Accurate mass measurement of DNA oligonucleotide ions using high-resolution time-of-flight mass spectrometry

Tannic Acid: a Novel Calibrator for Facile and Accurate Mass Measurement of Electrospray Ionization Mass Spectrometry

Accurate mass calibration is beneficial to the identification of the unknown compounds quickly and accurately. The ESI mass spectrum of tannic acid (TA) tends to a normal distribution of the cluster ion peaks in m/z range from 371.0368 to 1739.1169. Based on the interesting result, we reported the use of TA, a natural plant polyphenol, as a novel calibrator for electrospray ionization mass spectrometry (ESI MS), which has the following three advantages, including (1) easy preparation, (2) the calibration range of m/z 200~2000, and (3) the calibration error is around 3.00 ppm in positive ion mode, which is less than the use of sodium formate (SF) and Prod #88323 calibrators. This TA calibrator has great potential for the wide applications in biological, chemical, and pharmacal analysis.

A new oxygen modification cyclooctaoxygen binds to nucleic acids as sodium crown complex

BACKGROUND

Oxygen exists in two gaseous and six solid allotropic modifications. An additional allotropic modification of oxygen, the cyclooctaoxygen, was predicted to exist in 1990.

METHODS

Cyclooctaoxygen sodium was synthesized in vitro from atmospheric oxygen, or catalase effect-generated oxygen, under catalysis of cytosine nucleosides and either ninhydrin or eukaryotic low-molecular weight RNA. Thin-layer chromatographic mobility shift assays were applied on specific nucleic acids and the cyclooctaoxygen sodium complex.

RESULTS

We report the first synthesis and characterization of cyclooctaoxygen as its sodium crown complex, isolated in the form of three cytosine nucleoside hydrochloride complexes. The cationic cyclooctaoxygen sodium complex is shown to bind to nucleic acids (RNA and DNA), to associate with single-stranded DNA and spermine phosphate, and to be essentially non-toxic to cultured mammalian cells at 0.1-1.0mM concentration.

CONCLUSIONS

We postulate that cyclooctaoxygen is formed in most eukaryotic cells in vivo from dihydrogen peroxide in a catalase reaction catalyzed by cytidine and RNA. A molecular biological model is deduced for a first epigenetic shell of eukaryotic in vivo DNA. This model incorporates an epigenetic explanation for the interactions of the essential micronutrient selenium (as selenite) with eukaryotic in vivo DNA.

GENERAL SIGNIFICANCE

Since the sperminium phosphate/cyclooctaoxygen sodium complex is calculated to cover the active regions (2.6%) of bovine lymphocyte interphase genome, and 12.4% of murine enterocyte mitotic chromatin, we propose that the sperminium phosphate/cyclooctaoxygen sodium complex coverage of nucleic acids is essential to eukaryotic gene regulation and promoted proto-eukaryotic evolution.

Induced dual-nanospray: a novel internal calibration method for convenient and accurate mass measurement

Accurate mass information is of great importance in the determination of unknown compounds. An effective and easy-to-control internal mass calibration method will dramatically benefit accurate mass measurement. Here we reported a simple induced dual-nanospray internal calibration device which has the following three advantages: (1) the two sprayers are in the same alternating current field; thus both reference ions and sample ions can be simultaneously generated and recorded. (2) It is very simple and can be easily assembled. Just two metal tubes, two nanosprayers, and an alternating current power supply are included. (3)With the low-flow-rate character and the versatility of nanoESI, this calibration method is capable of calibrating various samples, even untreated complex samples such as urine and other biological samples with small sample volumes. The calibration errors are around 1 ppm in positive ion mode and 3 ppm in negative ion mode with good repeatability. This new internal calibration method opens up new possibilities in the determination of unknown compounds, and it has great potential for the broad applications in biological and chemical analysis.

On the formation and properties of interstrand DNA-DNA cross-links forged by reaction of an abasic site with the opposing guanine residue of 5'-CAp sequences in duplex DNA

