Isotopic Reagents Research Articles

Precise determination of Sm, Nd concentrations and Nd isotopic compositions at the nanogram level in geological samples by thermal ionization mass spectrometry

In this paper, a high sensitivity method for measurements of Nd isotopes as NdO+, on a TIMS using a single W filament with TaF5 as an ion emitter is presented. Although analyzing Nd isotopes as oxides (NdO+) is a well known technique, this is the first report to analyze Nd isotopic compositions as oxides using W filaments and the TaF5 emitter. When 0.5–1 ng loads of a Neodymium isotopic reference reagent, JNdi-1, were measured using this method, the ion yields were found to be mostly in excess of 15% and could be as high as 32%. Internal precision on 143Nd/144Nd could be better than 10 ppm (2SE) for 1 ng JNdi-1 loads and better than 15 ppm (2SE) for 0.5 ng JNdi-1 loads; thirteen replicates of 0.5–1 ng JNdi-1 loads yielded a 143Nd/144Nd value of 0.512112 ± 0.000028 (2SD). Compared with the previously reported NdO+ measurement method using the Re (or W) filaments + Silica-gel + H3PO4 loading techniques, this method has advantages including higher sensitivity, a more stable ion beam, and no need for oxygen gas to be bled into the ion source chamber. Sm isotopes were analyzed as Sm+ using the W filaments and the TaF5 emitter, and high sensitivity and good ion beam stability were also obtained. Several international rock reference materials, including an ultramafic rock reference material USGS PCC-1 that contains very low amounts of Sm and Nd, were analyzed with full column chemistry and the TaF5 method, and the results of Sm, Nd concentrations and Nd isotopic data are in good agreement with the reported values. Combined with a highly efficient and low-blank column chemistry to separate Nd from Sm, Ce, and Pr, this method holds potential to analyze Sm, Nd concentrations and Nd isotopic compositions of highly depleted peridotites; very small aliquots of minerals such as garnets; extra-terrestrial materials of limited sample size; and environmental samples that contain very low quantities of Sm and Nd.

Multiple Isotopic Labels for Quantitative Mass Spectrometry

Quantitative mass spectrometry is often performed using isotopically labeled samples. Although the 4-trimethylammoniumbutyryl (TMAB) labels have many advantages over other isotopic tags, only two forms have previously been synthesized (i.e., a heavy form containing nine deuteriums and a light form without deuterium). In the present report, two additional forms containing three and six deuteriums have been synthesized and tested. These additional isotopic tags perform identically to the previously reported tags; peptides labeled with the new TMAB reagents coelute from reversed-phase HPLC columns with peptides labeled with the lighter and heavier TMAB reagents. Altogether, these four tags allow for multivariate analysis in a single liquid chromatography/mass spectrometry analysis, with each isotopically tagged peptide differing in mass by 3 Da per tag incorporated. The synthetic scheme is described in simple terms so that a biochemist without specific training in organic chemistry can perform the synthesis. The interpretation of tandem mass spectrometry data for the TMAB-labeled peptides is also described in more detail. The additional TMAB isotopic reagents described here, together with the additional description of the synthesis and analysis, should allow these labels to be more widely used for proteomics and peptidomics analyses.

Prevention of Amino Acid Conversion in SILAC Experiments with Embryonic Stem Cells

Recent studies using stable isotope labeling with amino acids in culture (SILAC) in quantitative proteomics have made mention of the problematic conversion of isotope-coded arginine to proline in cells. The resulting converted proline peptide divides the heavy peptide ion signal causing inaccuracy when compared with the light peptide ion signal. This is of particular concern as it can effect up to half of all peptides in a proteomic experiment. Strategies to both compensate for and limit the inadvertent conversion have been demonstrated, but none have been shown to prevent it. Additionally, these methods combined with SILAC labeling in general have proven problematic in their large scale application to sensitive cell types including embryonic stem cells (ESCs) from the mouse and human. Here, we show that by providing as little as 200 mg/liter L-proline in SILAC media, the conversion of arginine to proline can be rendered completely undetectable. At the same time, there was no compromise in labeling with isotope-coded arginine, indicating there is no observable back conversion from the proline supplement. As a result, when supplemented with proline, correct interpretation of "light" and "heavy" peptide ratios could be achieved even in the worst cases of conversion. By extending these principles to ESC culture protocols and reagents we were able to routinely SILAC label both mouse and human ESCs in the absence of feeder cells and without compromising the pluripotent phenotype. This study provides the simplest protocol to prevent proline artifacts in SILAC labeling experiments with arginine. Moreover, it presents a robust, feeder cell-free, protocol for performing SILAC experiments on ESCs from both the mouse and the human.

