Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry

A method has been developed to identify oligonucleotide-peptide heteroconjugates by accurate mass measurements using MS. The fractional mass (the decimal fraction mass value following the monoisotopic nominal mass) for peptides and oligonucleotides is different due to their differing molecular compositions. This property has been used to develop the general conditions necessary to differentiate peptides and oligonucleotides from oligonucleotide-peptide heteroconjugates. Peptides and oligonucleotides generated by the theoretical digestion of various proteins and nucleic acids were plotted as nominal mass versus fractional mass. Such plots reveal that three nucleotides cross-linked to a peptide produce enough change in the fractional mass to be recognized from non-cross-linked peptides at the same nominal mass. Experimentally, a Cytochrome c digest was spiked with an oligonucleotide-peptide heteroconjugate and conditions for analyzing the sample using liquid chromatography (LC)-MS were optimized. Upon analysis of this mixture, all detected masses were plotted on a fractional mass plot and the heteroconjugate could be readily distinguished from non-cross-linked peptides. The method developed here can be incorporated into a general proteomics-like scheme for identifying protein-nucleic acid cross-links, and this method is equally applicable to characterizing cross-links generated from protein-DNA and protein-RNA complexes.     

Generation of mass tags by the inherent electrochemistry of electrospray for protein mass spectrometry

We present herein a review of our work on the on-line electrochemical generation of mass tags toward cysteine residues in peptides and proteins. Taking advantage of the inherent electrochemical nature of electrospray generated from a microfabricated microspray emitter, selective probes for cysteine were developed and tested for on-line nonquantitative mass tagging of peptides and proteins. The nonquantitative aspect of the covalent tagging thus allows direct counting of free cysteines in the mass spectrum of a biomolecule through additional adduct peaks. Several substituted hydroquinones were investigated in terms of electrochemical properties, and their usefulness for on-line mass tagging during microspray experiments were assessed with L-cysteine, peptides, and intact proteins. Complementarily, numerical simulations were performed to properly understand the respective roles of mass transport, kinetics of electrochemical-chemical reactions, and design of the microspray emitter in the mass tagging overall efficiency. Finally, the on-line electrochemical tagging of cysteine residues was applied to the analysis of tryptic peptides of purified model proteins for protein identification through peptide mass fingerprinting.     

Identification of the 'wrong' active pharmaceutical ingredient in a counterfeit Halfan drug product using accurate mass electrospray ionisation mass spectrometry,accurate mass tandem mass spectrometry and liquid chromatography/mass spectrometry

Methodology is presented for identifying an unknown active (pharmaceutical) ingredient (AI) in a counterfeit drug product. A range of mass spectrometric techniques, i.e., accurate mass mass spectrometry, tandem mass spectrometry (MS/MS) and liquid chromatography/mass spectrometry (LC/MS), has been employed to determine the AI in a counterfeit Halfan suspension, an antimalarial drug. In particular, use of LockSpray accurate mass MS/MS allowed identification of parts of the molecule from fragments, hence limiting the number of possible elemental compositions for the nominal mass of 278 found for the AI in the counterfeit product. The analysis of the isotope pattern observed for the protonated molecule further reduced the number of possible elemental compositions. A literature search for readily commercially available compounds of molecular formula C(12)H(14)N(4)O(2)S suggested that the AI was either sulfamethazine or sulfisomidine. An LC/MS separation of those two compounds and reference MS/MS spectra obtained for sulfamethazine and sulfisomidine led to the conclusion that the AI in the counterfeit Halfan suspension is sulfamethazine, which is an antibacterial agent.     

Chromatographic mass of a polymer and its use for determining the molecular mass characteristics

The method has been proposed for determining the molecular characteristics of flexible-chain polymers that obey the universal calibration principle and for which there are available experimental data on the intrinsic viscosity. This method is based on studying the dependence of the hydrodynamic volume M _n[η], M _w[η], M _z[η], and M _η[η] on parameter a in the Mark-Kuhn-Houwink equation. It has been found that, for parameter a varying in the range from 0.5 to 0.8, the weight-average hydrodynamic volume M _w[η] remains almost unchanged. This allows estimation of M _w based on a single intrinsic viscosity value. The notion of the chromatographic mass of a polymer is advanced and is employed for determining other molecular mass parameters.     

Comparison of mass resolution criteria in mass spectrometry

For a single peak, mass spectral resolution can be expressed in terms of peak width or ratio of peak position to peak width. Alternatively, for two equally intense peaks of equal width, resolution can be defined as the minimum peak separation such that the height of the valley between the combined peaks is less than a specified ratio (1%, 10%, 50%, 100%) of the individual (or combined) peak maximum. All these definitions depend on peak shape. Conversion formulae between various mass resolution criteria are presented for each of eight spectral peak shapes: Gaussian, triangular, trapezoidal, Lorentzian (absorption-mode, magnitude-mode, and sine-apodized magnitude-mode), and sinc (absorption-mode and magnitude-mode). From these formulae, mass resolutions based upon different criteria are readily compared for the same or different line shapes.     

Reactions in the source of a mass spectrometer: The mass spectrum of 1-chlorobenzotriazole

The mass spectrum of 1-chlorobenzotriazole contains ions derived from benzotriazole, a product of an exchange reaction with water in the source of the mass spectrometer. Relatively intense ions derived from iodine, iodine monobromide and other inter-halogen compounds are also observed. These species are produced by oxidation of involatile halide coatings in the source region by 1-chlorobenzotriazole. It is suggested that anomalous peaks produced by oxidation-reduction reactions in the source may be expected in the spectrum of any organic oxidant.     