We recently reported that the aldehyde residue of an abasic (Ap) site in duplex DNA can generate an interstrand cross-link via reaction with a guanine residue on the opposing strand. This finding is intriguing because the highly deleterious nature of interstrand cross-links suggests that even small amounts of Ap-derived cross-links could make a significant contribution to the biological consequences stemming from the generation of Ap sites in cellular DNA. Incubation of 21-bp duplexes containing a central 5'-CAp sequence under conditions of reductive amination (NaCNBH(3), pH 5.2) generated much higher yields of cross-linked DNA than reported previously. At pH 7, in the absence of reducing agents, these Ap-containing duplexes also produced cross-linked duplexes that were readily detected on denaturing polyacrylamide gels. Cross-link formation was not highly sensitive to reaction conditions, and the cross-link, once formed, was stable to a variety of workup conditions. Results of multiple experiments including MALDI-TOF mass spectrometry, gel mobility, methoxyamine capping of the Ap aldehyde, inosine-for-guanine replacement, hydroxyl radical footprinting, and LC-MS/MS were consistent with a cross-linking mechanism involving reversible reaction of the Ap aldehyde residue with the N(2)-amino group of the opposing guanine residue in 5'-CAp sequences to generate hemiaminal, imine, or cyclic hemiaminal cross-links (7-10) that were irreversibly converted under conditions of reductive amination (NaCNBH(3)/pH 5.2) to a stable amine linkage. Further support for the importance of the exocyclic N(2)-amino group in this reaction was provided by an experiment showing that installation of a 2-aminopurine-thymine base pair at the cross-linking site produced high yields (15-30%) of a cross-linked duplex at neutral pH, in the absence of NaCNBH(3).

The effects of molecular weight distribution and sample preparation on matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of petroleum macromolecules

To date there have been no systematic, quantitative investigations of the effect of sample preparation on the matrix-assisted laser desorption/ionization time-of-flight (MALDI) mass spectrometry response for polydisperse systems. To this end, the interrelationships between sample preparation, analyte molecular weight distribution (MWD) and solubility, and signal response were investigated for mixtures of alkylated polycyclic aromatic hydrocarbon (PAH) oligomers, the constituents of petroleum pitch that serve as precursors for advanced carbon materials. These PAH oligomers served as a useful analyte system for study, as their solvent solubilities decrease significantly with each increasing oligomeric unit. Molecular weight standards consisting of relatively pure dimer and trimer cuts of the starting M-50 petroleum pitch were produced using a dense-gas/supercritical extraction (DGE/SCE) technique and were then used to produce oligomeric mixtures of well-defined composition for study. Both traditional, solvent-based and newer, solvent-free sample preparation methods were evaluated, and their effects on both homogeneity and signal response were determined. While solvent-free sample preparation methods produced homogeneous samples and reproducible results regardless of the MWD of the analyte, solvent-based samples that contained more than one oligomeric cut produced non-homogeneous samples and poor reproducibilities. The differing solubilities of dimer, trimer, and tetramer oligomers in a given solvent (e.g., CS(2) or toluene) were found to be the cause of the inhomogeneities observed in solvent-based sample preparation. A quantitative analysis study performed with dimer/trimer mixtures over a wide range of compositions via solvent-free sample preparation indicates that linear, reproducible calibration curves can be generated and used to calculate the molecular composition of unknown dimer/trimer mixtures with confidence.

DETECTING LOW-LEVEL SYNTHESIS IMPURITIES IN MODIFIED PHOSPHOROTHIOATE OLIGONUCLEOTIDES USING LIQUID CHROMATOGRAPHY - HIGH RESOLUTION MASS SPECTROMETRY

An LC-MS method based on the use of high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS) for profiling oligonucleotides synthesis impurities is described.Oligonucleotide phosphorothioatediesters (phosphorothioate oligonucleotides), in which one of the non-bridging oxygen atoms at each phosphorus center is replaced by a sulfur atom, are now one of the most popular oligonucleotide modifications due to their ease of chemical synthesis and advantageous pharmacokinetic properties. Despite significant progress in the solid-phase oligomerization chemistry used in the manufacturing of these oligonucleotides, multiple classes of low-level impurities always accompany synthetic oligonucleotides. Liquid chromatography-mass spectrometry has emerged as a powerful technique for the identification of these synthesis impurities. However, impurity profiling, where the entire complement of low-level synthetic impurities is identified in a single analysis, is more challenging. Here we present an LC-MS method based the use of high resolution-mass spectrometry, specifically Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS or FTMS). The optimal LC-FTMS conditions, including the stationary phase and mobile phases for the separation and identification of phosphorothioate oligonucleotides, were found. The characteristics of FTMS enable charge state determination from single m/z values of low-level impurities. Charge state information then enables more accurate modeling of the detected isotopic distribution for identification of the chemical composition of the detected impurity. Using this approach, a number of phosphorothioate impurities can be detected by LC-FTMS including failure sequences carrying 3'-terminal phosphate monoester and 3'-terminal phosphorothioate monoester, incomplete backbone sulfurization and desulfurization products, high molecular weight impurities, and chloral, isobutyryl, and N(3) (2-cyanoethyl) adducts of the full length product. When compared with low resolution LC-MS, ~60% more impurities can be identified when charge state and isotopic distribution information is available and used for impurity profiling.

