Identification and sequencing analysis of intact proteins via collision-induced dissociation and quadrupole time-of-flight mass spectrometry

Identifying unknown proteins has become a central focal point for proteomic and biopharmaceutical development laboratories. Our laboratory investigated using quadrupole time-of-flight mass spectrometry (Qq/TOFMS) for the analysis of intact proteins for the purpose of identifying unknowns while limiting the number of sample-handling steps between protein extraction and identification. Eight standard proteins, both unmodified and disulfide-bonded and ranging in mass from 5 to 66 kDa, were analyzed using nanoelectrospray and collision-induced dissociation to generate peptide sequence tags. An MS analysis, followed by MS/MS analyses on two to five individual protein charge states, were obtained to make an identification. Peptide sequence tags were extracted from the MS/MS data and used, in conjunction with molecular mass and source origin, to obtain protein identifications using the web-based search engine ProteinInfo (www.proteometrics.com). All of the proteins were unambiguously identified from the input data, after which, all of the major product ions were identified for structural information. In most cases, N- and/or C-terminal ions, and also stretches of consecutive product ions from the protein interior, were observed. This method was applied to the analysis and identification of an unknown detected via reversed-phase high-performance liquid chromatography.     

Optimization of a quadrupole ion storage trap as a source for time‐of‐flight mass spectrometry

Designs of a quadrupole ion trap (QIT) as a source for time‐of‐flight (TOF) mass spectrometry are evaluated for mass resolution, ion trapping, and laser activation of trapped ions. Comparisons are made with the standard hyperbolic electrode ion trap geometry for TOF mass analysis in both linear and reflectron modes. A parallel‐plate design for the QIT is found to give significantly improved TOF mass spectrometer performance. Effects of ion temperature, trapped ion cloud size, mass, and extraction field on mass resolution are investigated in detail by simulation of the TOF peak profiles. Mass resolution (m/Δm) values of several thousand are predicted even at room temperature with moderate extraction fields for the optimized design. The optimized design also allows larger radial ion collection size compared with the hyperbolic ion trap, without compromising the mass resolution. The proposed design of the QIT also improves the ion–laser interaction volume and photon collection efficiency for fluorescence measurements on trapped ions. Copyright © 2011 John Wiley & Sons, Ltd.     

Ion-trap versus quadrupole for analysis of quaternary ammonium herbicides by LC-MS

Summary An ion-trap mass spectrometer for determination of quaternary ammonium herbicides in water samples is evaluated. Implementation of the method previously optimized in a quadrupole mass spectrometer (VG Platform II) in an ion-trap (LCQ) required modifications to the sample inlet of the electrospray source. Quality parameters were established and detection limits, after trace enrichment, range 5–50 ng L⁻¹. Good reproducibilities (day-to-day and run-to-run) <12% were obtained. The method was applied to analysis of spiked samples and the results were comparable with those determined using a quadrupole mass spectrometer.     

Charge state dependent collision-induced dissociation of native and reduced porcine elastase

The [M + 20H](20+)-[M + 12H](12+) charge states of native and reduced porcine elastase, a 25.9 kDa serine protease, were subjected to collisional activation in a quadrupole ion trap. For most charge states, ion parking was used to increase the number of parent ions over that yielded directly by electrospray. Ion-ion proton transfer reactions were used to reduce product ion charge states largely to +1 to simplify spectral interpretation. Both forms of the protein show charge state dependent fragmentation behavior. The native protein, which contains four disulfide linkages, shows almost no evidence for fragmentation within the regions of the protein linked by disulfide bonds. However, at the lowest charge states studied, evidence for cleavage of a least one of the disulfide bonds was evident in the appearance of a c-type ion. The highest charge states of native elastase showed several prominent cleavages C-terminal to valine residues. As the charge state decreased, however, preferential cleavages at acidic amino acid residues became important. The reduced form of the protein did not show particularly prominent cleavages at valine residues. However, many of the same preferential cleavages at acidic amino acid residues noted for the native protein were also observed in the same charge states of the reduced protein. The reduced protein also showed additional cleavages from regions of the protein that are ordinarily protected by disulfide linkages in the native form.     

