J 2022

MSMetaEnhancer: A Python package for mass spectra metadata annotation

TROJÁK, Matej, Helge HECHT, Martin ČECH and Elliott James PRICE

Basic information

Original name

MSMetaEnhancer: A Python package for mass spectra metadata annotation

Authors

Edition

Journal of Open Source Software, 2022

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Organization unit

Faculty of Science

DOI

Tags

International impact, Reviewed
Změněno: 2/11/2022 16:35, Helge Hecht, M.Sc.

Abstract

V originále

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