Ribonucleotide and ribonucleoside determination by ambient pressure ion mobility spectrometry

Detection limits and reduced mobilities for 12 ribonucleotides and 4 ribonucleosides were measured by ambient pressure electrospray ionization-ion mobility spectrometry (ESI-IMS). With the instrument used in this study it was possible to separate some of these compounds within mixtures. Detection limits reported for ribonucleotides and ribonucleosides ranged from 15 to 300 pmol and the reduced mobilities ranged from 41 to 56 suggesting that ambient pressure ESI-IMS may be used for their rapid and sensitive separation and detection. This report demonstrates that it was possible to use ion mobility spectrometry (IMS) to obtain a spectrum for the separation of nucleotides and nucleosides in less than 1 min. The application holds great promise for nucleotide analysis in the area of separating DNA fragments in genome sequencing and also for forensics DNA typing examinations used for the identification of blood stains in crime scenes and paternity testing.

MALDI-TOF MS profiling of annonaceous acetogenins in Annona muricata products for human consumption

Annonaceous acetogenins are proposed as environmental neurotoxicants consumed through medicinal and alimentary habits and responsible for atypical parkinsonian syndromes observed in tropical areas. Potential sources of exposure still have to be determined, as, to date, only a few batches of products for human consumption were searched for these compounds. To assess the presence of acetogenins, we propose a fast, sensitive and accurate method of screening, using MALDI-TOF MS, with minimal sample preparation. Development of the technique is discussed. Its application to leaves of herbal tea, pulp and bottled nectar of Annona muricata is presented.

Characterization of synthetic oligonucleotides containing biologically important modified bases by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Oligonucleotides containing modified bases are commonly used for biochemical and biophysical studies to assess the impact of specific types of chemical damage on DNA structure and function. In contrast to the synthesis of oligonucleotides with normal DNA bases, oligonucleotide synthesis with modified bases often requires modified synthetic or deprotection conditions. Furthermore, several modified bases of biological interest are prone to further damage during synthesis and oligonucleotide isolation. In this article, we describe the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to the characterization of a series of modified synthetic oligonucleotides. The potential for and limits in obtaining high mass accuracy for confirming oligonucleotide composition are discussed. Examination of the isotope cluster is also proposed as a method for confirming oligonucleotide elemental composition. MALDI-TOF-MS analysis of the unpurified reaction mixture can be used to confirm synthetic sequence and to reveal potential problems during synthesis. Analysis during and after purification can yield important information on depurination and base oxidation. It can also reveal unexpected problems that can occur with nonstandard synthesis, deprotection, or purification strategies. Proper characterization of modified oligonucleotides is essential for the correct interpretation of experiments performed with these substrates, and MALDI-TOF-MS analysis provides a simple yet extensive method of characterization that can be used at multiple stages of oligonucleotide production and use.

Metabolite identification of small interfering RNA duplex by high-resolution accurate mass spectrometry

On-line liquid chromatography/electrospray ionization high-resolution mass spectrometry (LC/ESI-HRMS) using an LTQ-Orbitrap mass spectrometer was employed to investigate the metabolite profiles of a model siRNA duplex designated HBV263. The HBV263 duplex was incubated in rat and human serum and liver microsomes in vitro. The siRNA drug and its metabolites were then extracted using a liquid-liquid extraction followed by solid-phase extraction (LLE-SPE), and analyzed by LC/ESI-MS. High-resolution accurate mass data enabled differentiation between two possible metabolite sequences with a monoisotopic molecular mass difference of less than 1 Da. ProMass deconvolution software was used to provide semi-automated data processing. In vitro serum and liver microsome incubation samples afforded different metabolite patterns: the antisense strand of the duplex was degraded preferentially in rat and human serum, while the sense strand of the duplex was less stable in rat and human liver microsomes.