Phosphopeptide detection and sequencing by matrix-assisted laser desorption/ionization quadrupole time-of-flight tandem mass spectrometry

A prototype matrix-assisted laser desorption/ionization quadrupole time-of-flight (MALDI-TOF) tandem mass spectrometer was used to sequence a series of phosphotyrosine-, phosphothreonine- and phosphoserine-containing peptides. The high mass resolution and mass accuracy of the instrument allowed the localization of one, three or four phosphorylated amino acid residues in phosphopeptides up to 3.1 kDa. Tandem mass spectra of two different phosphotyrosine peptides permitted amino acid sequence determination and localization of one and three phosphorylation sites, respectively. The phosphotyrosine immonium ion at m/z 216.04 was observed in these MALDI low-energy CID tandem mass spectra. Elimination of phosphate groups was evident from the triphosphorylated peptide but not from the monophosphorylated species. The main fragmentation pathway for the synthetic phosphothreonine-containing peptide and for phosphoserine-containing peptides derived from beta-casein and ovalbumin was the beta-elimination of phosphoric acid with concomitant conversion of phosphoserine to dehydroalanine and phosphothreonine to 2-aminodehydrobutyric acid. Peptide fragment ions of the b- and y-type allowed, in all cases, the localization of phosphorylation sites. Ion signals corresponding to (b-17), (b-18) and (y-17) fragment ions were also observed. The abundant neutral loss of phosphoric acid (-98 Da) is useful for femtomole level detection of phosphoserine-peptides in crude peptide mixtures generated by gel in situ digestion of phosphoproteins.     

Protein identification via ion-trap collision-induced dissociation and examination of low-mass product ions

A whole-protein tandem mass spectrometry approach for protein identification based on precursor ion charge state concentration via ion/ion reactions, ion-trap collisional activation, ion/ion proton-transfer reactions involving the product ions, and mass analysis over a narrow m/z range (up to m/z 2000) is described and evaluated. The experiments were carried out with a commercially available electrospray ion-trap instrument that has been modified to allow for ion/ion reactions. Reaction conditions and the approach to searching protein databases were developed with the assumption that the resolving power of the mass analyzer is insufficient to distinguish charge states on the basis of the isotope spacings. Ions derived from several charge states of cytochrome c, myoglobin, ribonuclease A, and ubiquitin were used to evaluate the approach for protein identification and to develop a two-step procedure to database searching to optimize specificity. The approach developed with the model proteins was then applied to whole cell lysate fractions of Saccharomyces cerevisiae. The results are illustrated with examples of assignments made for three a priori unknown proteins, each selected randomly from a lysate fraction. Two of the three proteins were assigned to species present in the database, whereas one did not match well any database entry. The combination of the mass measurement and the product ion masses suggested the possibility for the oxidation of two methionine residues of a protein in the database. The examples show that this limited whole-protein characterization approach can provide insights that might otherwise be lacking with approaches based on complete enzymatic digestion.     

Using collision-induced dissociation with corrections for the ion number of degrees of freedom for quick comparisons of relative bonding strength

The number of degrees of freedom-dependent stability of ions and ion-neutral non-covalent complexes under collision-induced dissociation (CID) conditions was studied in a quadrupole ion trap mass spectrometer. It was found that the stability of ions as probed by energy-variable CID has a linear dependence on the total number of degrees of freedom for the ions (or ion-neutral complexes) with the same (or nearly the same) bonding energy. The slope of such a stability vs number of degrees of freedom dependence correlates with the binding energy. Proton-bound amine dimers display the lowest slope as they have weak bonds. Breaking covalent bonds will result in much greater slopes. In addition to the binding energy, the vibrational frequencies of the ion also affect the stability vs number of degrees of freedom behavior. Studying such a dependence of the CID stability in a system paves the way for direct relative binding energy comparisons. The application of this approach is demonstrated by testing the relative heme affinities of anti-malaria drugs and related compounds.     

Tandem mass spectrometry of Cu(II) complexes: the effects of ligand donor group on dissociation

A quadrupole ion trap mass spectrometer was used to study the dissociation patterns of Cu(II) complexes with various linear podand ligands. Cu(II) complexes having different combinations of nitrogen-, oxygen- and sulfur-containing terminal functionality attached to a diethylenetriamine (DIEN) framework were ionized by electrospray and collision-induced dissociation (CID) was used to generate product ions. Regardless of the particular functional groups present, the complexes undergo predominantly heterolytic cleavages of carbon-carbon bonds along the DIEN backbone with Cu remaining coordinated to one of the two terminal functional groups. Upon dissociation, Cu's preference to remain coordinated to a particular functional group follows the trend thioether > amine > imidazole > pyridine > ether. A simple evaluation of this trend based upon metal-functional group binding affinity appears not to be adequate for fully explaining these observations. The tendency of Cu(II) to be reduced upon dissociation helps explain the observed trend, as does the flexibility of the functional group, which affects its ability to orient its dipole effectively toward the metal.     

