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

Jan Přívratský,Jiří Novák

doi:10.1186/s13321-021-00530-2

Abstract

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 open-source 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 stand-alone 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.

Highlights

Nonribosomal peptides (NRPs) are natural products commonly produced by bacteria and fungi [1]
We focus on high-resolution tandem mass spectra of NRPs and siderophores with NRP/PK structures [6, 7]
We present MassSpecBlocks [34]—an opensource and web-based tool for easy construction of NRP/PK sequence (Fig. 2) and building block (Additional file 1: Fig. S1) databases, which can be used in CycloBranch software to compare the experimental tandem mass spectra of NRPs/PKs with theoretical spectra [6, 7]

Summary

Introduction

Nonribosomal peptides (NRPs) are natural products commonly produced by bacteria and fungi [1]. We present MassSpecBlocks [34]—an opensource and web-based tool for easy construction of NRP/PK sequence (Fig. 2) and building block (Additional file 1: Fig. S1) databases, which can be used in CycloBranch software to compare the experimental tandem mass spectra of NRPs/PKs with theoretical spectra [6, 7]. Users can search compounds in public databases using one of the following properties—a name, a molecular formula, a monoisotopic mass, a database identifier, and a molecular structure in SMILES format (if the corresponding API supports the respective feature). NRP/PK sequences have the following properties: a compound name, a structure type (linear, cyclic, branched, branch-cyclic, linear-polyketide, cyclic-polyketide, and other), a sequence of building blocks, a formula and monoisotopic mass of the neutral molecule, lists of families and organisms, terminal modifications, and a reference into a public database. As in the case of NRPs, we determined if the polyketide was linear or cyclic

Results

Conclusion

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