Influence of internal standard charge state on the accuracy of mass measurements in orthogonal acceleration time-of-flight mass spectrometers

Accuracy of mass measurements performed in orthogonal acceleration time-of-flight (oa-TOF) mass spectrometers highly depends on the quality of the signal and the internal calibration. The use of two reference compounds which bracket the targeted unknown, give rise to ions with sufficient signal-to-noise ratio while avoiding detector saturation and produce signals of similar intensity as compared to the target is a common requirement which allow a 5 ppm accuracy on a routine basis. Ion charge state is demonstrated here to be an additional and particularly critical parameter. Using internal references of lower charge state than the target ion systematically yielded overestimated data. Errors measured for quadruply charged molecules were in the range 16-18 ppm when mass calibrants were singly charged ions while accuracy was below 5 ppm when references and target ions were in the same charge state. Magnitude of errors was found to increase with the difference in charge state. This phenomenon arises from the orthogonal acceleration of ions in the TOF analyzer, an interface implemented in all TOF mass spectrometers to accommodate continuous beam ionization sources.

Bacterial genotyping by 16S rRNA mass cataloging

Background

It has recently been demonstrated that organism identifications can be recovered from mass spectra using various methods including base-specific fragmentation of nucleic acids. Because mass spectrometry is extremely rapid and widely available such techniques offer significant advantages in some applications. A key element in favor of mass spectrometric analysis of RNA fragmentation patterns is that a reference database for analysis of the results can be generated from sequence information. In contrast to hybridization approaches, the genetic affinity of any unknown isolate can in principle be determined within the context of all previously sequenced 16S rRNAs without prior knowledge of what the organism is. In contrast to the original RNase T₁ cataloging method, when digestion products are analyzed by mass spectrometry, products with the same base composition cannot be distinguished. Hence, it is possible that organisms that are not closely related (having different underlying sequences) might be falsely identified by mass spectral coincidence. We present a convenient spectral coincidence function for expressing the degree of similarity (or distance) between any two mass-spectra. Trees constructed using this function are consistent with those produced by direct comparison of primary sequences, demonstrating that the inherent degeneracy in mass spectrometric analysis of RNA fragments does not preclude correct organism identification.

Results

Neighbor-joining trees for important bacterial pathogens were generated using distances based on mass spectrometric observables and the spectral coincidence function. These trees demonstrate that most pathogens will be readily distinguished using mass spectrometric analyses of RNA digestion products. A more detailed, genus-level analysis of pathogens and near relatives was also performed, and it was found that assignments of genetic affinity were consistent with those obtained by direct sequence comparisons. Finally, typical values of the coincidence between organisms were also examined with regard to phylogenetic level and sequence variability.

Conclusion

Cluster analysis based on comparison of mass spectrometric observables using the spectral coincidence function is an extremely useful tool for determining the genetic affinity of an unknown bacterium. Additionally, fragmentation patterns can determine within hours if an unknown isolate is potentially a known pathogen among thousands of possible organisms, and if so, which one.

Microbial identification by mass cataloging

Background

The public availability of over 180,000 bacterial 16S ribosomal RNA (rRNA) sequences has facilitated microbial identification and classification using hybridization and other molecular approaches. In their usual format, such assays are based on the presence of unique subsequences in the target RNA and require a prior knowledge of what organisms are likely to be in a sample. They are thus limited in generality when analyzing an unknown sample.

Herein, we demonstrate the utility of catalogs of masses to characterize the bacterial 16S rRNA(s) in any sample. Sample nucleic acids are digested with a nuclease of known specificity and the products characterized using mass spectrometry. The resulting catalogs of masses can subsequently be compared to the masses known to occur in previously-sequenced 16S rRNAs allowing organism identification. Alternatively, if the organism is not in the existing database, it will still be possible to determine its genetic affinity relative to the known organisms.

Results

Ribonuclease T₁ and ribonuclease A digestion patterns were calculated for 1,921 complete 16S rRNAs. Oligoribonucleotides generated by RNase T₁ of length 9 and longer produce sufficient diversity of masses to be informative. In addition, individual fragments or combinations thereof can be used to recognize the presence of specific organisms in a complex sample. In this regard, 140 strains out of 1,921 organisms (7.3%) could be identified by the presence of a unique RNase T₁-generated oligoribonucleotide mass. Combinations of just two and three oligoribonucleotide masses allowed 54% and 72% of the specific strains to be identified, respectively. An initial algorithm for recovering likely organisms present in complex samples is also described.

Conclusion

The use of catalogs of compositions (masses) of characteristic oligoribonucleotides for microbial identification appears extremely promising. RNase T₁ is more useful than ribonuclease A in generating characteristic masses, though RNase A produces oligomers which are more readily distinguished due to the large mass difference between A and G. Identification of multiple species in mixtures is also feasible. Practical applicability of the method depends on high performance mass spectrometric determination, and/or use of methods that increase the one dalton (Da) mass difference between uracil and cytosine.

Development of a quality control method for the characterization of oligonucleotides by capillary zone electrophoresis-electrospray ionization-quadrupole time of flight-mass spectrometry

A capillary zone electrophoresis-negative electrospray ionization-quadrupole time of flight-mass spectrometric method was developed for the characterization of oligonucleotides after synthesis, using model compounds. The major difficulty is the adduction of metal cations to the polyanionic backbone of the oligonucleotide sample, resulting in complex spectra and decreased sensitivity. Several approaches were investigated to circumvent this problem. Separation was performed in an ammonium carbonate buffer. During separation, the interfering metal ions were exchanged for ammonium ions, which are less tightly bound to the oligonucleotide when ionized. The influence of the addition of piperidine and imidazole or trans-1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid (CDTA) to the running buffer for further reduction of cation adduction was investigated. Addition of CDTA to the buffer system resulted in a deconvoluted spectrum with very little adducts. On-line sample stacking proved vital to preconcentrate the samples. The pH and the concentration of the ammonium carbonate buffer as well as the electrophoresis voltage were optimized to achieve the best signal response for the oligonucleotides and a maximum reduction of the cation adducts as well as a short analysis time. Finally, the sheath liquid composition was examined for further improvement of the signal. The developed method was used to analyze different oligonucleotides (5000-9200 Da) in light of its use as a final quality control method for oligonucleotides in terms of purity and sequence homogeneity of the synthesized products. In all cases, very little adducts were observed in the deconvoluted spectra, and the relative errors of the measured molecular masses ranged from 3 to 35 ppm.

Detection of DNA Sequence Variations in Homo- and Heterozygous Samples via Molecular Mass Measurements by Electrospray Ionization Time-of-Flight Mass Spectrometry

The potential of ion-pair reversed-phase high-performance liquid chromatography on-line hyphenated to electrospray ionization time-of-flight mass spectrometry for the characterization of polymerase chain reaction (PCR) amplified nucleic acids was evaluated. For that purpose, a "SNP toolbox" was constructed by cloning and PCR-mediated site-directed in vitro mutagenesis at nucleotide position (ntp) 16,519 of a sequence-verified fragment of the human mitochondrial genome (ntps 15,900-599). Confirmatory sequencing demonstrated that within the sequences of the clones one and the same base was mutated to all other bases. Using these clones or equimolar mixtures of these clones as PCR templates, 51-401-bp-long amplicons were generated, which were used to determine the upper size limits of PCR products for the unequivocal detection of sequence variations in homo- and heterozygous samples. Based on the high mass spectrometric performance of the applied time-of-flight mass spectrometer, the unequivocal genotyping of all kinds of single base exchanges in PCR amplicons from heterozygous samples with lengths up to 254 base pairs (bp) was demonstrated. Considering homozygous samples, the successful genotyping of single base substitutions in up to 401-bp-long PCR products was possible. Consequently, the described hyphenated technique represents one of the most powerful mass spectrometric genotyping assays available today.

Characterization of synthetic nucleic acids by electrospray ionization quadrupole time-of-flight mass spectrometry

The potential of electrospray ionization quadrupole-quadrupole-time-of-flight mass spectrometry (ESI-QqTOF-MS) for the characterization of synthetic nucleic acids was evaluated. Oligonucleotides ranging in size from 12 up to 51 nucleotides were analyzed via direct infusion MS as well as via liquid chromatography (LC) online hyphenated to MS. These experiments proved the outstanding mass spectrometric performance of the TOF mass analyzer in regard of accuracy, reproducibility, resolution, and sensitivity. During a 1-min run, the monoisotopic mass of (dT)(24) was measured with a maximum relative mass deviation of 7.64 ppm proving the high mass accuracy of the TOF analyzer. Over a period of 1 h, mean deviations were determined in the range between -3.58 ppm and 3.06 ppm demonstrating the high stability of the applied external calibration. The molecular mass of a 51-mer was measured with a deviation smaller than 3.23 ppm from the theoretical value. The resolution exceeded a value of m/Deltam = 20 000 (m is the measured mass and Deltam the full peak width at half-maximum), which enabled the separation of the isotopic peaks of all investigated oligonucleotides. Because of the outstanding transmission and detection efficiency of the TOF mass analyzer, detection limits in the amol/microl to low fmol/microl range were reached. The usability of LC-ESI-QqTOF-MS for the qualitative and quantitative analysis of synthetic oligonucleotide mixtures was demonstrated.