In-source fragmentation and accurate mass analysis of multiclass flavonoid conjugates by electrospray ionization time-of-flight mass spectrometry

In-source collision-induced dissociation (CID) fragmentation features of multiclass flavonoid glycoconjugates were examined using liquid chromatography electrospray time-of-flight mass spectrometry. Systematic experiments were performed to search for optimal conditions for in-source fragmentation in both positive and negative ion modes. The objective of the study was to attain uniformly appropriate conditions for a wide range of analytes independently of the aglycone, the attached sugar part and the type of bond between the aglycone and the glycan moieties (O- or C-glycosides). Studied substances included representatives of flavonols, flavones, flavanones and anthocyanins and, regarding their glycan parts, mono-, di- and triglycosides with varying distribution of carbohydrate moieties (di-O-glycosides, O-diglycosides, O,C-diglycosides). The breakdown properties of the analytes along with the abundances of the characteristic diagnostic ions required for structural elucidation of complex flavonoid derivatives were evaluated. An optimized value was found for the instrument parameter (fragmentor voltage) affecting the in-source CID fragmentation of the analytes [230 V (ESI+) and 330 V (ESI-)]. Thus, appropriate performance in terms of both highly sensitive full-scan acquisition and fragmentation information was obtained for all the investigated flavonoids. In addition, singularities in the abundance of selected diagnostic ions (e.g. Y(0), Y(1) and Y*) due to variations in the interglycosidic linkage (rutinoside-neohesperidoside) in the glycan part were found and are also evaluated and discussed in detail. The combination of in-source CID fragmentation with high mass accuracy MS detection establishes a working basis for the development of versatile and useful LC-MS methods for wide-scope screening, non-targeted detection and tentative identification of flavonoid derivatives.     

Mass spectrometry and planetary exploration: A brief review and future projection

Since the inception of mass spectrometry more than a century ago, the field has matured as analytical capabilities have progressed, instrument configurations multiplied, and applications proliferated. Modern systems are able to characterize volatile and nonvolatile sample materials, quantitatively measure abundances of molecular and elemental species with low limits of detection, and determine isotopic compositions with high degrees of precision and accuracy. Consequently, mass spectrometers have a rich history and promising future in planetary exploration. Here, we provide a short review on the development of mass analyzers and supporting subsystems (eg, ionization sources and detector assemblies) that have significant heritage in spaceflight applications, and we introduce a selection of emerging technologies that may enable new and/or augmented mission concepts in the coming decades.     

Characterization of tropane and cinnamamide alkaloids from Scopolia tangutica by high‐performance liquid chromatography with quadrupole time‐of‐flight tandem mass spectrometry

Scopolia tangutica is a traditional Chinese medicine used for antispasmodic, anesthesia, analgesia, and sedation. Its medicinal activity is associated to alkaloid constituents, including tropane and cinnamamide types. Low content of alkaloids in plant makes them difficult to be isolated and identified. The present work developed an effective method to quickly characterize alkaloids from Scopolia tangutica by high‐performance liquid chromatography coupled with quadrupole time‐of‐flight tandem mass spectrometry. Thirteen reference compounds were studied for their fragmentation pathways, including five tropane alkaloids and eight cinnamamide ones. Alkaloid constituent was analyzed by an optimized high‐performance liquid chromatography method and mass spectrometry analysis to achieve systematic characterization of alkaloids from Scopolia tangutica. As a result, 53 compounds were identified, including 21 tropane alkaloids (eight new ones), 18 caffeoyl ones (ten new ones) and 14 dicaffeoyl ones (seven new ones). It was important to provide rich information in phytochemical study and structure‐guided isolation of important compounds from this plant.     

Detection of singly- and doubly-charged quaternary ammonium drugs in equine urine by liquid chromatography/tandem mass spectrometry

Quaternary ammonium drugs (QADs) are anticholinergic agents some of which are known to have been abused or misused in equine sports. A recent review of literature shows that the screening methods reported thus far for QADs mainly cover singly-charged QADs. Doubly-charged QADs are extremely polar substances which are difficult to be extracted and poorly retained on reversed-phase columns. It would be ideal if a comprehensive method can be developed which can detect both singly- and doubly-charged QADs. This paper describes an efficient liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for the simultaneous detection and confirmation of 38 singly- and doubly-charged QADs at sub-parts-per-billion (ppb) to low-ppb levels in equine urine after solid-phase extraction.     

