Electrospray Ion Trap Mass Spectrometer Research Articles

UV fragmentation and ultrafast dynamics of trinuclear silver/1-methylthymine and silver/1-methyluracil metal-base pairs in an ion trap

We report on gas phase UV action spectroscopy and photodynamics of [Ag3(1MT-H/1MU-H)2]+ comprised of a linear silver string and two deprotonated 1-methyl-thymine/uracil (1MT/1MU) ligands. We applied pump–probe femtosecond laser photofragmentation in an electrospray ion trap mass spectrometer and high-level ab initio calculations at the level of approximate coupled-cluster singles-doubles theory. The experimental UV band at 283/275nm is assigned to a red shifted 1ππ∗ nucleobase located transition. Relaxation of the 1ππ∗ state occurs with time constants of 0.2/1.1ps and 0.2/4.2ps for the 1MT and 1MU complexes, respectively, on a similar ultrafast time scale as non-metalated uracil derivatives.

An On-Line Platform for the Analysis of Permethylated Oligosaccharides Using Capillary Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry.

Permethylation is one of the most practical modifications for mass spectrometric analysis of carbohydrates. In this study, we showed a facile platform for the on-line permethylation and analysis of acidic N-glycans using capillary liquid chromatography-electrospray ionization-tandem mass spectrometry to elucidate the N-glycan structures derived from glycoprotein samples. Two capillaries, individually packed with NaOH and C18 powder, were coupled to electrospray ion trap mass spectrometer. Prior to mass spectrometry, oligosaccharides were permethylated in NaOH-packed capillary by methyl iodide, and the permethylated glycans were consequently extracted from residual reagents, such as NaOH and methyl iodide, in C18-capillary, instead of using conventional chloroform extraction. After permethylation and purification, the permethylated glycans were released from C18 capillary by acetonitrile, and sprayed into mass spectrometer. Using this on-line strategy, a picomolar range of sialylated N-glycans from bovine fetuin were analyzed by tandem mass spectrometry.

Mass spectrometric characterization of gentamicin components separated by the new European Pharmacopoeia method

Liquid chromatography combined with pulsed electrochemical detection (LC–PED) is the method of choice in the European Pharmacopoeia for the determination of gentamicin and its related substances. A recently approved improved LC–PED method, with a reversed-phase C 18 column and a mobile phase consisting of trifluoroacetic acid (TFA), pentafluoropropionic acid (PFPA), sodium hydroxide and acetonitrile, showed better separation and more sensitive detection of the gentamicin components than the previous method using a polymer column. More unknown peaks can be separated from the main components and from each other. As the LC–PED method cannot be directly coupled to a mass spectrometer (MS), the unknown substances were collected after the LC column, desalted and analyzed by MS. The structures of the unknown compounds were deduced based on comparison of their fragmentation patterns with those of reference substances investigated by MS n experiments using an electrospray ion trap mass spectrometer. A comparison was also made with an already previously published LC–MS method using a volatile mobile phase.

Isotope coded protein label quantification of serum proteins—Comparison with the label-free LC–MS and validation using the MRM approach

Protein quantification based upon mass spectrometry is gaining ground in diverse applications of biological and clinical relevance. The present article focuses on one of the most complex biological fluids – serum – and provides a novel ICPL based quantification protocol. The results are compared to a label-free (data independent alternate scanning) absolute quantification method. The validation is performed using MRM based protein quantification technique. Regarding the ICPL approach, serum samples used in this study were depleted of high abundant proteins, labeled with ICPL and fractionated according to their respective pI (3–5, 5–7 and 7–12). The samples were further subjected to tryptic digestion followed by treatment with the Glu-C enzyme. The peptides were analyzed on a 2D-nano-LC system using four different concentrations of salt injections (45, 75, 150 and 500 mM ammonium acetate). The LC system was connected on-line with the electrospray ion-trap mass spectrometer. For the label-free quantification the serum samples were depleted and digested with trypsin. A proteome-wide comparison was performed using highly reproducible LC and data independent alternate scanning in conjunction with a high mass accuracy orthogonal time-of-flight mass spectrometer. Selected proteins, found by both methods, were validated using the MRM approach. For this purpose non-depleted tryptically digested serum samples were analyzed by LC coupled with a triple-quadrupole MS. The relative protein quantification using ICPL and mass spectrometry allowed for the detection of approximately 200 proteins, whereas about 2/3 of those contained the ICPL label and could therefore be quantified. Label-free approach used no fractionation, less sample and was able to identify and quantify over 110 proteins. The identified proteins covered generally 3–4 orders of magnitude of protein concentration in human serum. Changes in relative abundance of eight proteins were validated using MRM. This study, for the first time, shows the ability of the relative protein quantification based upon ICPL and 2D-LC–MS/MS to quantify serum biomarkers. It provides two additional label-free approaches that could validate and bring additional value to the label-based results, offering a starting point for comprehensive proteomics studies aiming at revealing biomarkers of clinical relevance.

