Envelope: interactive software for modeling and fitting complex isotope distributions

<p>Abstract</p> <p>Background</p> <p>An important aspect of proteomic mass spectrometry involves quantifying and interpreting the isotope distributions arising from mixtures of macromolecules with different isotope labeling patterns. These patterns can be quite complex, in particular with <it>in vivo </it>metabolic labeling experiments producing fractional atomic labeling or fractional residue labeling of peptides or other macromolecules. In general, it can be difficult to distinguish the contributions of species with different labeling patterns to an experimental spectrum and difficult to calculate a theoretical isotope distribution to fit such data. There is a need for interactive and user-friendly software that can calculate and fit the entire isotope distribution of a complex mixture while comparing these calculations with experimental data and extracting the contributions from the differently labeled species.</p> <p>Results</p> <p>Envelope has been developed to be user-friendly while still being as flexible and powerful as possible. Envelope can simultaneously calculate the isotope distributions for any number of different labeling patterns for a given peptide or oligonucleotide, while automatically summing these into a single overall isotope distribution. Envelope can handle fractional or complete atom or residue-based labeling, and the contribution from each different user-defined labeling pattern is clearly illustrated in the interactive display and is individually adjustable. At present, Envelope supports labeling with ²H, ¹³C, and ¹⁵N, and supports adjustments for baseline correction, an instrument accuracy offset in the m/z domain, and peak width. Furthermore, Envelope can display experimental data superimposed on calculated isotope distributions, and calculate a least-squares goodness of fit between the two. All of this information is displayed on the screen in a single graphical user interface. Envelope supports high-quality output of experimental and calculated distributions in PNG or PDF format. Beyond simply comparing calculated distributions to experimental data, Envelope is useful for planning or designing metabolic labeling experiments, by visualizing hypothetical isotope distributions in order to evaluate the feasibility of a labeling strategy. Envelope is also useful as a teaching tool, with its real-time display capabilities providing a straightforward way to illustrate the key variable factors that contribute to an observed isotope distribution.</p> <p>Conclusion</p> <p>Envelope is a powerful tool for the interactive calculation and visualization of complex isotope distributions for comparison to experimental data. It is available under the GNU General Public License from <url>http://williamson.scripps.edu/envelope/</url>.</p

Total calcium absorption is similar from infant formulas with and without prebiotics and exceeds that in human milk-fed infants

<p>Abstract</p> <p>Background</p> <p>1) To evaluate calcium absorption in infants fed a formula containing prebiotics (PF) and one without prebiotics (CF). 2) To compare calcium absorption from these formulas with a group of human milk-fed (HM) infants.</p> <p>Methods</p> <p>A dual tracer stable isotope method was used to assess calcium absorption in infants exclusively fed CF (n = 30), PF (n = 25) or HM (n = 19). Analysis of variance was used to analyze calcium intake, fractional calcium absorption, and the amount of calcium absorbed.</p> <p>Results</p> <p>Calcium intake (Mean ± SEM) for PF was 534 ± 17 mg/d and 557 ± 16 mg/d for CF (p = 0.33). Fractional calcium absorption was 56.8 ± 2.6 % for PF and 59.2 ± 2.3 % for CF (p = 0.49). Total calcium absorbed for PF was 300 ± 14 mg/d and 328 ± 13 mg/d for CF (p = 0.16). For HM infants calcium intake was 246 ± 20 mg/d, fractional calcium absorption was 76.0 ± 2.9 % and total calcium absorbed was 187 ± 16 mg/d (p <0.001, compared to either PF or CF).</p> <p>Conclusions</p> <p>Despite lower fractional calcium absorption of CF and PF compared to HM, higher calcium content in both led to higher total calcium absorption compared to HM infants. No significant effect of prebiotics was observed on calcium absorption or other markers of bone mineral metabolism.</p