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A new scoring function for top-down spectral deconvolution

Background: Top-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isotopomer envelopes from highly charged ions, which may overlap with one another. As a result, spectral deconvolution, which converts a complex top-down mass spectrum into a monoisotopic mass list, is a key step in top-down spectral interpretation. Results: In this paper, we propose a new scoring function, L-score, for evaluating isotopomer envelopes. By combining L-score with MS-Deconv, a new software tool, MS-Deconv+, was developed for top-down spectral deconvolution. Experimental results showed that MS-Deconv+ outperformed existing software tools in top-down spectral deconvolution. Conclusions: L-score shows high discriminative ability in identification of isotopomer envelopes. Using L-score, MS-Deconv+ reports many correct monoisotopic masses missed by other software tools, which are valuable for proteoform identification and characterization.

59 BASIC BIOLOGICAL SCIENCES↗

GlycReSoft: A Software Package for Automated Recognition of Glycans from LC/MS Data

Glycosylation modifies the physicochemical properties and protein binding functions of glycoconjugates. These modifications are biosynthesized in the endoplasmic reticulum and Golgi apparatus by a series of enzymatic transformations that are under complex control. As a result, mature glycans on a given site are heterogeneous mixtures of glycoforms. This gives rise to a spectrum of adhesive properties that strongly influences interactions with binding partners and resultant biological effects. In order to understand the roles glycosylation plays in normal and disease processes, efficient structural analysis tools are necessary. In the field of glycomics, liquid chromatography/mass spectrometry (LC/MS) is used to profile the glycans present in a given sample. This technology enables comparison of glycan compositions and abundances among different biological samples, i.e. normal versus disease, normal versus mutant, etc. Manual analysis of the glycan profiling LC/MS data is extremely time-consuming and efficient software tools are needed to eliminate this bottleneck. In this work, we have developed a tool to computationally model LC/MS data to enable efficient profiling of glycans. Using LC/MS data deconvoluted by Decon2LS/DeconTools, we built a list of unique neutral masses corresponding to candidate glycan compositions summarized over their various charge states, adducts and range of elution times. Our work aims to provide confident identification of true compounds in complex data sets that are not amenable to manual interpretation. This capability is an essential part of glycomics work flows. We demonstrate this tool, GlycReSoft, using an LC/MS dataset on tissue derived heparan sulfate oligosaccharides. The software, code and a test data set are publically archived under an open source license.

Environmental Molecular Sciences Laboratory↗

Isotope Ratio Monitoring Gas Chromatography Mass Spectrometry (IRM-GCMS)

On Earth, the C-13 content of organic compounds is depleted by roughly 13 to 23 permil from atmospheric carbon dioxide. This difference is largely due to isotope effects associated with the fixation of inorganic carbon by photosynthetic organisms. If life once existed on Mars, then it is reasonable to expect to observe a similar fractionation. Although the strongly oxidizing conditions on the surface of Mars make preservation of ancient organic material unlikely, carbon-isotope evidence for the existence of life on Mars may still be preserved. Carbon depleted in C-13 could be preserved either in organic compounds within buried sediments, or in carbonate minerals produced by the oxidation of organic material. A technique is introduced for rapid and precise measurement of the C-13 contents of individual organic compounds. A gas chromatograph is coupled to an isotope-ratio mass spectrometer through a combustion interface, enabling on-line isotopic analysis of isolated compounds. The isotope ratios are determined by integration of ion currents over the course of each chromatographic peak. Software incorporates automatic peak determination, corrections for background, and deconvolution of overlapped peaks. Overall performance of the instrument was evaluated by the analysis of a mixture of high purity n-alkanes of know isotopic composition. Isotopic values measured via IRM-GCMS averaged withing 0.55 permil of their conventionally measured values.