Chromatographic fingerprint analysis and characterization of furocoumarins in the roots of Angelica dahurica by HPLC/DAD/ESI-MS n technique

A high performance liquid chromatography–diode array detection–electrospray ionization tandem mass spectrometry (HPLC/DAD/ESI-MS n ) method was used for the chromatographic fingerprint analysis and characterization of furocoumarins in the roots of Angelica dahurica for the first time. Nine “common peaks” were identified by comparing with the retention time, UV and MS spectra of reference furocoumarins. The software “Similarity Evaluation System for Chromatographic Fingerprint of TCM” was used to evaluate the similarities of 13 batches of Baizhi samples collected from Henan, Zhejiang, Sichuan and Anhui provinces of China. The results indicated that the samples from different batches had similar HPLC fingerprints, and the method could be applied for the quality control of the roots of Angelica dahurica. In addition, a total of 20 furocoumarins were identified or tentatively characterized by HPLC/DAD/ESI-MS n technique, and their fragmentation patterns in an electrospray ion trap mass spectrometer were also summarized.

Sequencing peptides by electrospray ion-trap mass spectrometry: A useful tool in synthesis of Axinastatin 3

Abstract Axinastatin 3 as a potential anticancer agent was synthesized by chemical methods. In an electrospray ion-trap mass spectrometer, using one stage of tandem mass spectrometry (MS/MS), the linear peptide intermediate was sequenced via the complementarities of y and b ions. Then, using multistep MS/MS (to MS6), the cyclic peptide was sequenced through sequentially removing one amino acid residue in each stage of MS/MS. The difference of the fragmentation mechanisms and the sequencing approaches between them is discussed.

Separation of basic compounds of pharmaceutical interest by using nano-liquid chromatography coupled with mass spectrometry

Nano-liquid chromatography–mass spectrometry (nano-LC–MS) was evaluated for the separation of basic compounds of pharmaceutical interest. The separation of selected β-blockers, namely nadolol, oxprenolol, alprenolol and propranolol in the presence of terbutaline was performed using two 75 μm I.D. capillaries packed with two different RP 18 stationary phases (SP). The best results concerning resolution and efficiency were achieved using the SP where free silanol groups were not present. As expected, this latter SP proved to be very efficient and symmetry factors were observed mainly in the case of the more retained analytes. Baseline resolution of all studied basic compounds was achieved with the Cogent ® bidentate C 18 silica phase (CBC 18) eluting analytes at 800 nL/min with a mobile phase containing 500 mM ammonium acetate pH 4.5–water–methanol (1:8:91, v/v/v). The separated basic compounds were revealed using on-column UV detector at 205 nm and electrospray-ion-trap mass spectrometer (ESI-MS). The packed capillary was connected to the MS through a commercial sheath liquid interface or a sheathless nano-spray interface and in both cases the sensitivity was studied and the results compared. Limit of detection (LOD) as low as 0.1 ng/mL was measured for nadolol using the sheathless nano-spray interface and the capillary column packed with the CBC 18 stationary phase.

De Novo Biosynthetic Profiling of High Abundance Proteins in Cystic Fibrosis Lung Epithelial Cells

In previous studies with cystic fibrosis (CF) IB3-1 lung epithelial cells in culture, we identified 194 unique high abundance proteins by conventional two-dimensional gel electrophoresis and mass spectrometry (Pollard, H. B., Ji, X.-D., Jozwik, C. J., and Jacobowitz, D. M. (2005) High abundance protein profiling of cystic fibrosis lung epithelial cells. Proteomics 5, 2210-2226). In the present work we compared the IB3-1 cells with IB3-1/S9 daughter cells repaired by gene transfer with AAV-(wild type)CFTR. We report that gene transfer resulted in significant changes in silver stain intensity of only 20 of the 194 proteins. However, simultaneous measurement of de novo biosynthetic rates with [(35)S]methionine of all 194 proteins in both cell types resulted in the identification of an additional 31 CF-specific proteins. Of the 51 proteins identified by this hybrid approach, only six proteins changed similarly in both the mass and kinetics categories. This kinetic portion of the high abundance CF proteome, hidden from direct analysis of abundance, included proteins from transcription and signaling pathways such as NFkappaB, chaperones such as HSC70, cytoskeletal proteins, and others. Connectivity analysis indicated that approximately 30% of the 51-member hybrid high abundance CF proteome interacts with the NFkappaB signaling pathway. In conclusion, measurement of biosynthetic rates on a global scale can be used to identify disease-specific differences within the high abundance cystic fibrosis proteome. Most of these kinetically defined proteins are unaffected in expression level when using conventional silver stain analysis. We anticipate that this novel hybrid approach to discovery of the high abundance CF proteome will find general application to other proteomic problems in biology and medicine.

