An open-source, cross-platform and stand-alone tool for mass spectrometry data analysis.
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README.md

CycloBranch

An open-source, cross-platform and stand-alone tool for mass spectrometry data analysis.

Main features

  • designed for identification of small molecules
  • de novo sequencing
    • non-ribosomal peptides (NRPs) [1]
    • siderophores (including metals) [2]
    • supports linear, cyclic, branched, and branch-cyclic structures
    • based on custom databases of building blocks
      • 19 proteinogenic amino acids (20 including isomers)
      • 287 NRP blocks (512 including isomers)
  • dereplication / database search
    • conventional mass spectra (MS)
    • liquid-chromatography mass spectra (LC-MS) [2]
      • batch-processing
    • imaging mass spectra (MSI)
      • pixel-by-pixel analysis of imaging mass spectra (imzML) [2]
      • fusion of imzML files with optical and histology images [3]
    • tandem mass spectra (MS/MS)
      • single spectra analysis
      • supports also a direct comparison of an experimental spectrum with a theoretical one

Supported file formats

  • mzML, imzML
    • profile or centroid spectra
    • profile spectra require OpenMS 2.x installed
  • mzXML
  • baf (Bruker)
  • raw (Thermo)
    • profile or centroid spectra
    • requires OpenMS 2.x including ProteoWizard installed
    • Windows only
  • raw (Waters)
    • centroid spectra
    • Windows only
  • mgf (Mascot Generic File format)
    • centroid spectra
  • txt
    • centroid spectra
    • tab separated mass-to-charge ratio and intensity on each line; multiple peaklists separated by an empty line

Homepage

http://ms.biomed.cas.cz/cyclobranch/

Publications