All-ion Fragmentation Research Articles

Morphological and molecular characterization of the cyanobiont-bearing dinoflagellate Sinophysis canaliculata from the Canary Islands (eastern central Atlantic)

Morphological and molecular characterization of the cyanobiont-bearing dinoflagellate Sinophysis canaliculata from the Canary Islands (eastern central Atlantic)

Single-Laboratory Validation Study of a Method for Screening and Identification of Phosphodiesterase Type 5 Inhibitors in Dietary Ingredients and Supplements Using Liquid Chromatography/Quadrupole-Orbital Ion Trap Mass Spectrometry: First Action 2015.12.

A single-laboratory validation study of a method for screening and identification of phosphodiesterase type 5 (PDE5) inhibitors in dietary ingredients and supplements is described. PDE5 inhibitors were extracted from the samples using a 50:50 (v/v) mixture of acetonitrile and water and centrifuged. Supernatant was diluted, filtered, and analyzed by LC-high-resolution MS. Data were collected in MS acquisition mode that combined full-scan MS experiment with all-ion fragmentation and data-dependent MS/MS product from the ion scan experiment. This approach enabled collection of MS and tandem MS (MS/MS) data for both targeted and nontargeted PDE5 inhibitors in a single chromatographic run. Software-facilitated identification of targeted analytes was performed based on the retention time, accurate mass, and isotopic pattern of pseudomolecular ions, and accurate masses of fragment ions using an in-house compound database. Detection and identification of other PDE5 inhibitors and novel analogs were performed by retrospective evaluation of MS and MS/MS experimental data. The method validation results obtained for evaluated matrixes fulfilled the probability of identification requirements and probability of detection requirements (for the pooled data) set at 90% (95% confidence interval) in the respective AOAC Standard Method Performance Requirements for identification and screening methods for PDE5 inhibitors. Limited data demonstrating the quantification capability of the method were also generated. Mean recovery and repeatability obtained for the evaluated PDE5 inhibitors were in the range 69-90% and 0.4-1.8%, respectively.

Simultaneous quantitative determination, identification and qualitative screening of pesticides in fruits and vegetables using LC-Q-Orbitrap™-MS

A method based on QuEChERS extraction and LC-quadrupole-Orbitrap™ MS detection was established utilising an improved fully non-targeted way of data acquisition with and without fragmentation. A full-scan acquisition event without fragmentation (resolving power 70 000) was followed by five consecutive fragmentation events (variable data independent acquisition – vDIA; resolving power 35 000) where all ions from the full-scan range are fragmented. Compared with fragmentation in a single event (all-ion fragmentation – AIF), this improves both selectivity and sensitivity for the fragment ions, which is beneficial for screening performance and identification capability. The method was validated, using the data from the same measurements, for two types of analysis: quantitation/identification and qualitative screening. The quantitative validation, performed according to the guidelines in SANCO/12571/2013, tested the performance of the method for 184 compounds in lettuce and orange at two spiking levels: 10 and 50 ng g−1. The validation showed that the vast majority of the compounds met the criteria for trueness and precision set in the SANCO guidance document. In the qualitative validation the same 184 compounds were used to test the untargeted screening capabilities of the method. In this validation the compounds were spiked at three levels into 11 different fruit and vegetable matrices, which were measured twice on separate days. Taking all data from the qualitative validation together, an overall detection rate of 92% was achieved at the 10 ng g−1 level, increasing to 98% at 200 ng g−1. A screening detection limit (as defined in the SANCO guidelines) of 10 ng g−1 could be achieved for 134 compounds. For 39 and two pesticides the SDL was 50 and 200 ng g−1, respectively. For the other nine compounds no SDL could be established. The identification (ion ratio) criteria as recommended in the SANCO document could be met for 93% of the detected pesticide/matrix/concentration combinations. The outcome of both validations shows that the described method can be used to combine quantitative analysis and the identification of frequently detected pesticides (so far typically done using triple quadrupole MS/MS) with a qualitative screening to be used for a wide range of less frequent detected compounds in one measurement.

Site-specific characterization and absolute quantification of pegfilgrastim oxidation by top-down high-performance liquid chromatography-mass spectrometry.