Endometrial Carcinoma Biomarker Discovery and Verification Using Differentially Tagged Clinical Samples with Multidimensional Liquid Chromatography and Tandem Mass Spectrometry

The utility of differentially expressed proteins discovered and identified in an earlier study (DeSouza, L., Diehl, G., Rodrigues, M. J., Guo, J., Romaschin, A. D., Colgan, T. J., and Siu, K. W. M. (2005) Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cleavable ICAT with multidimensional liquid chromatography and tandem mass spectrometry. J. Proteome Res. 4, 377-386) to discriminate malignant and benign endometrial tissue samples was verified in a 40-sample iTRAQ (isobaric tags for relative and absolute quantitation) labeling study involving normal proliferative and secretory samples and Types I and II endometrial cancer samples. None of these proteins had the sensitivity and specificity to be used individually to discriminate between normal and cancer samples. However, a panel of pyruvate kinase, chaperonin 10, and alpha1-antitrypsin achieved the best results with a sensitivity, specificity, predictive value, and positive predictive value of 0.95 each in a logistic regression analysis. In addition, three new potential markers were discovered, whereas two other proteins showed promising trends but were not detected in sufficient numbers of samples to permit statistical validation. Differential expressions of some of these candidate biomarkers were independently verified using immunohistochemistry.

Quantification of Cysteine Oxidation in Human Estrogen Receptor by Mass Spectrometry

Redox-dependent modifications of sulfhydryl groups within the two Cys4 zinc fingers of the estrogen receptor DNA-binding domain (ER-DBD) result in structural damage and loss of ER DNA-binding function, which parallels the situation observed in many ER-positive breast cancers. Quantitation of the redox status of cysteinyl thiols within ER-DBD employed cysteine-specific oxidants to induce varying degrees of oxidation in recombinant ER, followed by differential alkylation with the stable isotopic labeling reagents [12C2]-iodoacetic acid and [13C2]-bromoacetic acid. Subsequent proteolysis with LysC/Asp-N generated diagnostic peptides of which the C-terminal peptide of the second zinc finger is most strongly detected by mass spectrometry (MS) and serves as a suitable marker of ER-DBD redox status. Data were collected from two different MALDI-MS instruments: a time-of-flight and a linear ion trap (vMALDI-LIT). An analogous but larger synthetic peptide treated with three isotopic variants of the alkylating reagent modeled isotopic overlaps that might complicate the relative quantitation of cysteine oxidation. Despite the isotopic overlaps, excellent relative quantitation was achieved from MS data obtained from both instruments. This was also true of tandem MS/MS data from the vMALDI-LIT, which should facilitate selected reaction monitoring. Relative quantitation by MS also closely matched data from immunochemical methods.

Development of Reagents for Differential Protein Quantitation by Subtractive Parent (Precursor) Ion Scanning

We present a generic approach for quantitative differential proteomics that reduces data complexity in proteome analysis by automated selection of peptides for MS/MS analysis according to their isotope-labeling ratio. Isotopic reagents were developed that give products which fragment easily to generate a unique pair of signature ions. Using the ion-pair ratio, we show that it is possible to select only BSA peptides (with a 3:1 light heavy isotope ratio) for MS/MS when spiked in a whole yeast extract using Parent (precursor) Ion Quantitation Scanning (PIQS) for MS/MS.

