MSMetaEnhancer: A Python package for mass spectra metadata annotation
| Authors | |
|---|---|
| Year of publication | 2022 |
| Type | Article in Periodical |
| Magazine / Source | Journal of Open Source Software |
| MU Faculty or unit | |
| Citation | |
| Web | https://doi.org/10.21105/joss.04494 |
| Doi | http://dx.doi.org/10.21105/joss.04494 |
| Description | MSMetaEnhancer is a Python software package for the metadata enrichment of records in mass spectral library files commonly used as reference for chemical identification via mass spectrometry. Each record contains spectral information, i.e., peak mass to charge ratio (m/z) and intensities, alongside chemical & structural metadata, e.g., identifiers. The package uses matchms (Huber et al., 2020) for data IO and supports the open, text-based .msp format. It annotates given mass spectra records in the library file by adding missing metadata such as SMILES, InChI, and CAS numbers to the individual entries. The package retrieves the respective information by querying several external databases using existing metadata (e.g., SMILES or CAS number), converting different representations or database identifiers. Multiple databases and services are included, currently supporting the chemical identifier resolver (CIR), chemical translation service (CTS) (Wohlgemuth et al., 2010), ChemIDplus (Tomasulo, 2002), the Integrated Database for Small Molecules (IDSM) (Galgonek & Vondrášek, 2021), PubChem (Kim et al., 2021), and BridgeDb (van Iersel et al., 2010). Additionally, instead of querying external databases, computing the identifiers is also supported (e.g. molecular weight from SMILES). |
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