical tools, including glycopeptide fragmentation regimes and automated data analysis. Here, we used a small set of synthetic disialylated, biantennary N-glycopeptides to systematically tune Q-TOF instrument parameters towards optimal energy stepping collision induced dissociation (CID) of glycopeptides. A linear dependency of m/z-ratio and optimal fragmentation energy was found, showing that with increasing m/z-ratio, more energy is required for glycopeptide fragmentation. Based on these optimized fragmentation parameters, a method combining lower- and higher-energy CID was developed, allowing the online acquisition of glycan and peptide-specific fragments within a single tandem MS experiment. We validated this method analyzing a set of human immunoglobulins (IgA1+2, sIgA, IgG1+2, IgE, IgD, IgM) as well as bovine fetuin. These optimized fragmentation parameters also enabled software-assisted glycopeptide assignment of both N- and O-glycopeptides including information about the most abundant glycan compositions, peptide sequence and putative structures. Twenty-six out of 30 N-glycopeptides and four out of five O-glycopeptides carrying >110 different glycoforms could be identified by this optimized LC-ESI tandem MS method with minimal user input. The Q-TOF based glycopeptide analysis platform presented here opens the way to a range of different applications in glycoproteomics research as well as biopharmaceutical development and quality control.Graphical ᅟElectronic supplementary materialThe online version of this article (doi:10.1007/s13361-015-1308-6) contains supplementary material, which is available to authorized users.

The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics *

Hybrid quadrupole time-of-flight (QTOF) mass spectrometry is one of the two major principles used in proteomics. Although based on simple fundamentals, it has over the last decades greatly evolved in terms of achievable resolution, mass accuracy, and dynamic range. The Bruker impact platform of QTOF instruments takes advantage of these developments and here we develop and evaluate the impact II for shotgun proteomics applications. Adaption of our heated liquid chromatography system achieved very narrow peptide elution peaks. The impact II is equipped with a new collision cell with both axial and radial ion ejection, more than doubling ion extraction at high tandem MS frequencies. The new reflectron and detector improve resolving power compared with the previous model up to 80%, i.e. to 40,000 at m/z 1222. We analyzed the ion current from the inlet capillary and found very high transmission (>80%) up to the collision cell. Simulation and measurement indicated 60% transfer into the flight tube. We adapted MaxQuant for QTOF data, improving absolute average mass deviations to better than 1.45 ppm. More than 4800 proteins can be identified in a single run of HeLa digest in a 90 min gradient. The workflow achieved high technical reproducibility (R2 > 0.99) and accurate fold change determination in spike-in experiments in complex mixtures. Using label-free quantification we rapidly quantified haploid against diploid yeast and characterized overall proteome differences in mouse cell lines originating from different tissues. Finally, after high pH reversed-phase fractionation we identified 9515 proteins in a triplicate measurement of HeLa peptide mixture and 11,257 proteins in single measurements of cerebellum—the highest proteome coverage reported with a QTOF instrument so far.

Evaluation of Differences in MS/MS Spectra from Two Differentgeneration Q-TOF Instruments: Implications for Metabolomic Database Use

Generating reproducible fragmentation patterns is a problem in electrospray ionization mass spectrometry. Two generations of quadrupole time-of-flight(Q-TOF) instruments were selected to evaluate the reproducibility of tandem mass spectrometry(MS/MS) spectra:an old- and a new-generation instrument. Ninety-four MS/MS and MS/MS/MS spectra with information-rich product ions were obtained in positive- or negative-ion mode with two different-generation Q-TOF instruments, BioTOF-Q and micrOTOF- Q. Two principles were selected to optimize the collision energy. On the one hand, maximal structural information is obtained when the collision energy is increased; on the other hand, when most product ions show relative abundance of more than 10%, the lowest collision energy should be selected. The Paired-Samples T Test method was used to analysis these paired-spectra. We found that most product ions were the same and the profiles of the product ions were similar with both Q-TOF instruments. Interestingly, at the low signal to-noise ratio (S/N) of the precursor ion (ion intensity low to 180 counts), the profile of the MS/MS spectrum is very similar to that at a high S/N. Furthermore, when spectra were generated with micrOTOF-Q even before and after a four-year interval, the profiles and product ions were virtually identical. In summary, databases built with different-generation Q-TOF instruments may be universally applicable. Keywords: Reproducibility, two different-generation, quadrupole time-of-flight, tandem mass spectrometry, paired-samples t test, databases built.

