Integration of Trapped Ion Mobility Spectrometry and Ultraviolet Photodissociation in a Quadrupolar Ion Trap Mass Spectrometer
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There is a growing demand for lower-cost, benchtop analytical instruments with complementary separation capabilities for the screening and characterization of biological samples. In this study, we report on the custom integration of trapped ion mobility spectrometry and ultraviolet photodissociation capabilities in a commercial Paul quadrupolar ion trap multistage mass spectrometer (TIMS-QIT-MSn UVPD platform). A gated TIMS operation allowed for the accumulation of ion mobility separated ion in the QIT, followed by a mass analysis (MS1 scan) or m/z isolation, followed by selected collision induced dissociation (CID) or ultraviolet photodissociation (UVPD) and a mass analysis (MS2 scan). The analytical potential of this platform for the analysis of complex and labile biological samples is illustrated for the case of positional isomers with varying PTM location of the histone H4 tryptic peptide 4-17 singly and doubly acetylated and the histone H3.1 tail (1-50) singly trimethylated. For all cases, a baseline ion mobility precursor molecular ion preseparation was obtained. The tandem CID and UVPD MS2 allowed for effective sequence confirmation as well as the identification of reporter fragment ions associated with the PTM location; a higher sequence coverage was obtained using UVPD when compared to CID. Different from previous IMS-MS implementation, the novel TIMS-QIT-MSn UVPD platform offers a lower-cost alternative for the structural characterization of biological molecules that can be widely disseminated in clinical laboratories.Keywords:
Ion-mobility spectrometry
Ultraviolet
Quadrupole ion trap
Collision-induced dissociation
Electron-transfer dissociation
Characterization
Orbitrap
Quadrupole ion trap
Electron-transfer dissociation
Tandem mass tag
Collision-induced dissociation
Top-down proteomics
Hybrid mass spectrometer
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Abstract A short DC voltage pulse is applied to one endcap of a quadrupole ion‐trap mass spectrometer to activate trapped ions. High internal‐energy deposition is achieved as evidenced by 91 + /92 + peak ratios in excess of 20 for dissociation of the n‐butylbenzene molecular ion. 1 The amount of internal energy can be controlled directly by vaarying the amplitude of the pulse. Dissociation efficiencies are less than those typically observed for collision‐induced dissociation in the ion trap and range from 50% at low internal energy deposition to 5% at maximum internal energy deposition.
Quadrupole ion trap
Collision-induced dissociation
Tandem
Quadrupole mass analyzer
Internal energy
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Quadrupole ion trap
Collision-induced dissociation
Tandem
Top-down proteomics
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Two related methods for effecting electron-transfer dissociation (ETD) are described that involve either the storage of analyte cations in a linear ion trap while reagent anions are transmitted through the cations or storage of the reagent anions with transmission of the analyte cations. In the former approach, the ETD products are captured and stored in the linear ion trap for subsequent mass analysis. In the latter approach, the ETD products pass through the linear ion trap and must be collected or directly mass-analyzed by an external device. In the present study, another linear ion trap is placed in series with the ion trap where the ion/ion reaction was employed. A pulsed dual ion source approach coupled with a hybrid triple quadrupole/linear ion trap instrument was used to illustrate these methods. The two approaches give similar results in terms of the identities and relative abundances of the ETD products. Under optimum conditions, the two approaches also give comparable extents of ion/ion reactions for the same reaction time. Also, conversions of precursor ions to product ions over the same reaction time are similar to those noted for experiments in which ions of both polarities are stored simultaneously. These approaches, therefore, provide expanded experimental options for the use of ETD. An advantage of transmission mode experiments that they hold over mutual storage mode experiments is that they do not require that any specialized measures be taken to enable the simultaneous storage of oppositely charged ions.
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Electron-transfer dissociation
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Collision induced dissociation (CID) in a quadrupole ion trap mass spectrometer using the conventional 30 ms activation time is compared with high amplitude short time excitation (HASTE) CID using 2 ms and 1 ms activation times. As a result of the shorter activation times, dissociation of the parent ions using the HASTE CID technique requires resonance excitation voltages greater than conventional CID. After activation, the rf trapping voltage is lowered to allow product ions below the low mass cut-off to be trapped. The HASTE CID spectra are notably different from those obtained using conventional CID and can include product ions below the low mass cut-off for the parent ions of interest. The MS/MS efficiencies of HASTE CID are not significantly different when compared with the conventional 30 ms CID. Similar results were obtained with a two-dimensional (linear) ion trap and a three-dimensional ion trap.
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Collision-induced dissociation
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The concept and method for mass selective ion transfer and accumulation within quadrupole ion trap arrays have been demonstrated. Proof-of-concept experiments have been performed on two sets of ion trap arrays: (1) a linear ion trap with axial ion ejection plus a linear ion trap with radial ion ejection; (2) a linear ion trap with axial ion ejection plus a linear ion trap with axial ion ejection. In both sets of ion trap arrays, ions trapped in the first ion trap could be mass selectively transferred and accumulated into the second ion trap, while keeping other ions reserved in the first ion trap. Different operating modes have been implemented and tested, including transferring all ions, ions within a selected mass range, ions with a mass-to-charge ratio of 1, and randomly selected ions. Unit mass resolution for ion transfer and ∼90% ion transfer efficiency has been achieved. A new tandem mass spectrometry scheme for analyzing multiple precursor ions in a single sample injection has been demonstrated, which would improve instrument duty cycle and sample utilization rate (especially for very limited samples), potentially facilitate applications like single cell analyses, and improve electron transfer dissociation efficiency.