Kinetics of the hydrolysis of woody-fibrous mass

The possibility has been shown of obtaining fodder additives by the hydrolysis of woody-fibrous mass with dilute sulfuric acid solutions. The kinetics of hydrolysis have been studied, a calculation has been made of the effective rate constants of hydrolysis of the polysaccharide part of the woody-fibrous mass, and the range of variation of the effective activation energy of the process has been determined.Deceased.Siberian Scientific Research Institute of Cellulose and Board, Bratsk. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 687–690, September–October, 1990.     

Kinetics of the hydrolysis of woody-fibrous mass

The possibility has been shown of obtaining fodder additives by the hydrolysis of woody-fibrous mass with dilute sulfuric acid solutions. The kinetics of hydrolysis have been studied, a calculation has been made of the effective rate constants of hydrolysis of the polysaccharide part of the woody-fibrous mass, and the range of variation of the effective activation energy of the process has been determined.     

Flow injection of the lock mass standard for accurate mass measurement in electrospray ionization time-of-flight mass spectrometry coupled with liquid chromatography

A method of flow injection of the lock mass for accurate mass measurement using electrospray ionization time-of-flight mass spectrometry is described. The reference compound is introduced in the chromatographic effluent via a six-port valve placed post-column, prior to the split connector. Flow injection is performed in such a way that the reference elution peak is superimposed in the total ion current and partially overlaps that of the investigated analyte, allowing independent ionization of the two compounds and thus accurate mass measurement with no ion suppression effects. Different lock mass molecules can be injected in a single analytical run to target various analytes. The performance of this methodology is demonstrated in both isocratic and gradient liquid chromatography modes. The molecular ion of the flow-injected lock mass could also be used as a reference for mass measurement of the in-source fragments of the analytes. Good mass accuracy, within 4 mDa of the theoretical values, was obtained.     

Ortho-rearrangement in the mass spectra of diphenylmethanes

The mass spectra of all possible methyl substituted derivatives of 3,3′,5,5′-tetramethyl-4, 4′-dihydroxy-diphenylmethane are recorded. The direct influence of steric hindrance to free rotation about the aryl-methylene bonds results in the progressive importance of ortho-rearrangement in the ionization-dissociation pathways of these compounds.     

Determination of micelle mass by electrospray ionization mass spectrometry

By electrospray ionization (ESI) mass spectrometry, micelle solutions of sodium cholate were investigated in detail in the presence and absence of ethanol. The average aggregation number could be evaluated from the spectra acquired under conditions where soft collisions adequate to measure the micelle solution were induced, and the value agreed well with that obtained previously by other methods. From the dependence on ethanol content, it was also found that the average aggregation number in aqueous solution without organic solvent could be reliably estimated. The ESI method proved to be a useful tool for determining the micelle mass in the original aqueous phase.     

Landmarks in the theory of mass spectra

Statistical theories of mass spectra are based on two assumptions. The first one, which postulates efficient phase space sampling, is substantiated by various experimentation and is now theoretically much better understood. The efficiency of phase space sampling can be estimated and is found to be quite good. Much effort remains to be done concerning the second assumption. A new impetus should be given to the concept of transition state. A better understanding of the role played by the conservation of angular momentum, the exact significance of transition state switching, and the incorporation of quantum effects are set as goals for the future.     

Extension of the two-dimensional mass channel cluster plot method to fast separations utilizing low thermal mass gas chromatography with time-of-flight mass spectrometry

Implementation of a data reduction and visualization method for use with high-speed gas chromatography and time-of-flight mass spectrometry (GC-TOFMS) is reported. The method, called the “2D m/z cluster method” facilitates analyte detection, deconvolution, and identification, by accurately measuring peak widths and retention times using a fast TOFMS sampling frequency (500 Hz). Characteristics and requirements for high speed GC are taken into consideration: fast separations with narrow peak widths and high peak capacity, rapid data collection rate, and effective peak deconvolution. Transitioning from standard GC (10–60+ minute separations) to fast GC (1–10 min separations) required consideration of how to properly analyze the data. This report validates use of the 2D m/z cluster method with newly developed GC technology that produces ultra-fast separations (∼1 min) with narrow analyte peak widths. Low thermal mass gas chromatography (LTM-GC) operated at a heating rate of 250 °C/min coupled to a LECO Pegasus III TOFMS analyzed a 115 component test mixture in 120 s with peak widths-at-base, w_b (4σ), of 350 ms (average) to produce a separation with a high peak capacity, n_c ∼ 340 (at unit resolution R_s = 1). The 2D m/z cluster method is shown to separate overlapped analytes to a limiting R_s ∼ 0.03, so the effective peak capacity was increased nearly 30-fold to n_c ∼10,000 in the 120 s separation. The method, when coupled with LTM-GC-TOFMS, is demonstrated to provide unambiguous peak rank (i.e. the number of analytes per overlapped peak in the total ion current (TIC)), by visualizing locations of pure and chromatographically overlapped m/z. Hence, peak deconvolution and identification using MCR-ALS (multivariate curve resolution – alternating least squares) is demonstrated.     

Hybrid mass spectrometers for tandem mass spectrometry

Mass spectrometers that use different types of analyzers for the first and second stages of mass analysis in tandem mass spectrometry (MS/MS) experiments are often referred to as "hybrid" mass spectrometers. The general goal in the design of a hybrid instrument is to combine different performance characteristics offered by various types of analyzers into one mass spectrometer. These performance characteristics may include mass resolving power, the ion kinetic energy for collision-induced dissociation, and speed of analysis. This paper provides a review of the development of hybrid instruments over the last 30 years for analytical applications.