The characterization and absolute quantification of protein biopharmaceuticals and their product-related impurities, e.g., oxidation variants, is essential due to their potential impact on biological activity and immunogenicity. Here, we present site assignment and absolute quantification of oxidation variants of pegfilgrastim, a poly(ethylene glycol) modified recombinant human granulocyte-colony stimulating factor. Pegfilgrastim stressed with 1.0% hydrogen peroxide served as a model protein for developing a top-down high-performance liquid chromatography-mass spectrometry (HPLC-MS) platform that allowed direct site assignment of Met122, Met127, and Met138 oxidation within a total analysis time of 30 min. Three different absolute quantification methods, namely, UV absorption spectroscopy, full-scan MS, and all-ion fragmentation (AIF) MS were compared. Additionally, the monitoring of all generated fragment ions or selected sets of fragment ions were evaluated for the AIF method. Linearity of calibration curves from 5.0 to 25 ng μL(-1), 25 to 250 ng μL(-1), and 100 to 1000 ng μL(-1) was confirmed. The AIF method achieved a lower limit of detection of 0.85 ng μL(-1) and a lower limit of quantification of 2.54 ng μL(-1). On the basis of the comparison of relative standard deviations of interday measurements, AIF was concluded to be the method of choice for concentrations up to 50 ng μL(-1), and UV measurements should be carried out above this concentration. Finally, an expired pegfilgrastim batch was analyzed as a a real biopharmaceutical sample to confirm the feasibility of our approach for monitoring low levels of oxidation variants.

4-Methoxy-α-PVP: in silico prediction, metabolic stability, and metabolite identification by human hepatocyte incubation and high-resolution mass spectrometry.

Novel psychoactive substances are continuously developed to circumvent legislative and regulatory efforts. A new synthetic cathinone, 4-methoxy-α-PVP, was identified for the first time in illegal products; however, the metabolism of this compound is not known. Complete metabolic profiles are needed for these novel psychoactive substances to enable identification of their intake and to link adverse effects to the causative agent. This study assessed 4-methoxy-α-PVP metabolic stability with human liver microsomes (HLMs) and identified its metabolites after HLM and hepatocyte incubations followed by high-resolution mass spectrometry (HRMS). A Thermo QExactive high-resolution mass spectrometer (HRMS) was used with full scan data-dependent mass spectrometry, with (1) and without (2) an inclusion list of predicted metabolite, and with full scan and all-ion fragmentation (3) to identify potential unexpected metabolites. In silico predictions were performed and compared to in vitro results. Scans were thoroughly mined with different data processing algorithms using WebMetabase (Molecular Discovery). 4-Methoxy-α-PVP exhibited a long half-life of 79.7 min in HLM, with an intrinsic clearance of 8.7 µL min−1 mg−1. In addition, this compound is predicted to be a low-clearance drug with an estimated human hepatic clearance of 8.2 mL min−1 kg−1. Eleven 4-methoxy-α-PVP metabolites were identified, generated by O-demethylation, hydroxylation, oxidation, ketone reduction, N-dealkylation, and glucuronidation. The most dominant metabolite in HLM and human hepatocyte samples was 4-hydroxy-α-PVP, also predicted as the #1 in silico metabolite, and is suggested to be a suitable analytical target in addition to the parent compound.

A high-resolution accurate mass (HR/AM) approach to identification, profiling and characterization of in vitro nefazodone metabolites using a hybrid quadrupole Orbitrap (Q-Exactive).

This paper describes a strategy for the profiling and identification of metabolites based on chemical group classification using high-resolution accurate mass (HR/AM) full scan mass spectrometry (MS) and All-Ion fragmentation (AIF) MS2 data. The proposed strategy uses a hybrid quadrupole Orbitrap (Q-Exactive) employing stepped normalised collision energy (NCE) at 35% and 80% to produce key chemically diagnostic product ions from full coverage of the product ion spectrum. This approach allows filtering of high-resolution AIF MS2 data in order to identify parent-related compounds produced following incubation in rat liver microsomes (RLMs). An antidepressant drug, nefazodone (NEF), was selected as the model test compound to demonstrate the proposed workflow for metabolite profiling. This resulted in the identification of three indicative chemical groups within NEF: triazolone, phenoxy and chlorophenylpiperazine. High-resolution mass spectrometry provides increased specificity to distinguish between two characteristic product ion masses m/z 154.0975 (C7 H12 N3 O) and 154.0419 (C8 H9 NCl), which are not fully resolved by spectrometers operating at nominal mass resolution, indicative of compounds containing the triazolone and chlorophenylpiperazine moieties, respectively. This post-acquisition processing strategy provides comprehensive detection and identification of high- and low-level metabolites from an 'all-in-one' analysis. This enables functional groups to be systematically traced across a wide range of metabolites, leading to the successful identification of 28 in vitro NEF-related metabolites. In our hands this approach has been applied to agrochemical environmental fate and dietary metabolism studies, as well as metabolomics and biomarker analysis. Copyright © 2015 John Wiley & Sons, Ltd.

High-resolution mass spectrometry provides novel insights into products of human metabolism of organophosphate and brominated flame retardants.

The high resolution, accurate mass, and fast scanning features of the Orbitrap(TM) mass spectrometer, combined with the separation power of ultrahigh-performance liquid chromatography were applied for the first time to study the metabolic profiles of several organic flame retardants (FRs) present in indoor dust. To mimic real-life exposure, in vitro cultured HepG2 human hepatocyte cell lines were exposed simultaneously to various FRs in an indoor dust extract for 24h. Target parent FRs, hexabromocyclododecanes (α-, β-, and γ-HBCDs), tris-2-chloroethyl phosphate (TCEP), tris(1-chloro-2-propyl) phosphate (TCIPP), and tris(1,3-dichloro-2-propyl) phosphate (TDCIPP), were separated in a single run for the first time using alternating positive and negative heated ESI source. Further metabolite separation and identification was achieved using full scan (70,000 full width at half maximum (FWHM)), accurate mass (up to 1ppm) spectrometry. Structural confirmation was performed via all ion fragmentation (AIF) spectra using the optional higher collisional dissociation (HCD) cell and MS/MS analysis. First insights into human metabolism of HBCDs revealed several hydroxylated and debrominated phase I metabolites, in addition to conjugated phase II glucuronides. Furthermore, various hydroxylated, oxidized, and conjugated metabolites of chlorinated phosphorous FRs were identified, leading to the suggestion of α-oxidation as a significant metabolic pathway for these compounds.

Qualitative characterization of the rat liver mitochondrial lipidome using all ion fragmentation on an Exactive benchtop Orbitrap MS.

Untargeted lipidomics profiling by liquid chromatography-mass spectrometry (LC-MS) allows researchers to observe the occurrences of lipids in a biological sample without showing intentional bias to any specific class of lipids and allows retrospective reanalysis of data collected. Typically, and in the specific method described, a general extraction method followed by LC separation is used to achieve nonspecific class coverage of the lipidome prior to high-resolution accurate mass (HRAM) MS detection. Here we describe a workflow including the isolation of mitochondria from liver tissue, followed by mitochondrial lipid extraction and the LC-MS conditions used for data acquisition. We also highlight how, in this method, all-ion fragmentation can be used to identify species of lower abundances, often missed by data-dependent fragmentation techniques. Here we describe the isolation of mitochondria from liver tissue, followed by mitochondrial lipid extraction and the LC-MS conditions used for data acquisition.

Identification and quantification of phytochemicals in nutraceutical products from green tea by UHPLC–Orbitrap-MS

A method has been developed and validated for the simultaneous detection and quantification of phytochemicals in nutraceutical products obtained from green tea. For that purpose, ultra-high performance liquid chromatography coupled to single-stage Orbitrap high resolution mass spectrometry (UHPLC–Orbitrap-MS) has been used. A database containing 37 compounds has been used for the detection and identification of the target compounds. The developed methodology was based on solid–liquid extraction, using a mixture of methanol:H2O (80:20, v/v, pH 4), followed by dilution (10 times) with a mixture of ammonium acetate:methanol (50:50, v/v). Chromatographic conditions were optimised and full scan accurate mass data acquisition using electrospray ionisation in positive and negative ion mode was used. Moreover, all-ion fragmentation mode was used to get information of fragment ions, and they were used for identification purposes. The developed method was validated, obtaining repeatability (intra-day) and inter-day precision values (expressed as relative standard deviation, RSD) lower than 16% and 20%, respectively. Lower limits were also evaluated and limits of detection (LODs) ranged from 1 to 50μgL−1, while limits of quantification (LOQs) ranged from 2 to 150μgL−1. Recovery was performed at five levels and it ranged from 70% to 109%. Finally, this method was used to evaluate the phytochemical content in 10 samples (tablets or capsules), showing concentrations of (+)-catechin, (−)-epicatechin, gallic acid, (−)-gallocatechin and quercetin-3-O-rutinoside, ranging from 258 (C6) to 10,729 (C6) mgkg−1.

