Skip to content

Latest commit

 

History

History
74 lines (69 loc) · 4.34 KB

README.md

File metadata and controls

74 lines (69 loc) · 4.34 KB
Raw

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
  • baf (Bruker)
  • 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