RMassBank scripts

Michele Stravs, March 2023

Purpose

This is a suite of scripts used to run RMassBank for MassBank acquisitions at Uchem. In addition to the standard RMassBank functionality, it provides:

• a quick EIC + MS2 stick quality control
• peakshape filtering: extracting the EIC for every fragment to ensure it matches with the precursor EIC
• a review tool
• a script to handle multiplexed acquisitions, i.e. multiple spectra in a file.

Non-goals

This is not intended to work for:

• MS2 spectra from "regular" measurements, like DDA from normal samples etc. We need specific targeted MS2 measurements to get many MS2 scans per compound, so we can construct fragment EICs.
• TOF spectra. Honestly TOF data is just annoying and we use this for Orbitrap data.

Feature gaps

This does not adequately handle non-default data such as [M]+, [M+Na]+ etc.