MSMetaEnhancer: A Python package for mass spectra metadata annotation

TROJÁK, Matej, Helge HECHT, Martin ČECH and Elliott James PRICE. MSMetaEnhancer: A Python package for mass spectra metadata annotation. Journal of Open Source Software. 2022, vol. 7, No 79. Available from: https://dx.doi.org/10.21105/joss.04494.

Basic information

• Original name: MSMetaEnhancer: A Python package for mass spectra metadata annotation
• Authors: TROJÁK, Matej, Helge HECHT, Martin ČECH and Elliott James PRICE.
• Edition: Journal of Open Source Software, 2022.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Organization unit: Faculty of Science
• Doi: http://dx.doi.org/10.21105/joss.04494
• Tags: International impact, Reviewed

Abstract

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).

Links

• LM2018121, large research infrastructures: Name: RECETOX RI (Acronym: RECETOX RI)

Investor: Ministry of Education, Youth and Sports of the CR, RECETOX RI

• LM2018121, large research infrastructures: Name: Výzkumná infrastruktura RECETOX (Acronym: RECETOX RI)

Investor: Ministry of Education, Youth and Sports of the CR, RECETOX RI

• 857560, interní kód MU(CEP code: EF17_043/0009632): Name: CETOCOEN Excellence (Acronym: CETOCOEN Excellence)

Investor: European Union, Spreading excellence and widening participation