Tandem Mass Spectrometry Using the Atmospheric Pressure Electron Capture Dissociation Ion Source

Atmospheric pressure electron capture dissociation (AP-ECD) is an emerging technique capable of being adopted to virtually any electrospray mass spectrometer, without modification of the main instrument. To date, however, because the electron capture reactions occur in the ion source, AP-ECD has been limited by its apparent inability to select precursors prior to fragmentation, i.e., to perform tandem mass spectrometry (MS/MS) experiments. In this paper we demonstrate a novel AP-ECD-MS/MS method using an AP-ECD source on a Xevo G2-S quadrupole time-of-flight (Q-TOF) mass spectrometer from Waters Micromass. The method takes advantage of the tendency for electron capture reactions to generate charge-reduced "ECnoD" products, species that have captured an electron and have had a covalent bond cleaved yet do not immediately dissociate into separate products and so retain the mass of the precursor ion. In the method, ECnoD products from the AP-ECD source are isolated in the quadrupole mass filter and induced to dissociate through supplemental activation in the collision cell, and then the liberated ECD fragment ions are mass analyzed using the high-resolution TOF. In this manner, true MS/MS spectra may be obtained with AP-ECD even though all of the precursors in the source are subjected to electron capture reactions in parallel. Here, using a late-model Q-TOF instrument otherwise incapable of performing electron-based fragmentation, we present AP-ECD-MS/MS results for a group of model peptides and show that informative, high-sequence-coverage spectra are readily attainable with the method.

Structural characterization of product ions by electrospray ionization and quadrupole time-of-flight mass spectrometry to support regulatory analysis of veterinary drug residues in foods

Monitoring of veterinary drug residues in foods is often conducted using liquid chromatography/tandem mass spectrometry (LC/MS/MS). Results have high economic stakes for producers, but the ions monitored are usually selected due to signal intensities without structural interpretation. In this study, the ion transitions were characterized by high-resolution mass spectrometry. The 62 veterinary drugs from the LC/MS/MS method consisted of sulfonamides, β-lactams, phenicols, macrolides, tetracyclines, fluoroquinolones, non-steroidal anti-inflammatory drugs (NSAIDs), and corticosteroids. They were individually infused into a quadrupole time-of-flight (Q-TOF) mass spectrometer using electrospray ionization (ESI) operated in positive mode. The MS and collision-induced dissociation (CID) MS/MS spectra for each analyte were obtained for structural elucidation. The Q-TOF instrument was calibrated to obtain a mass accuracy error <5 ppm for the MS and MS/MS spectra. The use of high-resolution ESI-Q-TOF-MS for the generation of the MS/MS product ions allowed for the determination of chemical formulae for the analytes, some of which led to new findings. Assigned structures were based on rational interpretation of the most stable possible products with comparison with the scientific literature. In difficult cases, isotopically labeled drugs or hydrogen/deuterium (H/D) exchange experiments were used to help confirm the structures of the product ions. The use of ESI-Q-TOF-MS in this study has allowed structure elucidation of 186 MS/MS product ions previously selected for the LC/MS/MS analysis of 62 veterinary drugs. This serves to reduce the chances of false positives and negatives in the monitoring program, and provides justification and defense in regulatory enforcement actions.

Molecular level differentiation between end‐capped and intramolecular azofunctional oligo(ε‐caprolactone) positional isomers through liquid chromatography multistage mass spectrometry

AbstractEnd‐capped and intramolecular azofunctional oligocaprolactones were characterized at molecular level by liquid chromatography electrospray ionization mass spectrometry (ESI MS) and NMR spectroscopy. The Disperse Red 19 (DR19) azofunctional oligomers, DC, were synthesized by ring‐opening oligomerization of ε‐caprolactone (ε‐CL) initiated by the hydroxyl groups of DR19 azo dye. The reaction products consist of a minor fraction of end‐capped azo functional oligocaprolactone (α‐DC), that is, a single CL arm oligomer, and a major fraction of intramolecular azo functional oligocaprolactone (β‐DC), that is, a two CL arms oligomer. The chromatographic separation was used to discriminate between α‐DC and β‐DC, and the results were confirmed by MS/MS performed on an ESI ion trap instrument. The results supported by accurate mass data obtained for product ions using an ESI quadrupole time of flight instrument demonstrate the qualitative discrimination at the molecular level between intramolecular and end‐capped azofunctional oligoesters isomers through a relatively simple multistage mass spectrometry experiment. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012

Use of quadrupole time‐of‐flight mass spectrometry to determine proposed structures of transformation products of the herbicide bromacil after water chlorination

The herbicide bromacil has been extensively used in the Spanish Mediterranean region, and although plant protection products containing bromacil have been withdrawn by the European Union, this compound is still frequently detected in surface and ground water of this area. However, the fast and complete disappearance of this compound has been observed in water intended for human consumption, after it has been subjected to chlorination. There is a concern about the possible degradation products formed, since they might be present in drinking water and might be hazardous. In this work, the sensitive full-spectrum acquisition, high resolution and exact mass capabilities of hybrid quadrupole time-of-flight (QTOF) mass spectrometry have allowed the discovery and proposal of structures of transformation products (TPs) of bromacil in water subjected to chlorination. Different ground water samples spiked at 0.5 µg/mL were subjected to the conventional chlorination procedure applied to drinking waters, sampling 2-mL aliquots at different time intervals (1, 10 and 30 min). The corresponding non-spiked water was used as control sample in each experiment. Afterwards, 50 μL of the water was directly injected into an ultra-high-pressure liquid chromatography (UHPLC)/electrospray ionization (ESI)-(Q)TOF system. The QTOF instrument enabled the simultaneous recording of two acquisition functions at different collision energies (MS(E) approach): the low-energy (LE) function, fixed at 4 eV, and the high-energy (HE) function, with a collision energy ramp from 15 to 40 eV. This approach enables the simultaneous acquisition of both parent (deprotonated and protonated molecules) and fragment ions in a single injection. The low mass errors observed for the deprotonated and protonated molecules (detected in LE function) allowed the assignment of a highly probable molecular formula. Fragment ions and neutral losses were investigated in both LE and HE spectra to elucidate the structures of the TPs found. For those compounds that displayed poor fragmentation, product ion scan (MS/MS) experiments were also performed. On processing the data with specialized software (MetaboLynx), four bromacil TPs were detected and their structures were elucidated. To our knowledge, two of them had not previously been reported.

ETD in a Traveling Wave Ion Guide at Tuned Z-Spray Ion Source Conditions Allows for Site-Specific Hydrogen/Deuterium Exchange Measurements

The recent application of electron transfer dissociation (ETD) to measure the hydrogen exchange of proteins in solution at single-residue resolution (HX-ETD) paves the way for mass spectrometry-based analyses of biomolecular structure at an unprecedented level of detail. The approach requires that activation of polypeptide ions prior to ETD is minimal so as to prevent undesirable gas-phase randomization of the deuterium label from solution (i.e., hydrogen scrambling). Here we explore the use of ETD in a traveling wave ion guide of a quadrupole-time-of-flight (Q-TOF) mass spectrometer with a "Z-spray" type ion source, to measure the deuterium content of individual residues in peptides. We systematically identify key parameters of the Z-spray ion source that contribute to collisional activation and define conditions that allow ETD experiments to be performed in the traveling wave ion guide without gas-phase hydrogen scrambling. We show that ETD and supplemental collisional activation in a subsequent traveling wave ion guide allows for improved extraction of residue-specific deuterium contents in peptides with low charge. Our results demonstrate the feasibility, and illustrate the advantages of performing HX-ETD experiments on a high-resolution Q-TOF instrument equipped with traveling wave ion guides. Determination of parameters of the Z-spray ion source that contribute to ion heating are similarly pertinent to a growing number of MS applications that also rely on an energetically gentle transfer of ions into the gas-phase, such as the analysis of biomolecular structure by native mass spectrometry in combination with gas-phase ion-ion/ion-neutral reactions or ion mobility spectrometry.

Comparative study of low- versus high-resolution liquid chromatography-mass spectrometric strategies for measuring perfluorinated contaminants in fish

Perfluorinated compounds (PFCs) are usually monitored by high-performance liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) on triple quadrupole instruments. Although not yet widely implemented in the field, high-resolution mass spectrometry (HRMS) today appears as a valuable alternative for these halogenated chemicals due to their significant mass defect. Indeed, this second approach offers a way to cope with particular matrix effects caused by co-eluting and isobaric interferences affecting the measurement of some PFCs in fish. The present study compares three different LC-MS-related instruments and various signal acquisition modes, from low-resolution full-scan and selected ion-monitoring (SIM) mode on a triple quadrupole (QqQ) instrument to high-resolution full-scan or product ion-scan mode on orbital trap (LTQ-Orbitrap) or quadrupole-time-of-flight (Q-TOF) devices. Performances are compared for seven model compounds belonging to seven PFCs subclasses: perfluoralkylsulfonate, perfluoroalkylcarboxylate, perfluoroalkylsulfinate, perfluoroalkyl-sulfonamide, fluorotelomer saturated acid, fluorotelomer unsaturated acid and perfluoroalkylphosphonic acid. Low-resolution MS/MS was found to be unsurprisingly reliable for extended multi-residue monitoring. However, the high stability of PFCs leads to a relatively poor and non-specific fragmentation pathway in MS/MS. In addition, biliary acid-interfering compounds (e.g. taurochenodeoxycholic acid), which where encountered in the present case in fish samples but that may be present in other biological samples, were found particularly disturbing in low-resolution MS/MS. Indeed, these interferences presented the same retention time and diagnostic signals as PFOS, leading to a possible overestimation of the PFOS quantification in LC-MS/MS. On the other hand, high-resolution MS and MS/MS (LTQ-Orbitrap and Q-TOF) provided better results in terms of signal specificity and sensitivity. For instance, the estimated limits of detection (LOD) reached for PFOS on QqQ, Q-TOF and LTQ-Orbitrap instruments were 3.8, 0.7 and 0.5 pg injected, respectively.