Ion trap collisional activation of c and z* ions formed via gas-phase ion/ion electron-transfer dissociation

A series of c- and z*-type product ions formed via gas-phase electron-transfer ion/ion reactions between protonated polypeptides with azobenzene radical anions are subjected to ion trap collision activation in a linear ion trap. Fragment ions including a-, b-, y-type and ammonia-loss ions are typically observed in collision induced dissociation (CID) of c ions, showing almost identical CID patterns as those of the C-terminal amidated peptides consisting of the same sequences. Collisional activation of z* species mainly gives rise to side-chain losses and peptide backbone cleavages resulting in a-, b-, c-, x-, y-, and z-type ions. Most of the fragmentation pathways of z* species upon ion trap CID can be accounted for by radical driven processes. The side-chain losses from z* species are different from the small losses observed from the charge-reduced peptide molecular species in electron-transfer dissociation (ETD), which indicates rearrangement of the radical species. Characteristic side-chain losses are observed for several amino acid residues, which are useful to predict their presence in peptide/protein ions. Furthermore, the unique side-chain losses from leucine and isoleucine residues allow facile distinction of these two isomeric residues.     

Liquid chromatography-mass spectrometry/mass spectrometry method development for drug metabolism studies: Examining lipid matrix ionization effects in plasma

Glycerophosphocholines (GPCho's) are known to cause liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) matrix ionization effects during the analysis of biological samples (i.e. blood, plasma). We have developed a convenient new method, which we refer to as "in-source multiple reaction monitoring" (IS-MRM), for detecting GPCho's during LC-MS/MS method development. The approach uses high energy in-source collisionally induced dissociation (CID) to yield trimethylammonium-ethyl phosphate ions (m/z 184), which are formed from mono- and disubstituted GPCho's. The resulting ion is selected by the first quadrupole (Q1), passed through the collision cell (Q2) in the presence of collision gas at low energy to minimize fragmentation, and m/z 184 selected by the third quadrupole. This approach can be combined with standard multiple reaction monitoring (MRM) transitions with little compromise in sensitivity during method development and sample analysis. Hence, this approach was used to probe ionization matrix effects in plasma samples. The resulting information was employed to develop LC-MS/MS analyses for drugs and their metabolites with cycle times less than 5 min.     

The fate of b-ions in the two worlds of collision-induced dissociation

Fragment analysis of proteins and peptides by mass spectrometry using collision-induced dissociation (CID) revealed that the pairwise generated N-terminal b- and C-terminal y-ions have different stabilities resulting in underrepresentation of b-ions. Detailed analyses of large-scale spectra databases and synthetic peptides underlined these observations and additionally showed that the fragmentation pattern depends on utilized CID regime. To investigate this underrepresentation further we systematically compared resonant excitation energy and beam-type CID facilitated on different mass spectrometer platforms: (i) quadrupole time-of-flight, (ii) linear ion trap and (iii) three-dimensional ion trap. Detailed analysis of MS/MS data from a standard tryptic protein digest revealed that b-ions are significantly underrepresented on all investigated mass spectrometers. By N-terminal acetylation of tryptic peptides we show for the first time that b-ion cyclization reaction significantly contributes to b-ion underrepresentation even on ion trap instruments and accounts for at most 16% of b-ion loss.     

Simultaneous determination of asperosaponin VI and its active metabolite hederagenin in rat plasma by liquid chromatography-tandem mass spectrometry with positive/negative ion-switching electrospray ionization and its application in pharmacokinetic study