Analysis of furanocoumarins from Yemenite Dorstenia species by liquid chromatography/electrospray tandem mass spectrometry

A series of prevailing prenylated furanocoumarins from leaves of Dorstenia gigas and Dorstenia foetida (Moraceae) were investigated by liquid chromatography/electrospray tandem mass spectrometry. The mass spectral behavior of the furanocoumarins under positive ion electrospray conditions is discussed using both an ion trap and a triple quadrupole system. It is demonstrated that both methods represent valuable tools not only for the rapid classification of this type of compounds, but also with respect to their substitution pattern. Copyright © 2012 John Wiley & Sons, Ltd.     

Collision-induced dissociation pathways of yeast sphingolipids and their molecular profiling in total lipid extracts: a study by quadrupole TOF and linear ion trap-orbitrap mass spectrometry

The yeast Saccharomyces cerevisiae synthesizes three classes of sphingolipids: inositolphosphoceramides (IPCs), mannosyl-inositolphosphoceramides (MIPCs), and mannosyl-diinositolphosphoceramides (M(IP)2C). Tandem mass spectrometry of their molecular anions on a hybrid quadrupole time-of-flight (QqTOF) instrument produced fragments of inositol-containing head groups, which were specific for each lipid class. MS(n) analysis performed on a hybrid linear ion trap-orbitrap (LTQ Orbitrap) mass spectrometer with better than 3 ppm mass accuracy identified fragment ions specific for the amide-linked fatty acid and the long chain base moieties in individual molecular species. By selecting m/z of class-specific fragment ions for multiple precursor ion scanning, we profiled yeast sphingolipids in total lipid extracts on a QqTOF mass spectrometer. Thus, a combination of QqTOF and LTQ Orbitrap mass spectrometry lends itself to rapid, comprehensive and structure-specific profiling of the molecular composition of sphingolipids and glycerophospholipids in important model organisms, such as fungi and plants.     

Analysis of phenolic choline esters from seeds of Arabidopsis thaliana and Brassica napus by capillary liquid chromatography/electrospray‐ tandem mass spectrometry

Total phenolic choline ester fractions prepared from seeds of Arabidopsis thaliana and Brassica napus were analyzed by capillary LC/ESI‐QTOF‐MS and direct infusion ESI‐FTICR‐MS. In addition to the dominating sinapoylcholine, 30 phenolic choline esters could be identified based on accurate mass measurements, interpretation of collision‐induced dissociation (CID) mass spectra, and synthesis of selected representatives. The compounds identified so far include substituted hydroxycinnamoyl‐ and hydroxybenzoylcholines, respective monohexosides as well as oxidative coupling products of phenolic choline esters and monolignols. Phenolic choline esters are well separable by reversed‐phase liquid chromatography and sensitively detectable using electrospray ionization mass spectrometry in positive ion mode. CID mass spectra obtained from molecular ions facilitate the characterization of both the type and substitution pattern of such compounds. Therefore, LC/ESI‐MS/MS represents a valuable tool for comprehensive qualitative and quantitative analysis of this compound class. Copyright © 2008 John Wiley & Sons, Ltd.     

Atmospheric pressure chemical ionization mass spectrometry and in-source fragmentation of lutein esters

Negative-ion atmospheric pressure chemical ionization (APCI) mass spectrometry and in-source collisionally induced dissociation (CID) were employed to obtain structural information of lutein esters from marigold extract. Both molecular ions and structurally significant fragments corresponding to the loss of fatty acids were observed in high abundance in the current study. Six lutein diesters including lauroylmyristoyl-lutein (LML), dimyristoyl-lutein (dML), myristoylpalmitoyl-lutein (MPL), dipalmitoyl-lutein (dPL), palmitoylstearoyl-lutein (PSL) and distearoyl-lutein (dSL) were characterized in a marigold flower extract. Breakdown curves (plots of relative ion abundance vs. internal energy) of three lutein diesters were established by monitoring the relative ion abundance of molecular and fragment ions at different cone voltages during negative-ion APCI-LC/MS analysis.     

