Your browser doesn't support javascript.
loading
Protocol for community-created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure.
Vargas, Fernando; Weldon, Kelly C; Sikora, Nicole; Wang, Mingxun; Zhang, Zheng; Gentry, Emily C; Panitchpakdi, Morgan W; Caraballo-Rodríguez, Andrés Mauricio; Dorrestein, Pieter C; Jarmusch, Alan K.
Afiliación
  • Vargas F; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences and Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, 92093, USA.
  • Weldon KC; Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA.
  • Sikora N; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences and Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, 92093, USA.
  • Wang M; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92093, USA.
  • Zhang Z; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences and Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, 92093, USA.
  • Gentry EC; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences and Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, 92093, USA.
  • Panitchpakdi MW; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences and Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, 92093, USA.
  • Caraballo-Rodríguez AM; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences and Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, 92093, USA.
  • Dorrestein PC; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences and Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, 92093, USA.
  • Jarmusch AK; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences and Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, 92093, USA.
Rapid Commun Mass Spectrom ; 34(10): e8725, 2020 May 30.
Article en En | MEDLINE | ID: mdl-31930757
ABSTRACT
RATIONALE A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networking (GNPS). The MSMS-Chooser workflow is an open-source protocol for the creation of MS/MS reference spectra directly in the GNPS infrastructure.

METHODS:

An MSMS-Chooser Sample Template is provided and completed manually. The MSMS-Chooser Submission File and Sequence Table for data acquisition were programmatically generated. Standards from the Mass Spectrometry Metabolite Library (MSMLS) suspended in a methanol-water (11) solution were analyzed. Flow injection on an LC/MS/MS system was used to generate negative and positive mode data using data-dependent acquisition. The MS/MS spectra and Submission File were uploaded to MSMS-Chooser workflow in GNPS for automatic selection of MS/MS spectra.

RESULTS:

Data acquisition and processing required ~2 h and ~2 min, respectively, per 96-well plate using MSMS-Chooser. Analysis of the MSMLS, over 600 small molecules, using MSMS-Chooser added 889 spectra (including multiple adducts) to the public library in GNPS. Manual validation of one plate indicated accurate selection of MS/MS scans (true positive rate of 0.96 and a true negative rate of 0.99). The MSMS-Chooser output includes a table formatted for inclusion in the GNPS library as well as the ability to directly launch searches via MASST.

CONCLUSIONS:

MSMS-Chooser enables rapid data acquisition, data analysis (selection of MS/MS spectra), and a formatted table for inspection and upload to GNPS. Open file-format data (.mzML or.mzXML) from most mass spectrometry platforms containing MS/MS spectra can be processed using MSMS-Chooser. MSMS-Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Idioma: En Revista: Rapid Commun Mass Spectrom Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Idioma: En Revista: Rapid Commun Mass Spectrom Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos