COCONUT

logo The “COpolymer COmposition NUmbering Tool” is a tool for estimating the composition distribution from mass spectra of synthetic copolymers. It is based on Linear Programming and is capable of automatically resolving overlapping isotopes and isobaric ions. It also features spectral pre-processing methods: baseline correction, spectral smoothing and peak picking (centroiding). COCONUT provides an easy-to-use graphical user interface.

Installation

Download the latest version here, older version are available here.

COCONUT requires Java 7 to run. Extract the zip file it to any folder (for example, your user directory or D:\ for Windows). In the extracted folder you find the subfolder “bin”:

  • Windows: double-click on “coconut.bat” to start COCONUT. You might want to create a link to this file: Click and drag the file to the desktop, keeping the ALT key pressed. You can rename this link (the one on your desktop) as you like.
  • Linux: the file “coconut” is the bash start script for COCONUT. Move to the “bin” folder and type “./coconut”.

Update Log

Version 1.4.2 (2016-03-24)

  • Updated Look & Feel
  • Abundance correction:
    • Fixed: composition matrix export
    • Improved layout

Version 1.4 (2015-10-29)

  • Abundance correction:
    • New: Interval length for TPS support point selection now automatic
    • Fixed: Applying the correction to the composition matrix was broken

Version 1.3 (2015-09-24)

  • New feature: Abundance correction

Version 1.2 (2015-06-12)

  • New: Peak heights for peak intensity estimation (optional)
  • New: Threshold for baseline detection
  • New: Resizable window
  • Fixed: Peak picking threshold not set correctly, file menus and tooltips sometimes not showing

Version 1.1 (2015-02-17)

  • Ported GUI from SWT to AWT for better perfomance, stability and decreased file size

Gurobi

COCONUT is distributed with the free LP solver lp_solve, but also supports the efficient proprietary Gurobi LP solver. If you prefer COCONUT to use an existing Gurobi installation, you need to set the path to the “lib” subfolder of your Gurobi installation:

  • Windows: add the path to the Gurobi “lib” folder to the PATH environment variable. See here for example how to set the PATH variable.
  • Linux: add the path to the Gurobi “lib” folder to the LD_LIBRARY_PATH environment variable.

Literature

Martin S. Engler, Sarah Crotty, Markus J Barthel, Christian Pietsch, Ulrich S. Schubert and Sebastian Böcker
Abundance correction for mass discrimination effects in polymer mass spectra.
Rapid Commun Mass Spectrom, 30:1233-1241, 2016.

Martin S. Engler, Sarah Crotty, Markus J Barthel, Christian Pietsch, Katrin Knop, Ulrich S. Schubert and Sebastian Böcker
COCONUT – An Efficient Tool for Estimating Copolymer Compositions from Mass Spectra.
Anal Chem, 87(10):5223-5231, 2015.