Efficient calculation of exact mass isotopic distributions

This paper presents a new method for efficiently calculating the exact masses in an isotopic distribution using a dynamic programming approach. The resulting program, isoDalton, can generate extremely high isotopic resolutions as demonstrated by a FWHM resolution of 2 x 10(11). This resolution allows very fine mass structures in isotopic distributions to be seen, even for large molecules. Since the number of exact masses grows exponentially with molecular size, only the most probable exact masses are kept, the number of which is user specified.     

Determination of the elemental composition of a substance from low-resolution mass spectra with the aid of a computer

The possibility of using low- and medium-resolution mass spectra for determining the composition of -diketonates, coronands, and other types of substances was studied. Several versions of a microcomputer program were developed that helped to determine the empirical formula of an unknown compound from generated values of ionic mass and distribution moments of the isotopic peaks of a molecular and protonated quasimolecular ion.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 2, pp. 394–396, February, 1991.     

The isotopic mass defect: a tool for limiting molecular formulas by accurate mass

This paper describes the use of the relative isotopic mass defect, which is the mass defect between the monoisotopic mass of an element and the mass of its A + 1 or its A + 2 isotopic cluster. The relative isotopic mass defect is combined with the intensity of the isotopic cluster and a formula generator to find the correct molecular formula for unknown pesticides, using accurate mass measurements. This paper introduces the concept of the relative mass defect of isotopes and the isotopic mass average (IMA), especially for C, H, N, O, S, Cl, and Br, and how to correlate these measurements to the correct molecular formula of an unknown compound. A heuristic rule of ±3 × 10⁻³ u (+3 millimass units) is developed as a simple observational tool for viewing accurate mass data with four-decimal-place mass accuracy. This heuristic rule allows one to rapidly scan data “by eye” without the use of sophisticated software, and is a useful and rapid way of examining a molecular formula.     

An expert system for inferring structures of organic compounds from their mass spectra.

Development of an 'expert system' for elucidation of structures of acyclic organic compounds is described. An expert system is a computer program that embodies some of the heuristic problem-solving knowledge of human experts so that it can effectively be used as an aid to decision making. The expert system described in this paper is intended to assist a chemist in arriving at plausible structures, the input data being the mass spectrum, molecular formula and presence (if known) of functional groups. The program generates chemically possible structures for the given molecular formula and can use, where available, the constraints imposed by the mass spectrum of the compound and by any known functional groups. The program makes use of a new algorithm for obtaining a canonical representation of structures and a new heuristic for incorporating constraints of the mass spectrum. This work constitutes a case study of the application of artificial intelligence techniques in chemistry and the material presented highlights this motivation.     

Spectral accuracy of molecular ions in an LTQ/Orbitrap mass spectrometer and implications for elemental composition determination

In addition to mass accuracy, the ability of a mass spectrometer to faithfully measure the isotopic distribution of an ion, defined as spectral accuracy, is also important. Although time-of-flight mass spectrometers are reported to possess high spectral accuracy capability compared with other mass spectrometers, the Orbitrap has not yet been investigated. Ten natural products (moxidectin, erythromycin, digoxin, rifampicin, amphotericin B, rapamycin, gramicidin S, cyclosporin A, vancomycin, and thiostrepton) ranging in molecular weight from 639 to 1663 Da were measured on an LTQ/Orbitrap mass spectrometer with resolving power settings of 7.5, 15, 30, 60, and 100 K. The difference in the observed profile isotope pattern compared with the theoretical calculation after peak shape calibration, denoted spectral error, was calculated using the program MassWorks (Cerno Bioscience, Danbury, CT, USA). Spectral errors were least at 7.5 K resolving power (≤3%) but exceeded 10% for some compounds at 100 K. The increasing spectral error observed at higher resolving power for compounds with complex fine structure might be explained by the phenomena of isotopic beat patterns as observed in FTICR. Several compounds with prominent doubly charged ions allowed comparison of spectral accuracies of singly-versus doubly-charged ions. When using spectral error to rank elemental compositions with formula constraints (C_0–100H_0–200N_0–50O_0–50Cl_0–5S_0–5) and a mass tolerance ≤2 parts-per-million, the correct formula was ranked first 35% of the time. However, spectral error considerations eliminated >99% of possible elemental formulas for compounds with molecular weight >900 Da.     

The computer processing and interpretation of mass spectral information. VI—computing the isotopic spectrum of assumed composition

An interactive program for the computation of an isotopic spectrum of assumed composition whose empirical formula can be represented either as a set of chemical elements or in terms of structural fragments (super-elements) is described. The core of the program is a table of all isotopes of 82 elements of the periodic table and super-elements whose list is decided on by the user. The exact mass of isotopic peaks is determined by the program either from the position of the maximum value of the peak abundance or from the position of its centroid. The spectrum printout may be in one of several formats. The interaction with the program is very useful for operators of mass spectrometers in enabling them to estimate and verify assumptions about the elemental composition of spectrum peak groups.     