Proteomic Complex Detection Using Sedimentation

Protein-protein interactions are important in many cellular processes, but there are still relatively few methods to screen for novel protein complexes. Here we present a quantitative proteomics technique called ProCoDeS (Proteomic Complex Detection using Sedimentation) for profiling the sedimentation of a large number of proteins through a rate zonal centrifugation gradient. Proteins in a putative complex can be identified since they sediment faster than predicted from their monomer molecular weight. Using solubilized mitochondrial membrane proteins from Arabidopsis thaliana, the relative protein abundance in fractions of a rate zonal gradient was measured with the isotopic labeling reagent ICAT and electrospray mass spectrometry. Subunits of the same protein complex had very similar gradient distribution profiles, demonstrating the reproducibility of the quantitation method. The approximate size of the unknown complex can be inferred from its sedimentation rate relative to known protein complexes. ProCoDeS will be of use in screening extracts of tissues, cells, or organelle fractions to identify specific proteins in stable complexes that can be characterized by subsequent targeted techniques such as affinity tagging.

Dimethyl multiplexed labeling combined with microcolumn separation and MS analysis for time course study in proteomics

Stable-isotope labeling coupled with liquid-phase separation and MS analysis is a powerful technique for comparative proteomics. We developed a dimethyl labeling strategy (Anal. Chem. 2003, 75, 6843-6852 and J. Proteome Res. 2005, 4, 101-108) to label peptide N-terminus and epsilon-amino groups of Lys with water-soluble formaldehyde via reductive methylation, and an isotopic pair of formaldehyde is used for binary labeling on two sets of samples. In this study, this approach is extended to a four sample labeling by combining the binary isotopic reagents of formaldehyde (d0, d2) and the binary isotopic reducing reagents, sodium cyanoborohydride (d0, d3). To ensure sufficient mass difference, this multiplexed labeling is coupled with endoproteinase Lys-C instead of trypsin for digestion, resulting in at least two labeling sites with a mass difference of 4 Da for each pair of peptide digest. Moreover, multiplex dimethyl labeling was proved to have no significant isotopic effect during RP LC elution. This method was further applied for monitoring Lys-C digestion using hemoglobin as a model. Dimethyl labeled digests derived from seven time points (1-30 h) were grouped into two sets of sample mixtures, separated by nano-LC to reduce the complexity, and then analyzed by ESI-MS/MS. The temporal study reveals that Lys-C digestion was completed in 10-15 h for all detected peptides. The multiplex dimethyl method has not only provided a simultaneous detection mean for four sample sets but has also conserved all the advantages associated with the original binary method.

Method for Quantitative Proteomics Research by Using Metal Element Chelated Tags Coupled with Mass Spectrometry

The mass spectrometry-based methods with a stable isotope as the internal standard in quantitative proteomics have been developed quickly in recent years. But the use of some stable isotope reagents is limited by the relative high price and synthetic difficulties. We have developed a new method for quantitative proteomics research by using metal element chelated tags (MECT) coupled with mass spectrometry. The bicyclic anhydride diethylenetriamine-N,N,N',N' ',N' '-pentaacetic acid (DTPA) is covalently coupled to primary amines of peptides, and the ligand is then chelated to the rare earth metals Y and Tb. The tagged peptides are mixed and analyzed by LC-ESI-MS/MS. Peptides are quantified by measuring the relative signal intensities for the Y and Tb tag pairs in MS, which permits the quantitation of the original proteins generating the corresponding peptides. The protein is then identified by the corresponding peptide sequence from its MS/MS spectrum. The MECT method was evaluated by using standard proteins as model sample. The experimental results showed that metal chelate-tagged peptides chromatographically coeluted successfully during the reversed-phase LC analysis. The relative quantitation results were accurate for proteins using MECT. DTPA modification of the N-terminal of peptides promoted cleaner fragmentation (only y-series ions) in mass spectrometry and improved the confidence level of protein identification. The MECT strategy provides a simple, rapid, and economical alternative to current mass tagging technologies available.