A new liquid chromatography-tandem mass spectrometry (LC-MS/MS) method operated in the positive/negative electrospray ionization (ESI) switching mode has been developed and validated for the simultaneous determination of asperosaponin VI and its active metabolite hederagenin in rat plasma. After addition of internal standards diazepam (for asperosaponin VI) and glycyrrhetic acid (for hederagenin), the plasma sample was deproteinized with acetonitrile, and separated on a reversed phase C18 column with a mobile phase of methanol (solvent A)-0.05% glacial acetic acid containing 10 mM ammonium acetate and 30 μM sodium acetate (solvent B) using gradient elution. The detection of target compounds was done in multiple reaction monitoring (MRM) mode using a tandem mass spectrometry equipped with positive/negative ion-switching ESI source. At the first segment, the MRM detection was operated in the positive ESI mode using the transitions of m/z 951.5 ([M+Na](+))→347.1 for asperosaponin VI and m/z 285.1 ([M+H](+))→193.1 for diazepam for 4 min, then switched to the negative ESI mode using the transitions of m/z 471.3 ([M-H](-))→471.3 for hederagenin and m/z 469.4 ([M-H](-))→425.4 for glycyrrhetic acid, respectively. The sodiated molecular ion [M+Na](+) at m/z 951.5 was selected as the precursor ion for asperosaponin VI, since it provided better sensitivity compared to the deprotonated and protonated molecular ions. Sodium acetate was added to the mobile phase to make sure that abundant amount of the sodiated molecular ion of asperosaponin VI could be produced, and more stable and intensive mass response of the product ion could be obtained. For the detection of hederagenin, since all of the mass responses of the fragment ions were very weak, the deprotonated molecular ion [M-H](-)m/z 471.3 was employed as both the precursor ion and the product ion. But the collision energy was still used for the MRM, in order to eliminate the influences induced by the interference substances from the rat plasma. The validated method was successfully applied to study the pharmacokinetics of asperosaponin VI and its active metabolite hederagenin in rat plasma after oral administration of asperosaponin VI at a dose of 90 mg/kg.     

Matrix-assisted laser desorption/ionization mass spectrometry peptide sequencing utilizing selective N-terminal bromoacetylation

In tandem mass spectrometric peptide sequencing, simplifying the mass spectrum is often desirable. The b-series ions were distinguished from the y-series ions in the MALDI TOF-TOF spectra by incorporating a bromine-tag to the N-terminal amino group through rapid and selective acetylation using bromoacetic anhydride without blocking the lysine and tyrosine residues. The 51:49 ratio of Br-79 and Br-81 isotopes facilitated identification of ions carrying the tag. With the Br-tag in the b-series ions, N-terminal sequencing of tryptic peptides from hemoglobin as well as model peptides was straightforward. When the b-ions were low in intensity, ions without the Br-tag were identified as y-ions and used for sequencing.     

Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate

Selected or multiple reaction monitoring is a targeted mass spectrometry method (S/MRM-MS), in which many peptides are simultaneously and consistently analyzed during a single liquid chromatography-mass spectrometry (LC-S/MRM-MS) measurement. These capabilities make S/MRM-MS an attractive method to monitor a consistent set of proteins over various experimental conditions. To increase throughput for S/MRM-MS it is advantageous to use scheduled methods and unfractionated protein extracts. Here, we established the practically measurable dynamic range of proteins reliably detectable and quantifiable in an unfractionated protein extract from a human cell line using LC-S/MRM-MS. Initially, we analyzed S/MRM transition peak groups in terms of interfering signals and compared S/MRM transition peak groups to MS1-triggered MS2 spectra using dot-product analysis. Finally, using unfractionated protein extract from human cell lysate, we quantified the upper boundary of copies per cell to be 35 million copies per cell, while 7500 copies per cell represents a lower boundary using a single 35 min linear gradient LC-S/MRM-MS measurement on a current, standard commercial instrument.     

