**PYTHEAS**

Pytheas is a package developed for the automated analysis of tandem MS data for RNA, with a focus on flexible handling of isotope labeling and RNA modifications.

Features

- Support for more than 50 simultaneous RNA chemical modifications, as well as user-specified isotope labeling schemes
- False discovery rate assessment through a target/decoy approach
- Statistical analysis through automated descriptive plots, highlighting the most important features of the dataset and user customizable
- Numerous options to improve data analysis based on different chromatographic/MS experimental setups

Please cite the following paper when referencing Pytheas:

D’Ascenzo L., Popova M. A., Abernathy S., Sheng K., Limbach P. A., Williamson J. R., **Pytheas: a software package for the automated analysis of RNA sequences and modifications via tandem mass spectrometry,** Nat. Comm., in press (April 2022) doi: 10.1038/s41467-022-30057-5

GitHub repository: https://github.com/ldascenzo/pytheas

**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%^{15}N labeled + 40%^{15}N labeled + 60%^{15}N labeled + 80%^{15}N labeled) - Supports labeling based on elements (
*e.g.*^{15}N labeling of the entire peptide) or residues (*e.g.*^{13}C 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 Convolution**. *Analytical Chemistry*, **80**, 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; unlabeled, 50% ^{15}N labeled and fully ^{15}N Labeled.

Features

- Supports simultaneous calculation of isotope distributions for mixtures containing an arbitrary number of species (
*e.g.*Unlabeled + 20%^{15}N labeled + 40%^{15}N labeled + 60%^{15}N labeled + 80%^{15}N labeled) - Supports labeling based on elements (
*e.g.*^{15}N labeling of the entire peptide) or residues (*e.g.*^{13}C 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 Bioinformatics*, **9**: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 Convolution**.*Analytical Chemistry*,**80**, pp. 4906-4917 (2008).

- Edit Sperling, Anne E. Bunner, Michael T. Sykes and James R. Williamson.
- 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.