Electrospray ionization mass spectra of hemoglobin and transferrin by a magnetic sector mass spectrometer. Comparison with theoretical isotopic distributions.

Electrospray ionization mass spectra of human hemoglobin chains and of transferrin were acquired on a magnetic sector mass spectrometer. The observed molecular ion for each hemoglobin chain was in good agreement with the theoretical isotopic distribution at a reasonable resolution of 2000. The clear separation of a variant beta-chain in admixture with the normal counterpart at mass 15,867 that differed from it by 14 Da (0.09%) ensured that a smaller mass difference could be detected. The molecular ions for human transferrin were too broad compared with the theoretical shape to determine the molecular mass accurately, probably due to the heterogeneity of the carbohydrate moiety. A decrease in mass by neuraminidase digestion, however, determined the average number of sialic acids in the molecule.     

Automated reduction and interpretation of

Here a fully automated computer algorithm is applied to complex mass spectra of peptides and proteins. This method uses a subtractive peak finding routine to locate possible isotopic clusters in the spectrum, subjecting these to a combination of the previous Fourier transform/Patterson method for primary charge determination and the method for least-squares fitting to a theoretically derived isotopic abundance distribution for m/z determination of the most abundant isotopic peak, and the statistical reliability of this determination. If a predicted protein sequence is available, each such m/z value is checked for assignment as a sequence fragment. A new signal-to-noise calculation procedure has been devised for accurate determination of baseline and noise width for spectra with high peak density. In 2 h, the program identified 824 isotopic clusters representing 581 mass values in the spectrum of a GluC digest of a 191 kDa protein; this is >50% more than the number of mass values found by the extremely tedious operator-applied methodology used previously. The program should be generally applicable to classes of large molecules, including DNA and polymers. Thorough high resolution analysis of spectra by Horn (THRASH) is proposed as the program's verb.     

A quality index for reference mass spectra

A numerical rating for evaluating the quality of reference mass spectra used for retrieval and interpretive applications is proposed. The overall quality index is the product of seven quality factors: (1) source of the spectrum; (2) ionization conditions; (3) higher molecular weight impurities; (4) illogical neutral losses; (5) isotopic abundance accuracy; (6) number of peaks; and (7) lower mass limit of peaks. For quality factor 6 the number of peaks of abundances ≥1% was found to correspond to 15 more than the number of atoms in the molecule with a correlation coefficient of 0.482. The program has been found useful in preparing a data base of 41429 mass spectra; for the majority of spectra judged to be unsatisfactory by the program this arose from a low quality factor 6 value (too few peaks).     

土壤及蔬菜中微量汞的同位素稀释电感耦合等离子体质谱测定

建立了微波消解电感耦合等离子体质谱同位素稀释(ID/ICP-MS)测定微量汞的方法。考察了仪器参数及测量条件对汞同位素比值RHg(202Hg/200Hg)测量的影响,根据同位素比值测量误差的传递因子优化了富集同位素稀释剂(202Hg98%)的加入量,并以铊同位素比值(205Tl/203Tl)作为RHg(202Hg/200Hg)测量时发生质量歧视效应的校正因子;通过反同位素稀释法标定了富集汞同位素稀释剂的浓度。利用所建立的ID/ICP-MS方法测定了杨树叶(GBW07604)和湖积物(GBW07423)2种标准参考物中汞的含量,回收率分别为112%和100%。该方法具有准确度高、精密度好等优点,且样品前处理简便,适用于土壤及蔬菜等样品中微量及痕量汞的准确测定。     

Automated determination of precursor ion, product ion, and neutral loss compositions and deconvolution of composite mass spectra using ion correlation based on exact masses and relative isotopic abundances

After an accidental, deliberate, or weather-related dispersion of chemicals (dispersive event), rapid determination of elemental compositions of ions in mass spectra is essential for tentatively identifying compounds. A direct analysis in real time (DART)ion source interfaced to a JEOL AccuTOFmass spectrometer provided exact masses accurate to within 2 mDa for most ions in full scan mass spectra and relative isotopic abundances (RIAs) accurate to within 15-20% for abundant isotopic ions. To speed determination of the correct composition for precursor ions and most product ions and neutral losses, a three-part software suite was developed. Starting with text files of m/z ratios and their ion abundances from mass spectra acquired at low, moderate, and high collision energies, the ion extraction program (IEP) compiled lists for the most abundant monoisotopic ions of their exact masses and the RIAs of the +1 and +2 isotopic peaks when abundance thresholds were met; precursor ions; and higher-mass, precursor-related species. The ion correlation program (ICP) determined if a precursor ion composition could yield a product ion and corresponding neutral loss compositions for each product ion in turn. The input and output program (IOP) provided the ICP with each precursor ion:product ion pair for multiple sets of error limits and prepared correlation lists for single or multiple precursor ions. The software determined the correct precursor ion compositions for 21 individual standards and for three- and seven-component mixtures. Partial deconvolution of composite mass spectra was achieved based on exact masses and RIAs, rather than on chromatography.     