Split-Field Drift Tube/Mass Spectrometry and Isotopic Labeling Techniques for Determination of Single Amino Acid Polymorphisms

A combination of split-field drift tube/mass spectrometry and isotopic labeling techniques is evaluated as a means of identifying single amino acid polymorphisms (SAAPs) in proteins. The method is demonstrated using cytochromec (equine and bovine) and hemoglobin (bovine and sheep). For these studies, proteins from different species are digested with trypsin, and the peptides are labeled at primary amine groups [using either a light (H(3))- or heavy (D(3))-isotopic reagent]. SAAP analysis is carried out by mixing the light-labeled peptides of one species with the heavy-labeled peptides of the other and electrospraying the resulting mixture into a split-field drift tube/mass spectrometer. Peptides having the same sequence in both species appear as doublets in the mass spectrum [shifted in mass-to-charge (m/z) according to the number of incorporated labels]; additionally, these species have identical mobility distributions. Peptides having sequences that differ by one amino acid appear as peaks in the mass spectrum that are shifted in m/z according to the mass difference associated with the SAAP and the number of incorporated labels. The ion mobility distributions for these peptides (differing by only a single amino acid) can often be rationalized by their expected similarities or differences providing additional evidence that they are related. In all, 12 and 26 peptide variants (between species) corresponding to 5 and 11 amino acid polymorphisms have been identified for the cytochrome c and hemoglobin protein samples, respectively.

An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins

A procedure for determining the extent of phosphorylation at individual sites of multiply phosphorylated proteins was developed and applied to two polyphosphorylated proteins. The protocol, using simple chemical (Fischer methyl-esterification) and enzymatic (phosphatase) modification steps and an accessible isotopic labeling reagent (methyl alcohol- d 4), is described in detail. Site-specific phosphorylation stoichiometries are derived from the comparison of chemically identical but isotopically distinct peptide species analyzed by microspray liquid chomatography-mass spectrometry (μLC-MS) using a Micromass Q-TOF2 mass spectrometer. Ten phosphorylation sites were unambiguously identified in tryptic digests of both proteins, and phosphorylation stoichiometries were determined for eight of the ten sites using the isotope-coded strategy. The extent of phosphorylation was also estimated from the mass spectral peak areas for the phosphorylated and unmodified peptides, and these estimates, when compared with stoichiometries determined using the isotope-coded technique, differed only marginally (within ∼20%).

Bonding of multiple noble-gas atoms to CUO in solid neon: CUO(Ng)n (Ng=Ar, Kr, Xe; n=1, 2, 3, 4) complexes and the singlet-triplet crossover point.

Laser-ablated U atoms co-deposited with CO in excess neon produce the novel CUO molecule, which forms distinct Ng complexes (Ng=Ar, Kr, Xe) with the heavier noble gases. The CUO(Ng) complexes are identified through CO isotopic and Ng reagent substitution and comparison to results of DFT frequency calculations. The U[bond]C and U[bond]O stretching frequencies of CUO(Ng) complexes are slightly red-shifted from neon matrix (1)Sigma(+) CUO values, which indicates a (1)A' ground state for the CUO(Ng) complexes. The CUO(Ng)(2) complexes in excess neon are likewise singlet molecules. However, the CUO(Ng)(3) and CUO(Ng)(4) complexes exhibit very different stretching frequencies and isotopic behaviors that are similar to those of CUO(Ar)(n) in a pure argon matrix, which has a (3)A" ground state based on DFT vibrational frequency calculations. This work suggests a coordination sphere model in which CUO in solid neon is initially solvated by four or more Ne atoms. Up to four heavier Ng atoms successively displace the Ne atoms leading ultimately to CUO(Ng)(4) complexes. The major changes in the CUO stretching frequencies from CUO(Ng)(2) to CUO(Ng)(3) provides evidence for the crossover from a singlet ground state to a triplet ground state.

Accurate and precise lithium isotopic determinations of igneous rock samples using multi-collector inductively coupled plasma mass spectrometry

A second-generation multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) was applied to lithium isotopic measurements. The high sensitivity of the ICP-MS enabled high precision (±0.82‰, 2 σ) analyses with small amount of Li (∼45 ng Li). A single-step column separation protocol was established with which rapid purification of lithium from rock solutions can be carried out with reduced blank (<10 pg). The influence of potential sources of error for acquisition of lithium isotopic data introduced during the separation, such as matrix effects and isotopic fractionation due to incomplete recovery, were examined with an artificially mixed solution of a composition similar to that of basalt, which was doped with Li isotopic standard reagent. The examinations demonstrated that our protocol suffered from negligible isotopic fractionation. The Li isotopic ratios obtained by our method for seawater and standard rocks (JA-1, JB-2, and JB-3) agree well with those of previously reported data by Moriguti and Nakamura [1,2], which were determined using a four-step column separation method and thermal ionisation mass spectrometry (TIMS). Our separation protocol combined with a sensitive MC-ICP-MS will enable Li isotopic analyses on silicate rock with low Li contents, such as meteorite and peridotites with increased sample throughput.

A mass spectrometry study of n-octane: Electron impact ionization and ion-molecule reactions

Electron impact ionization of n-octane over an energy range of 10–70 eV and the subsequent ion-molecule reactions with the parent molecule have been studied using Fourier-transform mass spectrometry. Molecular ion and fragment ions C1+–C6+ are produced from the electron impact with a total ionization cross section of 1.4±0.2×10−15 cm2 between 60 and 70 eV. C3H7+ is the most abundant ion at most of the ionizing energies with the exception for E⩽16 eV where C6H13+ and C6H12+ are the most abundant. Among the fragment ions only C4H7+ and smaller ions react readily with the parent molecule, primarily producing C5H11+ and C4H9+, with rate coefficients of 0.32–2.4×10−9 cm3 s−1. Essentially all of the ions, including the molecular ion and the large fragment ions, undergo decomposition upon collision with neutral molecules after they are kinetically excited to an energy range of 1–5 eV, forming a variety of small hydrocarbon ions. Many of the decomposition product ions in turn are capable of further reacting with n-octane. Isotope reagents have been utilized in experiments to probe the type of the ion-molecule reactions studied.

Considerations in the determination of boron at low concentrations.

Experimental evidence now supports the nutritional essentiality of boron (B) in some biological systems, and accordingly, the need for reliable analytical B data is increasing. However, the accurate determination of B in biological materials is a formidable challenge at low concentrations (<1 mg B/kg). Recent studies still show significant analytical discrepancies in the analysis of animal tissues and fluids, despite the development of instrumental techniques such as TIMS, ICP-MS, ICP-ES, ICAP, SIMS, NA-MS, PGAA, NRA, and so forth, which have demonstrated detection limits approaching or exceeding (microg B/kg concentrations. Since boric acid is both volatile and ubiquitous in nature, the chemical and physical pathways for B contamination and its loss are manifold, especially during sample preparation. An added obstacle is the inadequacy of biological reference materials certified for B below mg B/kg. With an emphasis toward sample preparation and ICP-MS analysis, examples are provided in this article to help the analyst avoid common problems associated with the analysis of B from biological sources. Topics that are discussed include contamination from Teflon vessels during microwave digestion, losses owing to freeze-drying, B isotopic variations, standards preparation, reagent backgrounds, and instrumental interferences.

Simple and rapid determination of the acetaldehyde dehydrogenase (ALDH2) genotypes by nonradioactive single‐strand conformation polymorphism analysis

The genotyping of mitochondrial acetaldehyde dehydrogenase (ALDH2) is very important in alcohol studies. We describe an ALDH2 genotyping method based on nonradioactive single-strand conformation polymorphism (SSCP) analysis on mini-gels following amplification with a mutated primer set. The three ALDH2 genotypes were clearly and unambiguously distinguished. This method was applied to the ALDH2 genotyping of 129 unrelated Japanese. The allele frequency of ALDH2*2 was calculated to be 0.271, which was consistent with the previous data. The method proved to be simple, rapid and reliable, and dispensed with isotopic reagent and expensive restriction enzymes and equipment. The SSCP method described here is valuable in routine ALDH2 genotyping.