MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis

0543988 - MBÚ 2022 RIV GB eng J - Journal Article
Přívratský, J. - Novák, Jiří
MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis.
Journal of Cheminformatics. Roč. 13, č. 1 (2021), č. článku 51. ISSN 1758-2946. E-ISSN 1758-2946
R&D Projects: GA ČR(CZ) GA21-17044S
Institutional support: RVO:61388971
Keywords : Mass spectrometry * Building blocks * Nonribosomal petides * Polyketides * Siderophores * MassSpecBlocks * CycloBranch * Tanimoto similarity * SmilesDrawer
OECD category: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Impact factor: 8.489, year: 2021
Method of publishing: Open access
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00530-2

Nonribosomal peptides and polyketides are natural products commonly synthesized by microorganisms. They are widely used in medicine, agriculture, environmental protection, and other fields. The structures of natural products are often analyzed by high-resolution tandem mass spectrometry, which becomes more popular with its increasing availability. However, the characterization of nonribosomal peptides and polyketides from tandem mass spectra is a nontrivial task because they are composed of many uncommon building blocks in addition to proteinogenic amino acids. Moreover, many of them have cyclic and branch-cyclic structures. Here, we introduce MassSpecBlocks an opensource and web-based tool that converts the input chemical structures in SMILES format into sequences of building blocks. The structures can be searched in public databases PubChem, ChemSpider, ChEBI, NP Atlas, COCONUT, and Norine and edited in a user-friendly graphical interface. Although MassSpecBlocks can serve as a stand-alone database, our primary goal was to enable easy construction of custom sequence and building block databases, which can be used to annotate mass spectra in CycloBranch software. CycloBranch is an open-source, cross-platform, and standalone tool that we recently released for annotating spectra of linear, cyclic, branched, and branch-cyclic nonribosomal peptides and polyketide siderophores. The sequences and building blocks created in MassSpecBlocks can be easily exported into a plain text format used by CycloBranch. MassSpecBlocks is available online or can be installed entirely offline. It offers a REST API to cooperate with other tools.
Permanent Link: http://hdl.handle.net/11104/0321068