COMPLX: a computer algorithm for the detection of protein-ligand and other macromolecular complexes in mass spectra

A new algorithm has been designed and tested to identify protein, or any other macromolecular, complexes that have been widely reported in mass spectral data. The program takes advantage of the appearance of multiply charged ions that are common to both electrospray ionization and, to a lesser extent, matrix-assisted laser desorption/ionization (MALDI) mass spectra. The algorithm, known as COMPLX for the COMposition of Protein-Ligand compleXes, is capable of identifying complexes for any protein or macromolecule with a binding partner of molecular mass up to 100 000 Da. It does so by identifying ion pairs present in a mass spectrum that, when they share a common charge, have an m/z value difference that is an integer fraction of a ligand or binding partner molecular mass. Several additional criteria must be met in order for the result to be ranked in the output file including that all m/z values for ions of the protein or complex have progressively lower values as their assigned charge increases, the difference between the m/z values for adjacent charge states (z, z + 1) decrease as the assigned charge state increases, and the ratio of any two m/z values assigned to a protein or complex is equal to the inverse ratio of their charge. The entries that satisfy these criteria are then ranked according to the appearance of ions in the mass spectrum associated with the binding partner, the length of a continuous series of charges across any set of ions for a protein and complex and the lowest error recorded for the molecular mass of the ligand or binding partner. A diverse range of hypothetical and experimental mass spectral data were used to implement and test the program, including those recorded for antibody-peptide, protein-peptide and protein-heme complexes. Spectra of increasing complexity, in terms of the number of ions input, were also successfully analysed in which the number of input m/z values far exceeds the few associated with a macromolecular complex. Thus the program will be of value in a future goal of proteomics, where mass spectrometry already plays a central role, for the direct analysis of protein and other associations within biological extracts.     

Isotopologs and isotopomers: New analytical aspects of isotopic mass spectrometry in biology

Metabolic products of biological systems in most cases are polyatomic molecular structures containing polyisotopic elements (hydrogen, carbon, nitrogen, oxygen, sulfur, chorine, etc.) that are different in genesis and biosynthetic pathways. In the molecules carrying two and more atoms of polyisotopic element in different positions (sites), the probability of detection of isotopes by sites in the pool (array) of analyzed molecules may be different, i.e., there is intramolecular isotopic heterogeneity by the specified element. Detection and quantitative estimation of isotopic heterogeneity of polyisotopic elements in molecules by the methods of isotopic mass spectrometry is a novel source of information about the processes involving the respective polyisotopic element. An isotopic equation has been proposed, the coefficients of which are normalized peak intensities of isotopically different molecular ions in the mass spectrum of the analyte. Solutions of this equation reflect the abundance ratios of isotopic atoms of polyisotopic element by its positions in molecules comprising the analyzed pool. During homogenous (equally probable) distribution of isotopic atoms of the element by all of its sites in molecules of the analyzed pool, solutions of the isotopic equation are equal to each other. In the case of non-homogenous isotope distribution of the polyisotopic element in the pool of molecules, solutions of the isotopic equation take on different values and may be presented by both real and complex numbers. Solutions of the isotopic equation reflect the peculiarities of distribution of element isotopes in a molecule and possible pathways of formation of a pool of analyzed molecules under laboratory and natural conditions.     

A conversational mass spectral search and retrieval system—II: Combined search options

An interactive, conversational mass spectral search system based on 8782 uncertified electron-impact mass spectra and accessible over ordinary telephone lines, is described. Compounds whose mass spectra are in the file can be immediately identified and very useful structural inferences can be obtained for compounds that are not represented in the file. The file may be searched in a number of ways, including by peaks and intensities, molecular weight, complete and partial molecular formula, molecular weight plus peaks/intensities, molecular formula plus peaks/intensities and molecular weight plus molecular formula. Lastly, the complete spectrum of any compound in the file can be printed out.     