A Major Cell Wall Lipopeptide of Mycobacterium avium subspecies paratuberculosis

Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne disease in cattle and other ruminants, is proposed to be at least one of the causes of Crohn disease in humans. MAP and Mycobacterium avium subspecies avium, a closely related opportunistic environmental bacterium, share 95% of their genes and exhibit homologies of more than 99% between these genes. The identification of molecules specific for MAP is essential for understanding its pathogenicity and for development of useful diagnostic tools. The application of gas chromatography, mass spectrometry, and nuclear magnetic resonance led to the structural identification of a major cell wall lipopeptide of MAP, termed Para-LP-01, defined as C20 fatty acyl-D-Phe-N-Me-L-Val-L-Ile-L-Phe-L-Ala methyl ester. Variations of this lipopeptide with different fatty acyl moieties (C16 fatty acyl through C17, C18, C19, C21 to C22) were also identified. Besides the specificity of this lipopeptide for MAP, the presence of an N-Me-L-valine represents the first reported N-methylated amino acid within an immunogenic lipopeptide of mycobacteria. Sera from animals with Johne disease, but not sera from uninfected cattle, reacted with this lipopeptide, indicating potential biological importance.

Concanavalin A-captured Glycoproteins in Healthy Human Urine

Both the urinary proteome and its glycoproteome can reflect human health status, and more directly, functions of kidney and urinary tracts. Because the high abundance protein albumin is not N-glycosylated, the urine N-glycoprotein enrichment procedure could deplete it, and urine proteome could thus provide a more detailed protein profile in addition to glycosylation information especially when albuminuria occurs in some kidney diseases. In terms of describing the details of urinary proteins, the urine glycoproteome is even a better choice than the proteome itself. Pooled urine samples from healthy volunteers were collected and acetone-precipitated for proteins. N-Linked glycoproteins enriched with concanavalin A affinity purification were separated and analyzed by SDS-PAGE-reverse phase LC/MS/MS or two-dimensional LC/MS/MS. A total of 225 urinary proteins were identified based on two-hit criteria with reliability over 97% for each peptide. Among these proteins, 94 were identified in previous urine proteome works, 150 were annotated as glycoproteins in Swiss-Prot, and 43 were predicted as glycoproteins by NetNGlyc 1.0. A number of known biomarkers and disease-related glycoproteins were identified. Because changes in protein quantity or the glycosylation status can lead to changes in the concanavalin A-captured glycoprotein profile, specific urine glycoproteome patterns might be observed for specific pathological conditions as multiplex urinary biomarkers. Knowledge of the urine glycoproteome is important in understanding kidney and body function.

Use of teicoplanin stationary phase for the enantiomeric resolution of atenolol in human urine by nano-liquid chromatography–mass spectrometry

Nano-liquid chromatography (nano-LC) was used for the enantiomeric resolution of atenolol employing a teicoplanin modified silica stationary phase prepared in our laboratory. Experiments were carried out in a fused silica capillary of 75 μm i.d. packed with chiral modified silica particles of 5 μm diameter. Separated enantiomers were revealed by on-line UV detector at 205 nm or electrospray-ion-trap mass spectrometer (ESI-MS). Atenolol enantiomers were eluted utilizing a mobile phase with the following composition: 500 mM ammonium acetate pH 4.5/methanol/acetonitrile 1:60:39 (v/v/v) allowing to achieve good enantioresolution in a reasonable analysis time (about 8 min) with a flow rate of about 900 nL/min. After comparing the sensitivity of the nano-LC method using a conventional UV detector for capillary electrophoresis, a zeta cell (3 nL volume) employed in nano-LC and the ion-trap MS the method was validated with the MS detector offering the highest sensitivity (limit of detection (LOD) = 50 ng/mL; limit of quantification (LOQ) = 400 ng/mL for each atenolol enantiomer). (−)-Ψ-Nor-ephedrine was used as the internal standard. The method was successfully applied to the analysis of atenolol enantiomers present in human urine samples of a patient under atenolol therapy.

Determination of Diterpenoids and Flavonoids in Isodon rubescens by LC-ESI-MS-MS

The diterpenoids and flavonoids in Isodon rubescens were analyzed simultaneously by high-performance liquid chromatography coupled with electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS-MS) for the first time. The fragmentation pathway of rubescensin A (oridonin) and rubescensin B (ponicidin) in an electrospray ion trap mass spectrometer was also investigated. A total of 10 compounds, including five diterpenoids and five flavonoids, were identified or preliminarily characterized based on their mass spectra. Six of them were reported from Isodon species for the first time.

Channel Function Is Dissociated from the Intrinsic Kinase Activity and Autophosphorylation of TRPM7/ChaK1

TRPM7/ChaK1 is a unique channel/kinase that contains a TRPM channel domain with 6 transmembrane segments fused to a novel serine-threonine kinase domain at its C terminus. The goal of this study was to investigate a possible role of kinase activity and autophosphorylation in regulation of channel activity of TRPM7/ChaK1. Residues essential for kinase activity were identified by site-directed mutagenesis. Two major sites of autophosphorylation were identified in vitro by mass spectrometry at Ser(1511) and Ser(1567), and these sites were found to be phosphorylated in intact cells. TRPM7/ChaK1 is a cation-selective channel that exhibits strong outward rectification and inhibition by millimolar levels of internal [Mg(2+)]. Mutation of the two autophosphorylation sites or of a key catalytic site that abolished kinase activity did not alter channel activity measured by whole-cell recording or Ca(2+) influx. Inhibition by internal Mg(2+) was also unaffected in the autophosphorylation site or "kinase-dead" mutants. Moreover, kinase activity was enhanced by Mg(2+), was decreased by Zn(2+), and was unaffected by Ca(2+). In contrast, channel activity was inhibited by all three of these divalent cations. However, deletion of much of C-terminal kinase domain resulted in expression of an apparently inactive channel. We conclude that neither current activity nor regulation by internal Mg(2+) is affected by kinase activity or autophosphorylation but that the kinase domain may play a structural role in channel assembly or subcellular localization.

18O‐labeling quantitative proteomics using an ion trap mass spectrometer

We describe a method for simultaneous identification and quantitation of proteins within complex mixtures. The method consists of 18O-labeling, a simple stable isotope-coding that requires merely enzymatic digestion in 18O-water, in combination with a capillary-liquid chromatography electrospray ion-trap mass spectrometer. In a separate experiment using the same sample and a spike test, we demonstrate that the difference ration was calculated accurately using the 18O-labeling method even if the protein was part of a complex mixture. Our data also suggest that the accuracy of the quantitation can be improved by averaging the difference ratios of several peptides. In comparing our method with the isotope-coded affinity tag (ICAT) method, we show that the 18O-labeling method has the advantages of better recovery and fewer isotope effects. Therefore, the 18O-labeling method is a powerful tool for large-scale proteomics applications.

On-line strong cation exchange μ-HPLC-ESI-MS/MS for protein identification and process optimization

We have developed an on-line strong cation exchange (SCX)-ESI-MS/MS platform for the rapid identification of proteins contained in mixtures. This platform consists of a SCX precolumn followed by a nanoflow SCX column on-line with an electrospray ion trap mass spectrometer. We also used this platform to study the dynamics of peptide separation/extraction by SCX, in particular to understand the parameters affecting the performance of SCX in multidimensional chromatography. For example, we have demonstrated that the buffer typically used for tryptic digestion of protein mixtures can have a detrimental effect on the chromatographic behaviour of peptides during SCX separations, thereby affecting certain peptide quantitation approaches that rely on reproducible peptide fractionation. We have also demonstrated that band broadening results when a step (discontinuous) gradient approach is used to displace peptides from the SCX precolumn, reducing the separation power of SCX in multidimensional chromatography. In contrast, excellent chromatographic peak shapes are observed when a defined (continuous) gradient is used. Finally, using a tryptic digest of a protein extract derived from human K562 cells, we observed that larger molecular weight peptides are identified using this on-line SCX approach compared to the more conventional reverse phase (RP) LC/MS approach. Both methods used in tandem complement each other and can lead to a greater number of peptide identifications from a given sample.

Reactivity of the NS2/3(907-1206)ASK(4) protein with beta-mercaptoethanol studied by electrospray ion trap mass spectrometry.

