diff --git a/README.md b/README.md index b719b63..0351396 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,29 @@ # CycloBranch -An open-source and cross-platform tool for mass spectrometry data analysis. +An open-source, cross-platform and stand-alone tool for mass spectrometry data analysis. ## Main features - * *De novo* sequencing of nonribosomal peptides. - * Compound search (dereplication) in: + * 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) + * liquid-chromatography mass spectra (LC-MS) [2] + * batch-processing * imaging mass spectra (MSI) - * Image fusion - + * 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 @@ -38,6 +52,6 @@ An open-source and cross-platform tool for mass spectrometry data analysis. http://ms.biomed.cas.cz/cyclobranch/ ## Publications - * *J. Am. Soc. Mass Spectrom.* (2015), 26(10):1780-1786. DOI: [10.1007/s13361-015-1211-1](http://dx.doi.org/10.1007/s13361-015-1211-1) - * *BBA - Proteins Proteom.* (2017), 1865(7):768-775. DOI: [10.1016/j.bbapap.2016.12.003](http://dx.doi.org/10.1016/j.bbapap.2016.12.003) - * *Sci. Rep.* (2017), 7:16523. DOI: [10.1038/s41598-017-16648-z](http://dx.doi.org/10.1038/s41598-017-16648-z) + * [1] *J. Am. Soc. Mass Spectrom.* (2015), 26(10):1780-1786. DOI: [10.1007/s13361-015-1211-1](http://dx.doi.org/10.1007/s13361-015-1211-1) + * [2] *BBA - Proteins Proteom.* (2017), 1865(7):768-775. DOI: [10.1016/j.bbapap.2016.12.003](http://dx.doi.org/10.1016/j.bbapap.2016.12.003) + * [3] *Sci. Rep.* (2017), 7:16523. DOI: [10.1038/s41598-017-16648-z](http://dx.doi.org/10.1038/s41598-017-16648-z)