I have direct infusion positive mode MS1 data from the QExactive, multiple replicates gathered across several batches across many months. Most of the software / R packages I have seen like XCMS, MS-DIAL, etc. seem to deal primarily with LC-MS data. What would a data-processing pipeline for this data look like and is there already an established workflow in R for DIMS data? I would like to go from ThermoRAW files to a background corrected, deisotoped, adduct-collapsed matrix of samples vs features.