Rapid characterization of oligonucleotides by capillary liquid chromatography-nano electrospray quadrupole time-of-flight mass spectrometry

A fast quality control method is developed allowing the desalting and characterization of oligonucleotides by capillary liquid chromatography and on-line nano-electrospray ionization quadrupole time-of-flight mass spectrometry using column switching. The influence of addition of ammonium acetate, trans-1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid, formic acid or acetic acid to the sample, addition of ammonium acetate to the trapping solvent and variation of the trapping time on the further reduction of cation adduction was studied. Final conditions were the addition of 0.1 M ammonium acetate to the sample, the use of a trapping solvent consisting of 0.4 M aqueous 1,1,1,3,3,3-hexafluoro-2-propanol (HFLP) adjusted to pH 7.0 with triethylamine plus 10 mM ammonium acetate during 8 min and the elution of the oligonucleotides with 0.4 M HFIP in 50% methanol. The potential of the optimized procedure is demonstrated for different synthetic oligonucleotides.

PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings

Molecular diagnostics are revolutionising the clinical practice of infectious disease. Their effects will be significant in acute-care settings where timely and accurate diagnostic tools are critical for patient treatment decisions and outcomes. PCR is the most well-developed molecular technique up to now, and has a wide range of already fulfilled, and potential, clinical applications, including specific or broad-spectrum pathogen detection, evaluation of emerging novel infections, surveillance, early detection of biothreat agents, and antimicrobial resistance profiling. PCR-based methods may also be cost effective relative to traditional testing procedures. Further advancement of technology is needed to improve automation, optimise detection sensitivity and specificity, and expand the capacity to detect multiple targets simultaneously (multiplexing). This review provides an up-to-date look at the general principles, diagnostic value, and limitations of the most current PCR-based platforms as they evolve from bench to bedside.

Structural Characterization, Magnetic Properties, and Electrospray Mass Spectrometry of Two Jahn−Teller Isomers of the Single-Molecule Magnet [Mn12O12(CF3COO)16(H2O)4]

The syntheses and characterization of two new, highly soluble, single-molecule magnets [Mn12O12(CF3COO16(H2O)4].2CF3COOH.4H2O (1) and Mn12O12(CF3COO16(H2O)4].CF3COOH.7H2O (2) are reported. Compound 1 was isolated from the reaction of Mn12O12(CF3COO16(H2O)4] with trifluoroacetic acid in CH2Cl2. Compound 1 crystallizes in the tetragonal space group Ifourmacr; (No. 82) with unit cell parameters a = b = 18.128(3) A, c = 13.048(3) A, V = 4287.9(19) A3, Z = 2 and is isostructural to [Mn12O12(CH3COO)16(H2O)4]. Compound 2 was prepared from the reaction of Mn12O12(CF3COO16(H2O)4] with neat trifluoroacetic acid, and crystallizes in the monoclinic space group P2(1)/n (No. 14) with unit cell parameters a = 15.221(8) A, b = 21.870(12) A, c = 27.217(15) A, beta = 90.53(1) degrees, V = 9060(9) A3, and Z = 4. The dc magnetic susceptibility measurements in the 2-300 K temperature range support a high-spin ground state. The magnetization data collected in the 1-7 T field range from 1.8 to 4.0 K were best fit to the parameters S = 10, g = 2.15, D = -0.65 cm(-1), and E = 0 cm(-1) for 1 and S = 10, g = 1.87, D = -0.34 cm(-1), and E = -0.10 cm(-1) for 2. The ac susceptibility data for compound 1 reveal out-of-phase (chi(m)") signals in the 4-7 K temperature range, whereas the chi(m)" signals for compound 2 appear below temperatures of 4 K. This variation in blocking temperatures is a consequence of the two different crystallographic forms of compounds 1 and 2. Compound 1 exhibits the same structural geometry and distortions found in [Mn12O12(CH3COO)16(H2O)4], while compound 2 is of lower molecular symmetry with two Jahn-Teller axes of distortion being oriented along oxide ligands. This different structural arrangement facilitates a different tunneling pathway that leads to a lower effective barrier for magnetization reorientation for compound 2. The substitution of the acetate ligands by trifluoroacetic acid was monitored by mass spectrometry, which is a convenient tool for judging completion of the substitution process.