The present work reports a mass spectrometric investigation of the NS2/3 protein, a protease from hepatitis C virus (HCV). During routine protein manipulation, in the presence of 100 mM beta-mercaptoethanol and under denatured conditions, the protein was unexpectedly modified at its cysteine residues, and the increased molecular weight corresponded to one molecule of beta-mercaptoethanol bound. The modified protein, once refolded, was found to be less active than the unmodified one. The aim of this work was to investigate whether the reactivity of cysteines with beta-mercaptoethanol involves one specific, highly reactive residue of the sequence, or if the modification is a random process. Liquid chromatography (LC) coupled on-line with an electrospray ion trap mass spectrometer was used to identify the modification sites. It was found that five cysteines out of nine had reacted with beta-mercaptoethanol, none of them showing a significantly higher reactivity than the others. 95% of sequence coverage was obtained.

Investigation of the influence of charge derivatization on the fragmentation of multiply protonated peptides

The fragmentation of the multiply charged peptides b-chain of bovine insulin and glucagon have been investigated under low energy collision induced dissociation (CID) conditions using an electrospray ion trap mass spectrometer. The influence of charge state, specific amino acids such as aspartate or proline, the location of basic sites, and the derivatization on the fragmentation behavior has been the focus of interest. As a basis for understanding the fragmentation process, the concept of the mobile proton was applied. A set of different derivatives was used to manipulate the sites of protonation of the peptides in order to control and improve the fragmentation behavior. These results can be applied for de novo sequencing, although the sequence-specific fragmentation processes have significant influence on the dissociation behavior of the peptides.

Fragmentation mechanisms of oligodeoxynucleotides studied by H/D exchange and electrospray ionization tandem mass spectrometry

We used solution-phase hydrogen/deuterium (H/D) exchange and multistage tandem mass spectrometry (MS/MS) experiments in an electrospray ion-trap mass spectrometer operating in the negative-ion mode to investigate the consequences of the loss of a high proton-affinity (PA) base from T-rich tetra and hexadeoxynucleotides. The T-rich oligodeoxynucleotides containing one or two other nucleobases take advantage of the mass spectral inertness of T because fragmentation of a T-rich oligomer is simple, allowing a tight focus on those processes of interest. Furthermore, determination of T-rich oligodeoxynucleotides may be a starting point in the development of a mass spectrometric scheme to understand the mutagenicity of various types of DNA damage by UV radiation. For nine oligodeoxynucleotides, the nucleobases were charged by nearly exclusive D transfer and then expelled as neutral bases. Loss of the base located at the 3′ end is preferred over that from the 5′ terminus when the two bases are identical. The observation of partially exchanged fragments from a completely exchanged precursor ion proves intramolecular H/D exchange between hydrogen atoms that can exchange in water and those that cannot. The multiplicity of the product-ion peaks provides information on decomposition pathways and origins of the product ions and shows that the loss of base is the first step in all fragmentation of hexanucleotides, but is a competitive process for tetranucleotide fragmentation.

Identification of two-dimensional electrophoresis-separated proteins in human hepatoma cell by electrospray ion trap mass spectrometry

As one of the most important analytical methods in proteome research, mass spectrometry was utilized to identify proteins separated by two-dimensional electrophoresis in the human hepatoma cell line BEL-7404. The protein spots were excised from the gel, followed by in-gel digestion, and the peptide mappings were analyzed by liquid chromatography electrospray ion trap mass spectrometer. Nine proteins were identified via database searching, according to the molecular weights and amino acid sequences of peptides, among which two proteins have not been identified in the other liver-cell database. The sequence coverage was 21% –72%. Furthermore, the relationship between the expressed proteins and the liver carcinoma was discussed.

Multistep tandem mass spectrometry for sequencing cyclic peptides in an ion-trap mass spectrometer

Collisionally activated decomposition (CAD) of a protonated cyclic peptide produces a superposition spectrum consisting of fragments produced following random ring opening of the cyclic peptide to give a set of acylium ions (or isomeric equivalents) of the same m/z. Assignment of the correct sequence is often difficult owing to lack of selectivity in the ring opening. A method is presented that utilizes multiple stages of CAD experiments in an electrospray ion-trap mass spectrometer to sequence cyclic peptides. A primary acylium ion is selected from the primary product-ion spectrum and subjected to several stages of CAD. Amino-acid residues are sequentially removed, one at each stage of the CAD, from the C-terminus, until a b 2 ion is reached. Results are presented for seven cyclic peptides, ranging in sizes from four to eight amino-acid residues. This method of sequencing cyclic peptides eliminates ambiguities encountered with other MS/MS approaches. The power of the strategy lies in the capability to execute several stages of CAD upon a precursor ion and its decomposition products, allowing the cyclic peptide to be sequenced in an unambiguous, stepwise manner.