Immonium ion scanning for the discovery of post-translational modifications and its application to histones

This study investigates the use of immonium ion scanning for the discovery of methylated and acetylated peptides. Tandem mass spectrometry of modified and unmodified versions of identical peptides revealed ions of 98, 112 and 126 m/ z specifically in association with mono-, dimethylated and acetylated lysine, respectively. Ions of 143 m/ z were seen to be associated with monomethylated arginine, although were not unique to this amino acid. Use of immonium ion scanning with differing collision energies (35, 55, 75, 95, 115 eV) showed that where immonium ions are strong and unique for a modified amino acid, the discovery rate of modified peptides can be improved up to 4-fold over control analyses. The position of an amino acid in a peptide, being terminal or internal, also affected the efficiency of identification of modified peptides. Higher collision energy scanning was required for the most effective identification of peptides with internal modified residues. We conclude that immonium ion scanning, particularly with a range of collision energies, can improve the discovery efficiency of post-translational modifications in peptides.     

High throughput quantification of cholesterol and cholesteryl ester by electrospray ionization tandem mass spectrometry (ESI-MS/MS)

Analysis of free cholesterol (FC) is not well suited for electrospray ionization (ESI); however, cholesteryl ester (CE) form ammonium adducts in positive ion mode and generate a fragment ion of m/z 369 upon collision-induced fragmentation. In order to allow parallel analysis of FC and CE using ESI tandem mass spectrometry (ESI-MS/MS), we developed an acetyl chloride derivatization method to convert FC to cholesteryl acetate (CE 2:0). Derivatization conditions were chosen to provide a quantitative conversion of FC to CE 2:0 without transesterification of naturally occurring CE species. FC and CE were analyzed by direct flow injection analysis using a fragment of m/z 369 in a combination of selected reaction monitoring (SRM) and precursor ion scan for FC and CE, respectively. Quantification was achieved using deuterated D(7)-FC and CE 17:0/CE 22:0 as internal standards as well as calibration lines generated by addition of FC and naturally occurring CE species to the respective sample matrix. The developed assay showed a precision and detection limit sufficient for routine analysis. A run time of 1.3 min and automated data analysis allow high throughput analysis. Loading of human skin fibroblast and monocyte derived macrophages with stable isotope labeled FC showed a potential application of this method in metabolism studies. Together with existing mass spectrometry methodologies for lipid analysis, the present methodology will provide a useful tool for clinical and biochemical studies and expands the lipid spectrum that can be analyzed from one lipid sample on a single instrumental platform.     

A Study on Immonium Ions and Immonium-Related Ions Depending on Different Collision Energies as Assessed by Q-TOF MS

Immonium ions and immonium-related ions commonly appear in the mass spectra of peptide precursor ions. An overall understanding of the variation of the abundance of these ions is beneficial for the identification of unknown peptides. Here, four peptides from mass spectrometry (MS) of sucrose phosphorylase were selected as precursor ions, and the frequency of immonium ions and immonium-related ions in a dataset containing 130 MS/MS spectra were examined. Immonium ions and immonium-related ions were mainly produced from the further fragmentation of a-, b-, and y-ions. At the optimal collision energy (CE), the immonium ions of leucine at m/z 86, isoleucine at m/z 86, glutamine at m/z 101, arginine at m/z 129, tryptophan at m/z 159, proline at m/z 70, valine at m/z 72, glutamic acid at m/z 102, phenylalanine at m/z 120, and tyrosine at m/z 136, as well as the immonium-related ions of methionine at m/z 61, lysine at m/z 84, glutamine at m/z 84, and tyrosine at m/z 91 existed in higher abundance and had higher confidence level, therefore suggesting the presence of corresponding amino acid residues well. However, the immonium ions of serine at m/z 60 and threonine at m/z 74, although showing lower abundance, were stable at high CE and had higher confidence level, indicating the presence of serine and threonine residues, respectively. The immonium ion of asparagine at m/z 87 also was a good indicator for the existence of asparagine residue.     