Automated de novo sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry

We present the first global computer-aided sequencing algorithm for the de novo determination of short nucleic acid sequences. The method compares the fragment ion spectra generated by collision-induced dissociation of multiply charged oligodeoxynucleotide-ions to the m/z values predicted employing established fragmentation pathways from a known reference sequence. The closeness of matching between the measured spectrum and the predicted set of fragment ions is characterized by the fitness, which takes into account the difference between measured and predicted m/z values, the intensity of the fragment ions, the number of fragments assigned, and the number of nucleotide positions not covered by fragment ions in the experimental spectrum. Smaller values for the fitness indicate a closer match between the measured spectrum and predicted m/z values. In order to find the sequence most closely matching the experimental spectrum, starting from a given nucleotide composition all possible oligonucleotide sequences are assembled followed by identification of the correct sequence by the lowest fitness value. Using this concept, sequences of 5- to 12-mer oligodeoxynucleotides were successfully de novo determined. High sequence coverage with fragment ions was essential for obtaining unequivocal sequencing results. Moreover, the collision energy was shown to have an impact on the interpretability of tandem mass spectra by the de novo sequencing algorithm. Experiments revealed that the optimal collision energy should be set to a value just sufficient for complete fragmentation of the precursor ion.

Studies on the chemical synthesis of oligodeoxynucleotides containing the s5T(6-4)T photoproduct: side reactions derived from the methylsulfenyl thiol protection elucidated by MALDI mass spectrometry

Attempts to incorporate the phosphoramidite of the thymine-thymine (6-4) photoproduct C5 thiol analogue (s(5)T(6-4)T PP), whose sulfur atom was protected with the methylsulfenyl group, into oligodeoxynucleotides (ODNs), are reported. Using matrix-assisted laser desorption-ionisation mass spectrometry (MALDI-MS) coupled to enzymatic digestion, accurate mass measurements and tandem mass spectrometry experiments, we demonstrated that ODNs containing the (2-cyanoethylthio)(5)T(6-4)T PP were obtained. Supported by model reactions, these results were explained 1) by the incorporation, during oligonucleotide synthesis, of the sulfur deprotected phosphoramidite that arose from a Michaelis-Arbusov-type rearrangement, and 2) the Michael addition to the thiol of acrylonitrile released upon the cyanoethyl phosphotriester deprotection. To avoid the formation of the cyanoethyl adduct, the phosphotriester deprotection was carried out in the presence of a thiol in excess. This afforded the ODN containing the h(5)T(6-4)T PP.

Exact mass measurement on an electrospray ionization time-of-flight mass spectrometer: error distribution and selective averaging

An automated, accurate and reliable way of acquiring and processing flow injection data for exact mass measurement using a bench-top electrospray ionization time-of-flight (ESI-TOF) mass spectrometer is described. Using Visual Basic programs, individual scans were selected objectively with restrictions on ion counts per second for both the compound of interest and the mass reference peaks. The selected "good scans" were then subjected to two different data-processing schemes ("combine-then-center" and "center-then-average"), and the results were compared at various ion count limit settings. It was found that, in general, the average of mass values from individual scans is more accurate than the centroid mass value of the combined (same) scans. In order to acquire a large number of good scans in one injection (to increase the sampling size for statistically valid averaging), an on-line dilution chamber was added to slow down the typically rapid mass chromatographic peak decay in flow-injection analysis. This simple addition worked well in automation without the need for manual sample dilution. In addition, by dissolving the reference compound directly into the mobile phase, manual syringe filling can be eliminated. Twenty-seven samples were analyzed with the new acquisition and process routines in positive electrospray ionization mode. For the best method found, the percentage of samples with RMS error less than 5 ppm was 100% with repetitive injection data (6 injections per sample), and 95% with single injection data. Afterwards, 31 other test samples were run (with MW ranging from 310 to 3493 Da, 21 samples in ESI+ and 10 in ESI- mode) and processed with similar parameters and 100% of them were mass-calculated to RMS error less than 5 ppm also.

Quantitation of Underivatized Free Amino Acids in Mammalian Cell Culture Media Using Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry

In this investigation, a quantitative matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) method was developed for the analysis of underivatized free amino acids in mammalian cell culture media. Calibration curves were developed for 12 amino acids over the linear range of 1-100 microM with coefficients of determination ranging from r2 = 0.9220 to r2 = 0.9973. An aerospray method was utilized for the sample deposition method, and the matrix, alpha-cyano-4-hydroxycinnamic acid, served as the internal standard. This assay was used to analyze bioreactor samples from five time points in the process. Concentrations determined through interpolation of the calibration curves were comparable to those obtained via reversed-phase HPLC based analysis with an average percent difference of 19.71%. Repeatability and intermediate precision studies were also performed, and the relative standard deviations ranged from 0.5943 to 21.41 and 3.157 to 18.97, respectively.

