SOFTWARE

ISODIST

Isodist is a program which uses Fourier transform convolution to calculate the isotope distribution of peptide and nucleic acid species with complex labeling patterns, and least squares to fit the calculated distribution to a data set.

Features

  • Supports simultaneous calculation of isotope distributions for mixtures containing an arbitrary number of species (e.g. Unlabeled + 20% 15N labeled + 40% 15N labeled + 60% 15N labeled + 80% 15N labeled)
  • Supports labeling based on elements (e.g. 15N labeling of the entire peptide) or residues (e.g. 13C Leucine labeling)
  • Incorporates a least squares fitting routine to determine both the extent of labeling for the defined labeling pattern for a given species, and the relative amounts of different species in a mixture
  • Automatically corrects for peak width, a machine-based mass offset and non-zero baseline
  • Can be run in batch mode to quickly fit hundreds or thousands of different aquired spectra

Please cite the following paper when referencing isodist:

Edit Sperling, Anne E. Bunner, Michael T. Sykes and James R. Williamson. Quantitative Analysis of Isotope Distributions in Proteomic Mass Spectrometry Using Least-Squares Fourier Transform ConvolutionAnalytical Chemistry80, pp. 4906-4917 (2008).

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ENVELOPE

Envelope is an interactive program which uses Fourier transform convolution to calculate the isotope distribution of peptide and nucleic acid species with complex labeling patterns. It is capable of simultaneously calculating the isotope distribution for an arbitrary number of different labeling patterns for a single molecule, and can display experimental data alongside the calculated spectra.

Pictured: An Envelope Screenshot. The mass spectrum of ribosomal protein S2 residues 45-58 (+3) is displayed, including calculated isotope distributions for three differently labeled species; unlabeled50% 15N labeled and fully 15N Labeled.

Features

  • Supports simultaneous calculation of isotope distributions for mixtures containing an arbitrary number of species (e.g. Unlabeled + 20% 15N labeled + 40% 15N labeled + 60% 15N labeled + 80% 15N labeled)
  • Supports labeling based on elements (e.g. 15N labeling of the entire peptide) or residues (e.g. 13C Leucine labeling)
  • Load data files and calculate the goodness of fit of experimental and calculated spectra.
  • Adjust for baseline, peak width and offset in the M/Z domain
  • A “Live” mode supports real-time feedback of adjustments to labeling patterns (dependent on processor speed and the complexity of the system)
  • Publication quality PDF and PNG export. Click for samples: PDF PNG
  • Export calculated spectra as (m/z, intensity) pairs

Please cite the following paper when referencing Envelope:

Michael T. Sykes and James R. Williamson.  Envelope: interactive software for modeling and fitting complex isotope distributions.  BMC Bioinformatics9:446, doi: 10.1186/1471-2105-9-446 (2008)

More Information

  • Envelope uses the Fourier Transform Convolution method to calculate isotope distributions. More information on FTC can be found in the following reference:
    • Edit Sperling, Anne E. Bunner, Michael T. Sykes and James R. Williamson. Quantitative Analysis of Isotope Distributions in Proteomic Mass Spectrometry Using Least-Squares Fourier Transform ConvolutionAnalytical Chemistry80, pp. 4906-4917 (2008).
  • For batch processing and automated fitting of data, consider using isodist, based on the same FTC method.
  • Envelope relies on the FFTW library for Fourier Transforms.
  • Envelope is released under the GNU General Public License.

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