Analysis of high mass peptides using a novel matrix-assisted laser desorption/ionisation quadrupole ion trap time-of-flight mass spectrometer

A novel matrix-assisted laser desorption/ionisation quadrupole ion trap time-of-flight (MALDI QIT ToF) mass spectrometer has been used to analyse high mass peptide ions exceeding 2000 Da. Human adrenocorticotropic hormone (fragment 18-39) and oxidised bovine insulin chain B were utilised to evaluate the performance of the instrument both in MS and in MS/MS mode. Its ability to efficiently isolate ions and to fragment them using collisionally activated decomposition (CAD) has been demonstrated using mixtures diluted to the low-femtomole level on target. Additionally, multiple stage mass spectrometry (MS/MS/MS) provides a second-generation product ion spectrum in which new fragment ions are detected and new stretches of amino acids are identified.     

Orthogonal trap time-of-flight mass spectrometer using a collisional damping chamber

We report a new hybrid mass spectrometer, which is a combination of a quadrupole ion trap and an orthogonal time-of-flight (TOF) mass spectrometer. This new configuration consists of a collisional-damping chamber (CDC) inserted between an MSn-capable ion trap and a high-mass-accuracy orthogonal-TOF mass spectrometer. Because the CDC converted an ion packet into an energy-focused and quasi-continuous beam, a high mass resolution of over 10,000 and a high mass accuracy of better than 3 ppm were achieved. Moreover, the ratio of the maximum detectable m/z to the minimum detectable m/z, which is referred to here as the mass window, was improved to more than 10.     

Product ion scanning using a Q-q-Q linear ion trap (Q TRAP) mass spectrometer

The use of a Q-q-Q(linear ion trap) instrument to obtain product ion spectra is described. The instrument is based on the ion path of a triple quadrupole mass spectrometer with Q3 operable as either a conventional RF/DC quadrupole mass filter or a linear ion trap mass spectrometer with axial ion ejection. This unique ion optical arrangement allows de-coupling of precursor ion isolation and fragmentation from the ion trap itself. The result is a high sensitivity tandem mass spectrometer with triple quadrupole fragmentation patterns and no inherent low mass cut-off. The use of the entrance RF-only section of the instrument as accumulation ion trap while the linear ion trap mass spectrometer is scanning enhances duty cycles and results in increased sensitivities by as much as a factor of 20. The instrument is also capable of all of the triple quadrupole scans including multiple-reaction monitoring (MRM) as well as precursor and constant neutral loss scanning. The high product ion scanning sensitivity allows the recording of useful product ion spectra near the MRM limit of quantitation.     

Dual linear ion trap/orthogonal acceleration time-of-flight mass spectrometer with improved precursor ion selectivity

A new hybrid mass spectrometer based on dual linear ion traps (LITs) and an orthogonal acceleration time-of-flight mass spectrometer (oaTOF), that can achieve MS(n) analysis and high-mass-accuracy detection with high sensitivity, has been developed. Dual-LIT was necessary because, in a single LIT plus oaTOF combination, the LIT pressure favorable for high precursor selectivity in MS(n) analysis (less than 1 mTorr) was far different from an optimum damping pressure (50-100 mTorr) for efficient connection to the TOF mass spectrometer. A dual-LIT solved this problem of inconsistency of the optimum pressures by using the first LIT for MS(n) analysis and the second LIT for collisional damping. This dual-LIT/TOF instrument achieved high-sensitivity MS(n) analysis with high precursor-ion selectivity.     

Operation and application of a new time-of-flight e-gas secondary neutral mass spectrometer (ToF–SNMS)

The low-pressure rf plasma of a secondary neutral mass spectrometer (e-gas SNMS) was connected with a time-of-flight (ToF) mass spectrometer for the first time. As opposed to ToF–SIMS in e-gas SNMS, the primary ion pulse cannot be used for triggering the flight time measurement. Therefore, an extraction pulse is used which at a defined time loads an ion package from the beam of the post-ionised particles into the ToF spectrometer. The newly developed ToF–SNMS system is described, and first experimental results are presented.     