Dissociation of individual isotopic peaks: predicting isotopic distributions of product ions in MSn

Traditional practice in tandem mass spectrometry is to select the mono-isotopic ion for dissociation. However, high molecular weight compounds often have weak mono-isotopic peaks, which limit that approach. Furthermore, the traditional approach does not take advantage of the very rich store of information available in the isotopic patterns from the dissociation of individual non-mono-isotopic peaks. Interpretation of these isotopic patterns requires a theory capable of predicting the patterns. However, a general theory for the prediction of these patterns has been lacking. This paper shows that the patterns can be obtained from a certain vector product, the outer product, of the full isotopic distribution of the product ion with the full isotopic distribution of the complementary product. Unlike previous approaches, the method is applicable to systems of arbitrary isotopic complexity. The patterns are potentially useful for elucidation of dissociation pathways, elemental composition, and chemical structure. The paper presents several applications of the theory.     

Proteome analysis using selective incorporation of isotopically labeled amino acids

A method is described for identifying intact proteins from genomic databases using a combination of accurate molecular mass measurements and partial amino acid content. An initial demonstration was conducted for proteins isolated from Escherichia coli (E. coli) using a multiple auxotrophic strain of K12. Proteins extracted from the organism grown in natural isotopic abundance minimal medium and also minimal medium containing isotopically labeled leucine (Leu-D10), were mixed and analyzed by capillary isoelectric focusing (CIEF) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR). The incorporation of the isotopically labeled Leu residue has no effect on the CIEF separation of the protein, therefore both versions of the protein are observed within the same FTICR spectrum. The difference in the molecular mass of the natural isotopic abundance and Leu-D10 isotopically labeled proteins is used to determine the number of Leu residues present in that particular protein. Knowledge of the molecular mass and number of Leu residues present can be used to unambiguously identify the intact protein. Preliminary results show the efficacy of this method for unambiguously identifying proteins isolated from E. coli.     

水样中低含量氯的分离与同位素质谱法测定

采用阳离子交换树脂,动态和静态交换相结合,对低氯浓度样品特别是雨水中的氯进行分离、提纯的简易方法。氯的回收率大于97％,能满足氯同位素质谱测定需要。氯同位素采用基于Cs2Cl^ 离子的正热电离质谱法测定,结果表明分离过程无明显的同位素分馏,本方法为雨水的氯同位素地球化学研究提供了可能。     

Coupled Si and O isotope measurements of meteoritic material by laser fluorination isotope ratio mass spectrometry

We present a procedure for the determination of the isotopic ratios of silicon and oxygen from the same aliquot of anhydrous silicate material. The sample is placed in a bromine pentafluoride atmosphere as it is heated with a CO₂ laser system releasing silicon tetrafluoride and oxygen gasses. The oxygen gas is then purified to remove other reaction by‐products through several liquid nitrogen traps before being captured onto a molecular sieve and transferred to an isotope ratio mass spectrometer. The silicon tetrafluoride gas is then purified using a supplementary line by repeatedly freezing to ?196°C with liquid nitrogen and then thawing with an ethanol slurry at ?110°C through a series of metal and Pyrex traps. The purified gas is then condensed into a Pyrex sample tube before it is transferred to an isotope ratio mass spectrometer for silicon isotope ratio measurements. This system has silicon yields of greater than 90% for pure quartz, olivine, and garnet standards and has a reproducibility of ±0.1‰ (2σ) for pure quartz for both oxygen and silicon isotope measurements. Meteoritic samples were also successfully analyzed to demonstrate this system's ability to measure the isotopic ratio composition of bulk powders with precision. This unique technique allows for the fluorination of planetary material without the need for wet chemistry. Though designed to analyze small aliquots of meteoritic material (1.5 to 3 mg), this approach can also be used to investigate refractory terrestrial samples where traditional fluorination is not suitable.     

ExMS: Data Analysis for HX-MS Experiments

A previous paper considered the problems that presently limit the hydrogen exchange - mass spectrometry (HX-MS) method for studying the biophysical and functional properties of proteins. Many of these problems can be overcome by obtaining and analyzing hundreds of sequentially overlapping peptide fragments that cover the protein many times over (Mayne et al. J. Am. Soc. Mass Spectrom. 2011: ). This paper describes a computer program called ExMS that furthers this advance by making it possible to efficiently process crowded mass spectra and definitively identify and characterize these many peptide fragments. ExMS automatically scans through high resolution MS data to find the individual isotopic peaks and isotopic envelopes of a list of peptides previously identified by MS/MS. It performs a number of tests to ensure correct identification in spite of peptide overlap in both chromatographic and mass spectrometric dimensions and possible multi-modal envelopes due to static or dynamic structural heterogeneity or HX EX1 behavior. The program can automatically process data from many sequential HX time points with no operator intervention at the rate of ~2 sec per peptide per HX time point using desktop computer equipment, but it also provides for rapid manual checking and decision when ambiguity exists. Additional subroutines can provide a step by step report of performance at each test along the way and parameter adjustment, deconvolute isotopic envelopes, and plot the time course of single and multi-modal H-D exchange. The program will be available on an open source basis at: