Input peak file [mzML]Path to the Rscript executable (default: 'Rscript'). [,opt.]Identifications or features whose peptide ID's serve as calibration masses. [idXML,featureXML,opt.]Input file containing reference m/z values (text file with each line as: m/z ms-level charge) which occur in all scans. [csv,opt.]Output file [mzML]Optional output file containing peaks from 'in' which were matched to reference m/z values. Useful to see which peaks were used for calibration. [mzML,Inactive]Optional output file containing lock masses which were NOT found or accepted(!) in data from 'in'. Useful to see which peaks were used for calibration. [mzML,Inactive]Table of model parameters for each spectrum. [csv,Inactive]Plot image of model parameters for each spectrum. [png,Inactive]Table of pre- and post calibration errors. [csv,Inactive]Plot image of pre- and post calibration errors. [png,Inactive]The text sent to standard out during the execution of InternalCalibration.The text sent to standard error during the execution of InternalCalibration. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)