Fragmentation of N-linked glycans with a matrix-assisted laser desorption/ionization ion trap time-of-flight mass spectrometer

N-Linked glycans were ionized from several matrices with a Shimadzu-Biotech AXIMA-QIT matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometer. [M+Na]+ ions were produced from all matrices and were accompanied by varying amounts of in-source fragmentation products. The least fragmentation was produced by 2,5-dihydroxybenzoic acid and the most by alpha-cyano-4-hydroxycinnamic acid and 6-aza-2-thiothymine. Sialic acid loss was extensive but could be prevented by formation of methyl esters. Fragmentation produced typical low-energy-type spectra dominated by ions formed by glycosidic cleavages. MS(n) spectra (n = 3 and 4) were used to probe the pathways leading to the major diagnostic ions. Thus, for example, an ion that was formed by loss of the core GlcNAc residues and the 3-antenna was confirmed as being formed by a B/Y rather than a C/Z mechanism. The proposed structures of several cross-ring cleavage ions were confirmed and it was shown that MS3 spectra could be obtained from as little as 10 fmol of glycan.     

Rapid hydrocarbon analysis using a miniature rectilinear ion trap mass spectrometer

A miniature ion trap mass analyzer was applied to the analysis of traces of hydrocarbons and simple heteroatomics in the vapor phase and in aqueous solution. Vapors of acetone, acetic acid, acetonitrile, benzene, butanethiol, carbon disulfide, hexane, dichloromethane, naphthalene, toluene and xylenes were detected and quantified using solid sorbent trapping and, in some cases, by passage through a membrane interface. Aqueous solutions of benzene, toluene, xylenes, hexane and a petroleum naphtha distillate were examined using the membrane interface. Sampling, detection and identification of all compounds was completed in times of less than one minute. The gas-phase samples of toluene and benzene were detected at 200 ppt (limit of detection, LOD) for toluene and 600 ppt for benzene. Identification of benzene and xylene in aqueous solutions was readily achieved with LODs of 200 and 400 ppb, respectively. Quantification over a linear dynamic range of two orders of magnitude for the aqueous samples and three orders of magnitude for the vapor-phase samples was demonstrated.     

Photoinduced dissociation of electrospray-generated ions in an ion trap/time-of-flight mass spectrometer using a pulsed CO2 laser

An ion trap/time-of-flight (IT/TOF) mass spectrometer was developed and applied to infrared multiphoton dissociation (IRMPD) studies of ions generated by electrospray ionization. A pulsed 10.6- micro m laser beam from a CO(2) laser was used for excitation of trapped ions. Results from IRMPD of peptide ions show that this method provides useful information related to the amino acid sequence of analyzed peptides. Comparative studies show that IRMPD spectra are similar to those obtained using a 266-nm UV laser beam for excitation. However, in contrast to multiple-pulse excitation required at 266 nm, the energy of a single laser pulse in IRMPD is sufficient to induce dissociation of peptide ions. The laser power is practically an exclusive parameter that must be controlled in order to obtain IRMPD spectra that will provide the optimal structural information. It is further demonstrated that the IRMPD IT/TOF technique has the potential to probe the structural features of larger ions that cannot be readily fragmented by collision-induced dissociation (CID). A multiply charged ion of equine cytochrome c is successfully fragmented in a single laser pulse experiment. The IRMPD IT/TOF technique is also shown to be a promising tool for studying dissociation kinetics of peptide and protein ions. Unlike other methods that usually monitor the dissociation ion kinetics in a dissociation time frame of greater than milliseconds, the IT/TOF can promptly detect all product ions generated by the dissociation process, and thus monitor the dissociation process of peptides and proteins in a sub-millisecond time frame. This instrument allows us to determine the dissociation rates of cytochrome c ions using high-energy photoexcitation. It is found that the charge state of the protein ion has a significant effect on dissociation kinetics, which is consistent with that found under low-energy excitation experiments. It is shown that the increase in energy of a laser pulse from 130 to 180 mJ changes the dissociation rate constant for the +12 ion from k = 2.4 x 10(3) x s(-1) to k = 7.3 x 10(4) x s(-1). The +8 ion following excitation at 130 mJ dissociates slower with a rate constant of k = 2.6 x 10(2) x s(-1). The rate difference observed is attributed to conformational differences among the ions with different charge states.     

High resolution on a quadrupole ion trap mass spectrometer

By using a modified ion trap mass spectrometer, resolution in excess of 30,000 (FWHM) at m I z 502 is demonstrated. The method of increasing resolution in the ion trap mass spectrometer operated in the mass-selective instability mode depends on decreasing the rate of scanning the primary radio frequency amplitude as well as using resonance ejection at the appropriate frequency and amplitude. A theoretical basis for the method is introduced.     

Development and characterization of an electrospray ionization ion trap/linear time-of-flight mass spectrometer

On-line analysis of compounds from solution has been greatly facilitated by the advent of electrospray ionization mass spectrometry (ESI-MS). Although quadrupole mass analyzers are most commonly used with ESI at present, time-of-flight (TOF) mass spectrometers offer several potential advantages including high data acquisition rates, which are desirable for fast separation techniques. One method of coupling ESI and TOF uses an ion trap for temporary storage and accumulation of the electrosprayed ions prior to TOF mass analysis. Previous studies have not fully addressed the effects of several key variables on the analytical capabilities of this type of instrument. In this study, the characterization of an ion trap/linear TOF instrument for ESI is described. The behavior of various analytes is divided into two separate groups; each one is found to have its own optimal set of operating conditions. The reasons for the observed differences between groups are explored. Issues relevant to mass resolution, sensitivity, mass range, mass-to-charge ratio discrimination, and mass measurement accuracy are addressed. Finally, it is suggested that the analytical capability of this type of instrument could be significantly improved by changing the ion optics from the existing focusing lenses to a rf-only quadrupole lens.     

Diastereomeric differentiation of peptides with CuII and FeII complexation in an ion trap mass spectrometer

Complexation by transition metal ions (CuII and FeII) was successfully used to differentiate the diastereomeric YAGFL, YDAGFL and Y(D)AGF(D)L pentapeptides by electrospray ionization-ion trap mass spectrometry in the positive ion mode using low-energy collision conditions. This distinction was allowed by the stereochemical effects due to the (D)Leu/(L)Leu and the (D)Ala/(L)Ala residues yielding various steric interactions which direct relative dissociation rate constants of the binary [(M - H) + MeII]+ complexes (Me = Cu or Fe) subjected to low-energy, collision-induced dissociation processes. The interpretation of the collision-induced dissociation spectra obtained from the diastereomeric cationized peptides allowed the location of the deprotonated site(s), leading to the postulation of ion structures and fragmentation pathways for both the [(M - H) + CuII]+ and [(M - H) + FeII]+ complexes, which differed significantly. With CuII, consecutive fragmentations, initiated by the decarboxylation at C-terminus, were favored relative to sequence product ions. On the other hand, with FeII, competitive fragmentations resulting in abundant sequence product ions and significant internal losses were preferred. This could be explained by different localizations of the negative charge, which directs the orientation of both the [(M - H) + CuII]+ and [(M - H) + FeII]+ binary complexes fragmentations. Indeed, the free negative charge of the [(M - H) + CuII]+ ions was mainly located at one oxygen atom: either at the C-terminal carboxylic group or, to a minor extent, at the Tyr phenol group (i.e. zwitterionic forms). On the other hand, the negative charge of the [(M - H) + FeII]+ ions was mainly located at one of the nitrogen atoms of the peptide backbone and coordinated to FeII (i.e. salt non-zwitterionic form).Moreover, this study reveals the particular behavior of CuII reduced to CuI, which promotes radical losses not observed from the peptide-FeII complexes. Finally, this study shows the analytical potentialities of the complexation of transition metal ions with peptides providing structural information complementary to that obtained from low-energy, collision-induced dissociation processes of protonated or deprotonated peptides.     

Optimized precursor ion selection for labile ions in a linear ion trap mass spectrometer and its impact on quantification using selected reaction monitoring

The fragmentation of fragile ions during the application of an isolation waveform for precursor ion selection and the resulting loss of isolated ion intensity is well‐known in ion trap mass spectrometry (ITMS). To obtain adequate ion intensity in the selected reaction monitoring (SRM) of fragile precursor ions, a wider ion isolation width is required. However, the increased isolation width significantly diminishes the selectivity of the channels chosen for SRM, which is a serious problem for samples with complex matrices. The sensitive and selective quantification of many lipid molecules, including ceramides from real biological samples, using a linear ion trap mass spectrometer is also hindered by the same problem because of the ease of water loss from protonated ceramide ions. In this study, a method for the reliable quantification of ceramides using SRM with near unity precursor ion isolation has been developed for ITMS by utilizing alternative precursor ions generated by in‐source dissociation. The selected precursor ions allow the isolation of ions with unit mass width and the selective analysis of ceramides using SRM with negligible loss of sensitivity. The quantification of C18:0‐, C24:0‐ and C24:1‐ceramides using the present method shows excellent linearity over the concentration ranges from 6 to 100, 25 to 1000 and 25 to 1000 nM, respectively. The limits of detection of C18:0‐, C24:0‐ and C24:1‐ceramides were 0.25, 0.25 and 5 fmol, respectively. The developed method was successfully applied to quantify ceramides in fetal bovine serum. Copyright © 2014 John Wiley & Sons, Ltd.     

Thermospray liquid chromatography-mass spectrometry with a quadrupole ion trap mass spectrometer

A theromospray ion source using corona discharge ionization was interfaced to a quadrupole ion trap mass spectrometer via a multi-element lens system. Ions were injected into the trap periodically where they were stabilized by collisions with helium bath gas. Mass spectra were recorded on the trapped ions using the mass-selective instability scan mode. Data are shown for a peptide and a nucleoside and the effects of some experimental variables on the spectra are explored.     

A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight (Q-TOF) mass spectrometer for studying protein phosphorylation

A tandem quadrupole time-of-flight (Q-TOF) mass spectrometer has been programmed such that phosphorylated peptides can automatically be discovered and identified in a way similar to that of the use of precursor ion or neutral loss scanning, but without the need to scan the quadrupole mass filter. Instead, the method capitalizes on the innate capability of the Q-TOF to record mass spectra and product ion spectra quickly, with good sensitivity and with good mass accuracy. Alternate mass spectra, with and without fragmentation, are recorded at high and low collision energy with the quadrupole operating in wideband mode. The method of analysis is both compatible with and dependant on liquid chromatography for separation of complex mixtures. The method has been demonstrated by searching for the neutral loss of 98 Da (H3PO4) from phosphoserine and phosphothreonine residues, or for the phosphorylated immonium ion at m/z 216 from phosphotyrosine. The method also incorporates acquisition of the product ion spectrum from any candidate precursor ions, thereby allowing confirmation of the neutral loss or product ion and providing additional sequence information to assist identification of the protein and assign the site of phosphorylation.     

A novel approach for identification and characterization of glycoproteins using a hybrid linear ion trap/FT-ICR mass spectrometer

Combining source collision-induced dissociation (CID) and tandem mass spectral acquisition in a pseudo-MS(3) experiment using a linear ion trap results in a highly selective and sensitive approach to identifying glycopeptide elution from a protein digest. The increased sensitivity is partially attributed to the nonselective nature of source CID, which allows simultaneous activation of all charge states and coeluting glycoforms generating greater ion abundance for the mass-to-charge (m/z) 204 and/or 366 oxonium ions. Unlike source CID alone, a pseudo-MS(3) approach adds selectivity while improving sensitivity by eliminating chemical noise during the tandem mass spectral acquisition of the oxonium ions in the linear ion trap. Performing the experiments in the hybrid linear ion trap/Fourier transform-ion cyclotron resonance (FT-ICR) enables subsequent high-resolution/high-mass accuracy full-scan mass spectra (MS) and parallel acquisition of MS/MS in the linear ion trap to be completed in 2 s directly following the pseudo-MS(3) scan to collate identification and characterization of glycopeptides in one experimental scan cycle. Analysis of bovine fetuin digest using the combined pseudo-MS(3), high-resolution MS, and data-dependent MS/MS events resulted in identification of four N-linked and two O-linked glycopeptides without enzymatic cleavage of the sugar moiety or release of the sialic acids before analysis. In addition, over 95% of the total protein sequence was identified in one analytical run.     

Determination of high-energy fragmentation of protonated peptides using a beqq hybrid mass spectrometer

A hybrid tandem instrument of BEqQ geometry was used to determine high-energy decomposition of protonated peptides, such as side-chain fragmentation yielding d _n and w _n ions. The transmission through both E and Q of such product ions, formed in the second field-free region, permits improved mass resolution and confident mass assignment. The experimental technique may involve synchronous scanning of E and Q, or, for the purpose of identification of specific products, limited-range scanning of either E or Q with the other analyzer fixed. These techniques are not equivalent, with respect to product ion transmission, to the double focusing of product ions achieved with four-sector instruments but nevertheless represent a critical improvement over conventional mass-analyzed ion kinetic energy spectrometry analyses. Fragmentation of protonated peptides occurring in the second field-free region inside and outside the collision cell were distinguished by floating the collision cell above ground potential. Mass filtering using Q confirmed the mass assignments. The data indicate that product ions resulting from spontaneous decomposition are in some instances quantitatively more significant than those resulting from high-energy collisional activation. Furthermore, the differentiation of the products of low- and high-energy processes should facilitate spectral interpretation.     