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Assigning glycosylation sites of glycoproteins and their microheterogeneity is still a very challenging analytical task despite the rapid advancements in mass spectrometry. It is shown here that glycopeptide ions can be fragmented efficiently using the higher-energy C-trap dissociation (HCD) feature of a linear ion trap orbitrap hybrid mass spectrometer (LTQ Orbitrap). An attractive aspect of this dissociation option is the generation of distinct Y1 ions (peptide+GlcNAc), thus allowing unequivocal assignment of N-glycosylation sites of glycoproteins. The combination of the very informative collision-induced dissociation spectra acquired in the linear ion trap with the distinct features of HCD offers very useful information aiding in the characterization of the glycosylation sites of glycoproteins. The HCD activation energy needed to obtain optimum Y1 ions was studied in terms of glycan structure and charge state, and size and structure of the peptide backbone. The latter appeared to be primarily dictating the needed HCD energy. The distinct Y1 ion formation in HCD facilitated an easy assignment of such an ion and its subsequent isolation and dissociation through multiple-stage tandem mass spectrometry. The resulting MS(3) spectrum of the Y1 ion facilitates database searching and de novo sequencing thus prompting the subsequent identification of the peptide backbone and associated glycosylation sites. Moreover, fragment ions formed by HCD are detected in the Orbitrap, thus overcoming the 1/3 cut-off limitation that is commonly associated with ion trap mass spectrometers. As a result, in addition to the Y1 ion, the common glycan oxonium ions are also detected. The high mass accuracy offered by the LTQ Orbitrap mass spectrometer is also an attractive feature that allows a confident assignment of protein glycosylation sites and the microheterogeneity of such sites.
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Abstract Doubly protonated peptides that undergo an electron transfer reaction without dissociation in a linear ion trap can be subjected to beam‐type collisional activation upon transfer from the linear ion trap into an adjacent mass analyzer, as demonstrated here with a hybrid triple quadrupole/linear ion trap system. The activation can be promoted by use of a DC offset difference between the ion trap used for reaction and the ion trap into which the products are injected of 12–16 V, which gives rise to energetic collisions between the transferred ions and the collision/bath gas employed in the linear ion trap used for ion/ion reactions. Such a process can be executed routinely on hybrid linear ion trap/triple quadrupole tandem mass spectrometers and is demonstrated here with several model peptides as well as a few dozen tryptic peptides. Collisional activation of the peptide precursor ions that survive electron transfer frequently provides structural information that is absent from the precursor ions that fragment spontaneously upon electron transfer. The degree to which additional structural information is obtained by collisional activation of the surviving singly charged peptide ions depends upon peptide size. Little or no additional structural information is obtained from small peptides (<8 residues) due to the high electron transfer dissociation (ETD) efficiencies noted for these peptides as well as the extensive sequence information that tends to be forthcoming from ETD of such species. Collisional activation of the surviving electron transfer products provided greatest benefit for peptides of 8–15 residues. Copyright © 2007 John Wiley & Sons, Ltd.
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Due to their versatility, quadrupole ion traps have become popular mass spectrometers in the growing field of proteomics. High sensitivity, user friendliness and low cost are the key features that have contributed to the success of the technology. However, mass measurement accuracy, resolution and mass range are still not comparable to the analytical performances obtained on other mass spectrometers. In the past 5 years, researchers have tried to overcome these drawbacks, focusing their attention on two different aspects of ion-trap mass spectrometry, development of novel types of ion traps and manipulation of the gas-phase ion chemistry, in order to obtain alternative techniques for tandem mass spectrometry analysis. In the field of trapping devices, improvements in instrumental design have led to the linear ion trap, digital ion trap and orbitrap. Activation methods based on electrons, chemically produced by an anion or from irradiation with an electron beam, have demonstrated their utility in providing complementary sequence information for improving confidence in protein identification.
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Top-down proteomics
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Electron-transfer dissociation
Hybrid mass spectrometer
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Mass spectrometric identification and characterization of growth-promoting anabolic-androgenic steroids in biological matrices has been a major task for doping control as well as food safety laboratories. The fragmentation behavior of stanozolol, its metabolites 17-epistanozolol, 3'-OH-stanozolol, 4alpha-OH-stanozolol, 4beta-OH-stanozolol, 17-epi-16alpha-OH-stanozolol, 16alpha-OH-stanozolol, 16beta-OH-stanozolol, as well as the synthetic analogues 4-dehydrostanozolol, 17-ketostanozolol, and N-methyl-3'-OH-stanozolol, was investigated after positive electrospray ionization and subsequent collision-induced dissociation utilizing a quadrupole-linear ion trap and a novel linear ion trap-orbitrap hybrid mass spectrometer. Stable isotope labeling, H/D-exchange experiments, MS3 analyses and high-resolution/high mass accuracy measurements of fragment ions were employed to allow proposals for charge-driven as well as charge-remote fragmentation pathways generating characteristic product ions of stanozolol at m/z 81, 91, 95, 105, 119, 135 and 297 and 4-hydroxylated stanozolol at m/z 145. Fragment ions were generated by dissociation of the steroidal A- and B-ring retaining the introduced charge within the pyrazole function of stanozolol and by elimination of A- and B-ring fractions including the pyrazole residue. In addition, a charge-remote fragmentation causing the neutral loss of methanol was observed, which was suggested to be composed by the methyl residue at C-18 and the hydroxyl function located at C-17.
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Orbitrap
Collision-induced dissociation
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Ion trapping
Hybrid mass spectrometer
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