Utility of high performance liquid chromatography/electrospray/mass spectrometry of polar lipids in specifically Per-13C labeled Gram-negative bacteria DA001 as a tracer for acceleration of bioremediation in the subsurface

Specific fatty acids from phosphatidylglycerol (PG) and phosphatidylethanolamine (PE) recovered from a per 13C-labeled bacteria can be detected in environmental samples and used as measures of bacterial transport in the subsurface. Detection of palmitic acid (16:0) and oleic acid (18:1) at m/z 271 (255+16) and 299 (281+18) as negative ions in PG and PE separated by high performance liquid chromatography (HPLC) and detected after up-front collisionally induced dissociation (CID) utilizing electrospray (ES) mass spectrometry (MS) provided sufficient sensitivity and specificity for detection in the presence of the indigenous microbiota. Application of tandem mass spectrometry (MS/MS) in the multiple reaction monitoring (MRM) was use to monitor selected transitions. MRM can increase the sensitivity so that polar lipids recovered from cell densities currently at about 10(4) cells/sample can be detected. This technology provides a non-intrusive mechanism for monitoring the distribution of bacteria added to accelerate in situ bioremediation of subsurface sediments.     

Determination of ecabet in human plasma by high-performance liquid chromatography-tandem mass spectrometry

This paper describes a simple, robust and cost-effective assay for the determination of ecabet in human plasma. After a simple step of protein precipitation using methanol, plasma samples were analyzed by reverse phase high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) with valsartan as the internal standard (I.S.). Ecabet and the I.S. valsartan were separated on a Venusil MP C18 analytical column using methanol-10mM ammonium acetate (75:25, v/v, pH 3.0) as mobile phase at a flow rate of 1.0 mL/min. Ecabet and I.S. were eluted at 0.91 and 0.92 min, respectively, ionized in negative mode, and then detected by multiple reaction monitoring (MRM) essay. The MRM transitions of m/z 379.1-->m/z 277.1 and m/z 434.3-->m/z 350.1 were used to quantify ecabet and I.S., respectively. The assay was linear over the concentration range of 10-6000 ng/mL and was successfully applied to a pharmacokinetic study in healthy volunteers.     

N-Terminal amino acid side-chain cleavage of chemically modified peptides in the gas phase: a mass spectrometry technique for N-terminus identification

Although genome databases have become the key for proteomic analyses, de novo sequencing remains essential for the study of organisms whose genomes have not been completed. In addition, post-translational modifications present a challenge in database searching. Recognition of the b or y-ion series in a peptide MS/MS spectrum as well as identification of the b1 - and yn-1 -ions can facilitate de novo analyses. Therefore, it is valuable to identify either amino-acid terminus. In previous work, we have demonstrated that peptides modified at the epsilon-amino group of lysine as a t-butyl peroxycarbamate derivative undergo free radical promoted peptide backbone fragmentation under low-energy collision-induced dissociation (CID) conditions. Here we explore the chemistry of the N-terminal amino group modified as a t-butyl peroxycarbamate. The conversion of N-terminal amines to peroxycarbamates of simple amino acids and peptides was studied with aryl t-butyl peroxycarbonates. ESI-MS/MS analysis of the peroxycarbamate adducts gave evidence of a product ion corresponding to the neutral loss of the N-terminal side chain (R), thus identifying this residue. Further fragmentation (MS3) of product ions formed by N-terminal residue side-chain loss (-R) exhibited an m/z shift of the b-ions equal to the neutral loss of R, therefore labeling the b-ion series. The study was extended to the analysis of a protein tryptic digest where the SALSA algorithm was used to identify spectra containing these neutral losses. The method for N-terminus identification presented here has the potential for improvement of de novo analyses as well as in constraining peptide mass mapping database searches.     

Biological effectiveness of high-energy protons: target fragmentation.

High-energy protons traversing tissue produce local sources of high-linear-energy-transfer (LET) ions through nuclear fragmentation. We examine the contribution of these target fragments to the biological effectiveness of high-energy protons using the cellular track model. The effects of secondary ions are treated in terms of the production collision density using energy-dependent parameters from a high-energy fragmentation model. Calculations for mammalian cell cultures show that at high dose, at which intertrack effects become important, protons deliver damage similar to that produced by gamma rays, and with fragmentation the relative biological effectiveness (RBE) of protons increases moderately from unity. At low dose, where sublethal damage is unimportant, the contribution from target fragments dominates, causing the proton effectiveness to be very different from that of gamma rays with a strongly fluence-dependent RBE. At high energies, the nuclear fragmentation cross sections become independent of energy. This leads to a plateau in the proton single-particle-action cross section, below 1 keV/micron, since the target fragments dominate.     