Implementing visible 473 nm photodissociation in a Q-Exactive mass spectrometer: towards specific detection of cysteine-containing peptides.

Improvement of the fragmentation specificity may streamline data processing of bottom-up proteomic experiments by drastically reducing either the amount of MS/MS data to process in the discovery phase or the detection of interfering signals in targeted quantification. Photodissociation at appropriate wavelengths is a promising alternative technique to the non-discriminating conventional activation mode by collision. Here, we describe the implementation of visible LID at 473 nm in a Q-Exactive-Orbitrap mass spectrometer for the specific detection of cysteine-containing peptides tagged with a Dabcyl group. HCD cell DC offset and irradiation time were optimized to obtain high fragmentation yield and spectra free of contaminating CID product ions, while keeping the irradiation time scale compatible with chromatographic separation. With this optimized experimental set-up, the selective detection of cysteine-containing peptides in a whole tryptic hydrolysate of three combined proteins is demonstrated by comparing all ion fragmentation (AIF) spectra recorded online with and without laser irradiation.

Simultaneous electrochemical oxidation/ionization of a selenoxanthene revealed by on-line electrospray-high resolution mass spectrometry

The oxidation behavior of the antioxidant 9-phenyl-2,3,4,5,6,7,8,9-octahydro-1H-selenoxanthene (SEL) is studied by means of an instrumental on-line set-up consisting of an electrochemical (EC) thin-layer cell coupled directly to the electrospray ionization (ESI) source of a high resolution Orbitrap mass spectrometer (HR-MS). A potential ramp between 0 and 2500mV vs. Pd/H2 (10mV/s) was applied to the EC working electrode in order to screen for emerging oxidation products. Presentation of the obtained data as three-dimensional mass voltammograms visualizes the oxidation/ionization efficiency in dependency of the potential applied. EC oxidation gave rise to the formation of ten oxidation products including the dehydrogenated cationic SEL, various oxygenated as well as dimeric species. Molecular formulae could successfully be assigned for all oxidation products with deviations below 5ppm between calculated and measured m/z. Further characterization of the oxidation products was achieved by extending the system with online high pressure liquid chromatography (HPLC). All-ion fragmentation of the oxidation products was carried out to confirm the proposed structures. Electrochemical oxidation enabled a first prediction of possible phase-I metabolism reactions of SEL, which are likely to occur in vivo. Therefore, electrochemically assisted electrospray ionization enables method development for the identification of SEL and its potential metabolites by means of HPLC/ESI-MS.

Top-down MS for rapid methionine oxidation site assignment in filgrastim

Protein therapeutics have emerged as a major new class of pharmaceuticals. One important shelf-life-limiting factor of biopharmaceuticals is methionine oxidation, and therefore, it is important that analytical methods are able to thoroughly characterize all possible oxidized variants. Here, we present a fast and sensitive method to perform online methionine oxidation site assignment using granulocyte colony-stimulating factor (filgrastim) as a model. The method is based on top-down MS using the all-ion fragmentation mode of the Exactive benchtop mass spectrometer. Conditions that provide information on the intact mass of the protein as well as on fragment ions that allow unambiguous site assignment of methionine oxidation in filgrastim variants as low as 0.12 % of total peak area in a chromatographic time scale were identified. Using this method, we performed methionine oxidation site assignment in H2O2-stressed filgrastim and in filgrastim which was stored at intended conditions, respectively. We show that the relative abundance of oxidation species observed in filgrastim stored under intended conditions differs strikingly from the oxidized species observed after H2O2 stress. Additionally, we report an oxidized filgrastim variant that has not been previously described in the literature. FigureA top-down approach on an Exactive benchtop mass spectrometer in all-ion fragmentation mode is a highly attractive alternative to the traditional approach of isolation/bottom-up analysis for methionine oxidation site assignement in biopharmaceuticals. With a sensitivity as low as 0.12 % of total peak area and a throughput of about one sample per hour, the method is highly suitable for a thorough characterization of oxidized methionine residues

Label-free quantitative proteomics reveals regulation of interferon-induced protein with tetratricopeptide repeats 3 (IFIT3) and 5'-3'-exoribonuclease 2 (XRN2) during respiratory syncytial virus infection

A large quantitative study was carried out to compare the proteome of respiratory syncytial virus (RSV) infected versus uninfected cells in order to determine novel pathways regulated during viral infection. RSV infected and mock-infected HEp2 cells were lysed and proteins separated by preparative isoelectric focussing using offgel fractionation. Following tryptic digestion, purified peptides were characterized using label-free quantitative expression profiling by nano-ultra performance liquid chromatography coupled to electrospray ionisation mass spectrometry with collision energy ramping for all-ion fragmentation (UPLC-MSE). A total of 1352 unique cellular proteins were identified and their abundance compared between infected and non-infected cells. Ingenuity pathway analysis revealed regulation of several central cellular metabolic and signalling pathways during infection. Selected proteins that were found regulated in RSV infected cells were screened by quantitative real-time PCR for their regulation on the transcriptional level. Synthesis of interferon-induced protein with tetratricopeptide repeats 3 (IFIT3) and 5'-3'-exoribonuclease 2 (XRN2) mRNAs were found to be highly induced upon RSV infection in a time dependent manner. Accordingly, IFIT3 protein levels accumulated during the time course of infection. In contrast, little variation was observed in XRN2 protein levels, but different forms were present in infected versus non-infected cells. This suggests a role of these proteins in viral infection, and analysis of their function will shed further light on mechanisms of RNA virus replication and the host cell defence machinery.

Elemental formula annotation of polar and lipophilic metabolites using 13C, 15N and 34S isotope labelling, in combination with high‐resolution mass spectrometry

The unbiased and comprehensive analysis of metabolites in any organism presents a major challenge if proper peak annotation and unambiguous assignment of the biological origin of the peaks are required. Here we provide a comprehensive multi-isotope labelling-based strategy using fully labelled (13) C, (15) N and (34) S plant tissues, in combination with a fractionated metabolite extraction protocol. The extraction procedure allows for the simultaneous extraction of polar, semi-polar and hydrophobic metabolites, as well as for the extraction of proteins and starch. After labelling and extraction, the metabolites and lipids were analysed using a high-resolution mass spectrometer providing accurate MS and all-ion fragmentation data, providing an unambiguous readout for every detectable isotope-labelled peak. The isotope labelling assisted peak annotation process employed can be applied in either an automated database-dependent or a database-independent analysis of the plant polar metabolome and lipidome. As a proof of concept, the developed methods and technologies were applied and validated using Arabidopsis thaliana leaf and root extracts. Along with a large repository of assigned elemental compositions, which is provided, we show, using selected examples, the accuracy and reliability of the developed workflow.

Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation

The orbitrap mass analyzer combines high sensitivity, high resolution, and high mass accuracy in a compact format. In proteomics applications, it is used in a hybrid configuration with a linear ion trap (LTQ-Orbitrap) where the linear trap quadrupole (LTQ) accumulates, isolates, and fragments peptide ions. Alternatively, isolated ions can be fragmented by higher energy collisional dissociation. A recently introduced stand-alone orbitrap analyzer (Exactive) also features a higher energy collisional dissociation cell but cannot isolate ions. Here we report that this instrument can efficiently characterize protein mixtures by alternating MS and “all-ion fragmentation” (AIF) MS/MS scans in a manner similar to that previously described for quadrupole time-of-flight instruments. We applied the peak recognition algorithms of the MaxQuant software at both the precursor and product ion levels. Assignment of fragment ions to co-eluting precursor ions was facilitated by high resolution (100,000 at m/z 200) and high mass accuracy. For efficient fragmentation of different mass precursors, we implemented a stepped collision energy procedure with cumulative MS readout. AIF on the Exactive identified 45 of 48 proteins in an equimolar protein standard mixture and all of them when using a small database. The technique also identified proteins with more than 100-fold abundance differences in a high dynamic range standard. When applied to protein identification in gel slices, AIF unambiguously characterized an immunoprecipitated protein that was barely visible by Coomassie staining and quantified it relative to contaminating proteins. AIF on a benchtop orbitrap instrument is therefore an attractive technology for a wide range of proteomics analyses.