Table II. List of the basic quality parameters that the QCCalculator program uses to create a basic qcML. Parameters that are included for completeness but not actually metrics (like filename) are written in italics. For an overview on the exsisting qcML metrics see supplementary material.

Quality parameter/metric	Description	CV accession
MzML file	Name of the MS run file	MS:1000577
Instrument model	Vendor and model name	MS:1000031
Completion time	Date and time of MS run	MS:1000747
MS1 spectra count	Number of MS1 spectra	QC:0000006
MS2 spectra count	Number of MS2 spectra	QC:0000007
Chromatogram count	Number of chromatograms	QC:0000008
Total number of missed cleavages	Number of missed cleavages	QC:0000037
Total number of identified proteins	Number of identified proteins	QC:0000032
Total number of uniquely identified proteins	Number of unique proteins	QC:0000033
Total number of PSMs	Number of PSMs	QC:0000029
Total number of identified peptides	Number of identified proteins	QC:0000030
Total number of uniquely identified peptides	Number of identified peptides	QC:0000031
Mean delta ppm	Mean of ppm error	QC:0000040
Median delta ppm	Median of ppm error	QC:0000041
Id ratio	Ratio of recorded vs. identified MS2 plotted on M/Z over RT	QC:0000035
Number of features	Number of detected features	QC:0000046
MZ aquisition ranges	Value range limitations used for aquisition	QC:0000009
RT aquisition ranges	Value range limitations used for aquisition	QC:0000012
Id settings	The settings of the search engine used engine name and further parameters.	QC:0000026