An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology

Selected reaction monitoring (SRM) is an accurate quantitative technique, typically used for small-molecule mass spectrometry (MS). SRM has emerged as an important technique for targeted and hypothesis-driven proteomic research, and is becoming the reference method for protein quantification in complex biological samples. SRM offers high selectivity, a lower limit of detection and improved reproducibility, compared to conventional shot-gun-based tandem MS (LC-MS/MS) methods. Unlike LC-MS/MS, which requires computationally intensive informatic postanalysis, SRM requires preacquisition bioinformatic analysis to determine proteotypic peptides and optimal transitions to uniquely identify and to accurately quantitate proteins of interest. Extensive arrays of bioinformatics software tools, both web-based and stand-alone, have been published to assist researchers to determine optimal peptides and transition sets. The transitions are oftentimes selected based on preferred precursor charge state, peptide molecular weight, hydrophobicity, fragmentation pattern at a given collision energy (CE), and instrumentation chosen. Validation of the selected transitions for each peptide is critical since peptide performance varies depending on the mass spectrometer used. In this review, we provide an overview of open source and commercial bioinformatic tools for analyzing LC-MS data acquired by SRM.     

Novel approach in LC-MS/MS using MRM to generate a full profile of acyl-CoAs: discovery of acyl-dephospho-CoAs

A metabolomic approach to selectively profile all acyl-CoAs was developed using a programmed multiple reaction monitoring (MRM) method in LC-MS/MS and was employed in the analysis of various rat organs. The programmed MRM method possessed 300 mass ion transitions with the mass difference of 507 between precursor ion (Q1) and product ion (Q3), and the precursor ion started from m/z 768 and progressively increased one mass unit at each step. Acyl-dephospho-CoAs resulting from the dephosphorylation of acyl-CoAs were identified by accurate MS and fragmentation. Acyl-dephospho-CoAs were also quantitatively scanned by the MRM method with the mass difference of 427 between Q1 and Q3 mass ions. Acyl-CoAs and dephospho-CoAs were assayed with limits of detection ranging from 2 to 133 nM. The accuracy of the method was demonstrated by assaying a range of concentrations of spiked acyl-CoAs with the results of 80–114%. The distribution of acyl-CoAs reflects the metabolic status of each organ. The physiological role of dephosphorylation of acyl-CoAs remains to be further characterized. The methodology described herein provides a novel strategy in metabolomic studies to quantitatively and qualitatively profile all potential acyl-CoAs and acyl-dephospho-CoAs.     

A highly sensitive ultra performance liquid chromatography-tandem mass spectrometric (UPLC-MS/MS) technique for quantitation of protein free and bound efavirenz (EFV) in human seminal and blood plasma

A combined UPLC-tandem mass spectrometric (UPLC-MS/MS) technique has been validated for quantitation of protein free efavirenz (EFV) as well as total concentrations of EFV in human blood and seminal plasma. The analytical method possesses capabilities for concentration measurements of EFV ranging from 0.5 to 10,000ng/ml with an accuracy (%dev) of -5.2-8.0% and precision (%CV) of <8%. Standard curves were linear with coefficients of variation (r(2)) >0.98. The method employs a racemic fluorinated analog of EFV (F-EFV) as the internal standard. EFV and F-EFV were eluted from a reverse-phase UPLC column via gradient elution with detection via negative ion multiple reaction monitoring (MRM). EFV and F-EFV, respectively, were detected via the following MRM transitions: m/z 314.0>244.1 and m/z 298.0>227.9. The time required for the analysis of each sample was 8.0min. The analytical technique is capable of a reliable detection limit of ～15-20fmol of EFV injected on column.     

