CycloBranch

A tool for mass spectrometry data analysis.

About

• designed for identification of small molecules
• open-source, cross-platform, and stand-alone
• supported types of spectra
  • conventional mass spectra (MS)
  • liquid-chromatography mass spectra (LC-MS)
  • imaging mass spectra (MSI)
  • tandem mass spectra (MS/MS)
• main features
  • MS, LC-MS, MSI
    • dereplication / database search
    • prediction of elemental compositions of unknown compounds
    • fine isotopic structure
  • LC-MS
    • quantitation of small molecules
  • MSI
    • pixel-by-pixel analysis of imaging mass spectra (imzML)
    • fusion of imzML files with optical and histology images
  • MS/MS
    • single spectra only
    • analysis based on custom databases of building blocks (amino acids)
    • linear, cyclic, branched, and branch-cyclic non-ribosomal peptides (NRPs) and siderophores
    • direct comparison of experimental spectrum with theoretical spectrum
    • database search
    • de novo sequencing
      • 19 proteinogenic amino acids (20 including isomers)
      • 287 NRP blocks (512 including isomers)

Supported file formats

• mzML, imzML
  • profile or centroid spectra
  • profile spectra require OpenMS 2.x installed
• mzXML
  • centroid spectra
  • requires OpenMS 2.x installed
• baf (Bruker)
  • profile and centroid spectra
  • requires CompassXport 3.0 installed
  • Windows only
• raw (Thermo)
  • profile or centroid spectra
  • requires OpenMS 2.x including ProteoWizard installed
  • Windows only
• raw (Waters)
  • profile and 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

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

References and More Information

• quantitation of small molecules in LC-MS data
  • Novak J. et al. Quantitation of Small Molecules from Liquid Chromatography-Mass Spectrometric Accurate Mass Datasets using CycloBranch. Eur. J. Mass Spectrom., 29(2):102-110, 2023. DOI: 10.1177/14690667231164766
• molecular formula annotations
  • Novak J. et al. CycloBranch 2: Molecular Formula Annotations Applied to imzML Data Sets in Bimodal Fusion and LC-MS Data Files. Anal. Chem., 92(10):6844–6849, 2020. DOI: 10.1021/acs.analchem.0c00170
• configuration of the tool for different use cases
  • Pluhacek T. et al. Analysis of Microbial Siderophores by Mass Spectrometry. In Sanjoy K. Bhattacharya (ed.), Metabolomics: Methods and Protocols, Methods in Molecular Biology, 1996:131-153, Springer, 2019. DOI: 10.1007/978-1-4939-9488-5_12
• isotopic fine structure
  • Novak J. et al. CycloBranch: An open tool for fine isotope structures in conventional and product ion mass spectra. J. Mass Spectrom. 53(11):1097-1103, 2018. DOI: 10.1002/jms.4285
• fusion of imzML files with histology images
  • Luptakova D. et al. Non-invasive and Invasive Diagnoses of Aspergillosis in a Rat Model by Mass Spectrometry. Sci. Rep., 7:16523, 2017. DOI: 10.1038/s41598-017-16648-z
• dereplication in LC-MS and MSI datasets; de novo sequencing of siderophores
  • Novak J. et al. Batch-processing of Imaging or Liquid-chromatography Mass Spectrometry Datasets and De Novo Sequencing of Polyketide Siderophores. BBA - Proteins Proteom., 1865(7):768-775, 2017. DOI: 10.1016/j.bbapap.2016.12.003
• de novo peptide sequencing of NRPs
  • Novak J. et al. CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra. J. Am. Soc. Mass Spectrom., 26(10):1780-1786, 2015. DOI: 10.1007/s13361-015-1211-1