Freeman, K. H.↗

Acquisition and processing of data for isotope-ratio-monitoring mass spectrometry

Methods are described for continuous monitoring of signals required for precise analyses of 13C, 18O, and 15N in gas streams containing varying quantities of CO2 and N2. The quantitative resolution (i.e. maximum performance in the absence of random errors) of these methods is adequate for determination of isotope ratios with an uncertainty of one part in 10(5); the precision actually obtained is often better than one part in 10(4). This report describes data-processing operations including definition of beginning and ending points of chromatographic peaks and quantitation of background levels, allowance for effects of chromatographic separation of isotopically substituted species, integration of signals related to specific masses, correction for effects of mass discrimination, recognition of drifts in mass spectrometer performance, and calculation of isotopic delta values. Characteristics of a system allowing off-line revision of parameters used in data reduction are described and an algorithm for identification of background levels in complex chromatograms is outlined. Effects of imperfect chromatographic resolution are demonstrated and discussed and an approach to deconvolution of signals from coeluting substances described.

NASA Discipline Exobiology↗

In-Situ Reaction Monitoring for Lunar Applications Utilizing a Single Quadrupole Residual Gas Analyzer

With a revived focus to create a permeant presence on the moon and in preparation for future Mars exploration, it is imperative that all re-sources are utilized to their fullest potential. In-Situ Resource Utilization (ISRU) will be critical for future mission success as it would enable independent operation of missions while minimally relying on the complex supply chain created between the Earth, moon and Mars. One of the most critical resources that have been identified for ISRU is the creation of liquid oxygen (O2) for not only breathable air, but also for rocket fuel. On the moon and potentially Mars, one of the most O2 rich resources is in the presence of regolith. Although there are numerous minerals within regolith and various processes to extract O2, this is not the scope of this paper. Since the O2 extraction method can vary, a critical standardized analytical method is needed to verify O2 (or oxygenated precursor compounds) for extraction efficiency and purity. Our group utilizes a modified consumer off-the-shelf (COTS), Residual Gas Analyzer (RGA) Single Quadrupole Mass Spectrometer (QMS). Due to the current field mission requirements, the gas analysis module will need to rely only on mass-to-charge ratios (m/z) and peak intensities to differentiate and quantitate targeted gas-phase reactants or products, i.e. carbon monoxide (CO), carbon dioxide (CO2), methane (CH4) and hydrogen (H2). However, due to solar wind implanted volatiles and various other compounds present in lunar regolith, such as nitrogen (N2), helium (He), and deuterium (D2), deconvolution and quantification of isobaric compounds becomes quite difficult. Specifically, the presence of N2 makes quantification of CO, an oxygenated precursor, difficult due to both compounds having a peak at m/z 28. Approaches to differentiate isobaric components: Initially, the solution to overcome isobaric overlap was to use isotopic ratios, particularly be-tween carbon-13 and nitrogen-15. Although limited literature discuss isotopic composition and attempt to quantify the ratios, variation is particularly high and limited to a few lunar regolith samples. The following were identified as potential approaches to quantify isobaric species, N2 and CO, using our RGA. Threshold Ionization. CO and N2 both have peaks at m/z 28, but only N2 is capable of producing a peak at m/z 7. While a N2 peak at m/z 7 is generally rare, instrument parameters can be optimized in order to maximize the peak intensity. Typically a standard ionization energy of 70 eV is used to monitor a batch process and would produce reliable results for a majority of the reactants or products that we are interested in quantifying. However, to analyze the rare molecular fragment of N2 (N2+ at m/z 7), a different ionization energy may be beneficial. Threshold Ionization Mass Spectrometry (TIMS) will be explored to optimize the N2+ peak at m/z 7 by varying parameters such as ionization energy and pressure. Therefore, a quantitative value at m/z 7 will be used to determine the product gas concentration of N2, which will be subtracted from the total concentration determined at m/z 28 enabling us to approximate the amount of CO. Secondary Detector (infrared gas detector, IR). Another approach to quantitate and differentiate be-tween isobaric components is to leverage alternative modes of detection. Unlike mass spectrometry, which generally uses a separation step prior to analysis (i.e. gas chromatography), IR produces energy that is specifically absorbed depending on the bond and configuration of the molecule. This technique could be leveraged since it is generally only active on non-symmetric molecules, i.e. CO. Utilizing concentrations of CO determined from another detector could help correct concentrations of CO obtained from the QMS. However, the inclusion of another detector adds additional mission requirements, such as power, software changes and avionics updates that add additional cost and schedule requirements.

mass spectrometry↗