Determination of tobramycin in serum using liquid chromatography-tandem mass spectrometry and comparison with a fluorescence polarisation assay

We have developed a tandem mass spectrometry (LC-MS-MS) method for measuring tobramycin concentrations in serum samples and have compared it with a fluorescence polarisation immunoassay. After protein precipitation with acetonitrile supernatant was injected into the LC-MS-MS system. A C(18) cartridge (4x2 mm) was eluted with a step gradient of 20-100% methanol containing HFBA. The retention times were, tobramycin 1.05 min and sisomycin 1.05 min. The MRM transitions were: m/z 467.8>163 (tobramycin) and m/z 447.8>160 (sisomycin). The limit of quantification was 0.15 mg/l and the assay was linear up to 50 mg/l. Assay precision was <6% within and between batch.     

Determination of duloxetine in human plasma by liquid chromatography with atmospheric pressure ionization-tandem mass spectrometry and its application to pharmacokinetic study

A rapid, sensitive and accurate liquid chromatographic-tandem mass spectrometry (LC-MS-MS) method is described for the determination of duloxetine in human plasma. Duloxetine was extracted from plasma using methanol and separated on a C18 column. The mobile phase consisting of a mixture of acetonitrile and 5mM ammonium acetate (45:55, v/v, pH 3.5) was delivered at a flow rate of 0.3 ml/min. Atmospheric pressure ionization (API) source was operated in positive ion mode. Multiple reaction monitoring (MRM) mode using the transitions of m/z 298.1-->m/z 44.0 and m/z 376.2-->m/z 123.2 were used to quantify duloxetine and internal standard (I.S.), respectively. The linearity was obtained over the concentration range of 0.1-50.0 ng/ml and the lower limit of quantitation (LLOQ) was 0.1 ng/ml. This method was successfully applied to pharmacokinetic study of a duloxetine formulation product after oral administration to healthy human subjects.     

Stochastic radial dose distributions and track structure theory

Measured single-event distributions of the specific energy deposited in cylindrical volumes with simulated diameters down to 150 nm for (4)He and (12)C ions with energies of 25 MeV/nucleon and (16)O ions with 21 MeV/nucleon and radial distances up to 12 microm are presented. The mean specific energy per ion , the mean specific energy per target hit z(1)(r), and the relative frequency of target hits nu(r) as a function of radial distance are evaluated and compared with the corresponding quantities of the track structure model of Kiefer and Straaten (Phys. Med. Biol. 31, 1201-1209, 1986). Though there are some discrepancies in the absolute values, the radial dependence of , z(1)(r) and v(r) for (12)C and (16)O ions is reproduced satisfactorily. The model fails to describe the data for (4)He ions. A more detailed comparison of the radial shape of the mean specific energies calculated from the experimental data from the present work and data from the literature reveals a significant projectile charge dependence which is not included in track structure models.     

Development of a liquid chromatography/negative-ion electrospray tandem mass spectrometry assay for the determination of cilnidipine in human plasma and its application to a bioequivalence study

A simple method using a one-step liquid-liquid extraction (LLE) with methyl-t-butyl ether (MTBE) followed by high-performance liquid chromatography (HPLC) with negative-ion electrospray ionization tandem mass spectrometric (ESI-MS/MS) detection was developed for the determination of cilnidipine in human plasma using benidipine as an internal standard (IS). Acquisition was performed in multiple reaction monitoring (MRM) mode, by monitoring the transitions: m/z 491.1>121.8 for cilnidipine and m/z 504.2>122.1 for IS, respectively. Analytes were chromatographed on a CN column by isocratic elution using 10mM ammonium acetate buffer-methanol (30:70, v/v; adjusted with acetic acid to pH 5.0). Results were linear (r2=0.99998) over the studied range (0.1-20ng/ml) with a total LC-MS/MS analysis time per run of 3min. The developed method was validated and successfully applied to a cilnidipine bioequivalence study in 24 healthy male volunteers.