Ultra high performance liquid chromatography with quadrupole time-of-flight tandem mass spectrometry and liquid chromatography with tandem mass spectrometry combined with chemometric analysis as an approach for the quality evaluation of Mume Fructus

Mume Fructus is an important traditional Chinese medicine that has been widely used in the treatment of intestinal diseases and asthma for thousands of years. In order to evaluate the quality of Mume Fructus in different processing methods, the main chemical components in Mume Fructus were investigated and a method was established for simultaneous quantification of organic acids of Mume Fructus. First, an optimized ultra-performance liquid chromatography-quadrupole-time of flight tandem-mass spectrometry method was used to identify the structures of main components in Mume Fructus. A total of 41 chemical compounds were identified, including 11 organic acids, 13 flavonoids, and three fatty acids. The contents of 11 organic acids in 18 batches of Mume Fructus from different processing methods were simultaneously determined by a liquid chromatography with tandem mass spectrometry method. The results of quantitative and hierarchical cluster analysis indicated that Mume Fructus under different processing methods were rich in the above 11 organic acids and the contents were obviously different. Taken together, the proposed quality evaluation method was fast and comprehensively reflects the content of the main chemical components in Mume Fructus under different processing methods, and provides a useful reference for the quality control and evaluation of Mume Fructus.     

Identification of glucuronide conjugates of ketobemidone and its phase I metabolites in human urine utilizing accurate mass and tandem time-of-flight mass spectrometry

The glucuronide conjugates of ketobemidone, norketobemidone and hydroxymethoxyketobemidone were identified in human urine post-intravenous administration of Ketogan Novum. The human urine was extracted on a mixed-mode solid-phase micro-column before analysis with liquid chromatography/electrospray ionization time-of-flight mass spectrometry (LC/ESI-TOF-MS) and tandem MS (MS/MS). Accurate mass and collision-induced dissociation product ion spectra were used for identification of the glucuronide conjugates. Two different TOF mass spectrometers were used and the accurate mass measurements were performed on three separate days with each instrument. The accuracy of the mass measurements was better than 2.1 ppm for two out of three conjugates and the inter-day relative standard deviation was within +/-0.00049%. The MS/MS fragmentation patterns of the conjugates were in accordance with those of the synthetic aglycones and included peaks originating from the [M + H](+) ion of the respective aglycone.     

Application of liquid chromatography/quadrupole time-of-flight mass spectrometry (LC-QqTOF-MS) in the environmental analysis

This paper gives an overview of the potentials of liquid chromatography-hybrid quadrupole time-of-flight mass spectrometry (LC-QqTOF) in the environmental analysis. Examples of applications of QqTOF instruments for target analysis of pharmaceuticals and pesticides are presented and discussed, as well as applications aimed on the identification of unknown compounds present in environmental waters or on the elucidation of structures of biodegradation and photodegradation products. Specific issues such as uncertainty of mass measurement and quantitative performances are discussed in details.     

Evidence for linkage position determination in known feruloylated mono- and disaccharides using electrospray ion trap mass spectrometry

Various feruloylated arabinose- and galactose-containing mono- and disaccharides with known linkage configurations (2-O-(trans-feruloyl)-L-arabinopyranose, 5-O-(trans-feruloyl)-L-arabinofuranose, O-[2-O-(trans-feruloyl)-alpha-L-arabinofuranosyl]-(1-->5)-L-arabinofuranose, and O-[6-O-(trans-feruloyl)-beta-D-galactopyranosyl]-(1-->4)-D-galactopyranose) were analyzed by electrospray ionization mass spectrometry using an ion trap or a quadrupole time-of-flight (Q-TOF) mass analyzer. Collision-induced dissociation (CID) experiments using the two mass analyzers generated similar tandem mass spectrometric (MS/MS) fragmentation patterns. However, the ester-bond cleavage ions were more abundant using the Q-TOF mass analyzer. Compared with the positive ion mode, the negative ion mode produces simpler and more useful CID product-ion patterns. For arabinose-containing feruloylated compounds, results obtained with both analyzers show that it is possible to assign the location of the feruloyl group to the O-2 or O-5 of arabinosyl residues. In the characterization of the 2-O-feruloyl and 5-O-feruloyl linkages, the relative abundance of the cross-ring fragment ions at m/z 265 (-60 u or -62 u after 18O-labelling) and at m/z 217 (-108 u or -110 u after 18O-labelling) play a relevant role. For galactose-containing feruloylated compounds, losses of 60, 90 and 120 Da observed in MS3 experiment correspond to the production of 0,2A1, 0,3A1 and (0,2A1-60 Da) cross-ring cleavage ions, respectively, fixing the location of feruloyl group at the O-6 of the galactose residue.