ZnS nanomaterial characterization by MALDI-TOF mass spectrometry

We present a methodology for mass and size dispersity analysis by MALDI-TOF mass spectrometry of lyothermally grown 2.5-3.7 nm ZnS nanocrystals having a Zn blende crystal structure. These results correlate with information obtained by TEM and absorption spectroscopy. The use of MS methods to probe size and size dispersity provides a convenient method to rapidly analyze II-VI materials at the nanoscale. We believe these results represent the first mass spectrometric analysis of size and size dispersities on II-VI nanocrystals.

Gas-phase conformations of deprotonated trinucleotides (dGTT-, dTGT-, and dTTG-): the question of zwitterion formation

The gas-phase conformations of a series of trinucleotides containing thymine (T) and guanine (G) bases were investigated for the possibility of zwitterion formation. Deprotonated dGTT-, dTGT-, and dTTG- ions were formed by MALDI and their collision cross-sections in helium measured by ion mobility based methods. dTGT- was theoretically modeled assuming a zwitterionic and non-zwitterionic structure while dGTT- and dTTG- were considered "control groups" and modeled only as non-zwitterions. In the zwitterion, G is protonated at the N7 site and the two neighboring phosphates are deprotonated. In the non-zwitterion, G is not protonated and only one phosphate group is deprotonated. Two conformers, whose cross-sections differ by 17 +/- 2 A2, are observed for dTGT- in the 80 K experiments. Multiple conformers are also observed for dGTT- and dTTG- at 80 K, though relative cross-section differences between the conformers could not be accurately obtained. At higher temperatures (>200 K), the conformers rapidly interconvert on the experimental time scale and a single "time-averaged" conformer is observed in the ion mobility data. Theory predicts only one low-energy conformation for the zwitterionic form of dTGT- with a cross-section 8% smaller than experimental values. Additionally, the extra H+ on G does not bridge both phosphates. Thus, dTGT- does not appear to be a stable zwitterion in the gas-phase. Theory does, however, predict two low-energy conformers for the non-zwitterionic form of dTGT- that differ in cross-section by 18 +/- 3 A2, in good agreement with the experiment. In the smaller cross-section form (folded conformer), G and one of the T bases are stacked while the other T folds towards the stacked pair and hydrogen bonds to G. In the larger cross-section form (open conformer), the unstacked T extends away from the T/G stacked pair. Similar folded and open conformers are predicted for all three trinucleotides, regardless of which phosphate is deprotonated.

Electrospray ionization quadrupole time-of-flight mass spectrometry and quadrupole mass spectrometry for genotyping single nucleotide substitutions in intact polymerase chain reaction products in K-ras and p53

Single nucleotide polymorphisms (SNPs) and mutations were genotyped for both homozygous and heterozygous PCR products of p53, a tumor suppressor gene, and K-ras, an oncogene, using electrospray ionization (ESI) quadrupole time-of-flight (Q-TOF) mass spectrometry (MS) and ESI-quadrupole MS analysis. Mass accuracy was adequate for both instruments to detect genetic changes in homozygous PCR products, including the most difficult to distinguish (adenine [A] --> thymine [T] transversion). However, for the detection of A --> T shifts (9.0 Da difference) in heterozygous PCR products, the increased resolution of ESI-Q-TOFMS proved essential. Although, greater mass differences in heterozygotes (e.g. cytosine [C] <--> T or guanine [G] <--> A) can be discriminated using ESI-quadrupole MS analysis.

Sodium-tolerant matrix for matrix-assisted laser desorption/ionization mass spectrometry and post-source decay of oligonucleotides

A mixture of 2',4',6'-trihydroxyacetophenone in acetonitrile and aqueous triammonium citrate solution in a 1:1 molar proportion (0.2 M concentration) was found to be a good matrix for the detection of synthetic oligodeoxynucleotide samples. A high proportion of volatile solvent as well as the high salt content ensure fast co-crystallization of the matrix, co-matrix and analyte molecules. Matrix-assisted laser desorption/ionization (MALDI) mass spectra obtained in negative ion reflectron mode from samples prepared with this protocol show deprotonated molecules [M - H](-), rather than sodium adducts, as the most abundant ions even when up to 50 mM of sodium chloride is present in the sample. The matrix is shown to be effective for low mass modified single nucleotides as well as for longer oligodeoxynucleotides (up to 18mer). Post-source decay (PSD) mass spectra can also be obtained by increasing the laser fluence. Simple sequence information such as the identity and localization of a deleted base or the 5'/3' orientation can then easily be obtained. The calibration method and mass accuracy required are discussed depending on the type of information required.