RMassBank

RMassBank processes tandem mass spectrometry (MS/MS) data to extract, recalibrate, and format high-accuracy spectra for spectral interpretation and deposition to the MassBank database.

Key Features:

• Automated extraction and processing: Extracts tandem MS spectra from raw data files and performs formula assignment to MS/MS fragments.
• Spectrum recalibration and cleanup: Recalibrates MS/MS spectra using assigned fragment formulas and performs spectrum cleanup to reduce noise and improve mass accuracy.
• Compound information retrieval: Retrieves compound metadata from internet databases to annotate spectra.
• Export to MassBank records: Formats processed spectra as MassBank-compatible records for database deposition.

Scientific Applications:

• Pesticide analysis: Enables identification and molecular formula assignment for pesticide MS/MS spectra using reference spectra.
• Metabolomics: Improves reliability of metabolite identification by providing recalibrated high-accuracy MS/MS spectra.
• Proteomics: Enhances peptide and protein MS/MS spectral interpretation through recalibration and cleanup.
• Spectral database curation: Produces MassBank-ready records to support curation and expansion of MassBank (e.g., >944 spectra contributed).

Methodology:

Computational steps include extraction of tandem MS spectra, formula assignment to MS/MS fragments, recalibration of spectra using assigned fragments, spectrum cleanup, retrieval of compound information from internet databases, and formatting as MassBank records; the workflow was evaluated on 70 pesticide reference standards measured on an LTQ-Orbitrap XL at various collision energies, with recalibrated spectra ranking highest and the average rank for correct molecular formulas improving from 2.55 (uncalibrated) to 1.53 (recalibrated).