Development of a tabletop time-of-flight mass spectrometer with an ion attachment ionization technique

We report a new type of mass spectrometry based on a time-of-flight mass spectrometer combined with an ion attachment ionization technique (IA-TOF). In contrast to electron ionization mass spectra, IA-TOF mass spectra are not complicated by peaks due to fragmentation of the molecular ion; the adduct ion formed in IA does not fragment. We developed a tabletop IA-TOF system and evaluated its performance by analyzing specimens originally in the gas, liquid, and solid phases. We obtained fragment-free spectra covering a mass range up to m/z 3400 with a mass resolution of about 4700. Our IA-TOF system realizes accurate and versatile real-time mass spectrometry.     

Coupling of ion-molecule reactions with liquid chromatography on a quadrupole ion trap mass spectrometer

We report for the first time a coupling of gas-phase ion-molecule reactions with chromatographic separations on a quadrupole ion trap mass spectrometer. The interface was accomplished by using a pulsed valve for the introduction of a volatile neutral into the ion trap. The pulsed valve controller is synchronized with the mass spectrometer software. The setup requires some minor modifications to the vacuum system of the commercial quadrupole ion trap but most of the modifications are external to the mass spectrometer. Two applications of this interface are described: differentiation between two phosphoglucose positional isomers and detection of a phosphopeptide in a peptide mixture. Both applications are using the reactivity of trimethoxyborate towards a phosphate moiety in the negative ion mode. The detection of phosphopeptides hinges on our findings that non-phosphorylated peptide anions do not react with trimethoxyborate. This LC/MS detection can be easily visualized in terms of selected reaction monitoring.     

Mass spectrometric approaches for the characterization of proteins on a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer

This study demonstrates structural and conformational characterization of proteins by nanoflow electrospray ionization (nanoESI) mass spectrometry (MS) and tandem mass spectrometry (MS/MS) utilizing a quadrupole time-of-flight (Q-TOF) mass spectrometer (Micromass, Manchester, England). Model peptides were successfully sequenced at the 35 attomole (amol) level, and peptides derived from a tryptic in-gel digest of 25 femtomole (fmol) bovine serum albumin (BSA) were successfully sequenced. The results demonstrated that the MS/MS sensitivity of the Q-TOF clearly surpassed the detection limit of the silver stain. A silver destaining step greatly improved the mass analysis of peptides derived from in-gel digests. Interestingly, sequence analysis revealed BSA residue 424 (tyrosine) as a potential chlorination site. In addition, a modified procedure was successfully used to extract and measure the masses of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE)-resolved proteins in the 10-68.5 kDa range. The Q-TOF was also used to monitor conformational changes of proteins. These experiments demonstrated an acid-induced denaturation of BSA in the pH 3-4 range, and heat-induced unfolding of cytochrome c between 50 and 60 degrees C. Finally, Zn2+ binding was demonstrated for the carbonic anhydrase apoprotein. In summary, the wide range of applications and the high quality of the experimental data made the Q-TOF mass spectrometer a powerful analytical tool for protein characterization.     

Rapid screening and characterization of drug metabolites using a multiple ion monitoring-dependent MS/MS acquisition method on a hybrid triple quadrupole-linear ion trap mass spectrometer

A novel LC/MS/MS method that uses multiple ion monitoring (MIM) as a survey scan to trigger the acquisition of enhanced product ions (EPI) on a hybrid quadrupole-linear ion trap mass spectrometer (Q TRAP) was developed for drug metabolite identification. In the MIM experiment, multiple predicted metabolite ions were monitored in both Q1 and Q3. The collision energy in Q2 was set to a low value to minimize fragmentation. Results from analyzing ritonavir metabolites in rat hepatocytes demonstrate that MIM-EPI was capable of targeting a larger number of metabolites regardless of their fragmentation and retained sensitivity and duty cycle similar to multiple reaction monitoring (MRM)-EPI. MIM-based scanning methods were shown to be particularly useful in several applications. First, MIM-EPI enabled the sensitive detection and MS/MS acquisition of up to 100 predicted metabolites. Second, MIM-MRM-EPI was better than MRM-EPI in the analysis of metabolites that undergo either predictable or unpredictable fragmentation pathways. Finally, a combination of MIM-EPI and full-scan MS (EMS), as an alternative to EMS-EPI, was well suited for routine in vitro metabolite profiling. Overall, MIM-EPI significantly enhanced the metabolite identification capability of the hybrid triple quadrupole-linear ion trap LC/MS.