RMassBank

Version: 2.6.0

Website

https://bioconductor.org/packages/release/bioc/html/RMassBank.html

Description

This bioconductor package is designed to allow for easy upload of data onto MassBank. Initially MS/MS spectra are extracted from raw data files. Then using a .csv containing the compound information, RMassBank attempts to fit molecular formulas for every peak. This generates an array of metabolites, which is then aggregated into a list. A calibration curve is then calculated from this list and all spectra are then recalibrated. The recalibrated spectra are then reanalysed and aggregated and know electronic noise is removed. Peaks without a compound identification are then reanalysed, allowing for N2O as an additional element. After this peaks that are only found in a single spectra are removed. After this annotated spectra can be uploaded onto MassBank. Additionally XCMS can be used to extract the MS2 spectra (optionally the MS1) and then for peak picking. CAMERA can then be used to process the spectra.

Functionality

• Other Tools

Instrument Data Type

Approaches

• Targeted

Computer Skills

Advanced

Software Type

R Package

Interface

Command line Interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

Rcpp

Input Formats - Open

mzML, mzData

Input Formats - Proprietary

N/A

Published

2013

Last Updated

2018

License

Artistic-2.0

Paper

http://www.ncbi.nlm.nih.gov/pubmed/23303751

PMID

23303751