Table I. Example of a controlled vocabulary (cv) term and its implementation as a quality parameter in qcML XML. Each cv term has an id, a name and a definition. Additionally it may have relational references to other cv terms if it is hierarchically embedded, e.g. “total number of PSM” has the relation ‘a part of’ to the term “MS identification result details.” (a) An example term in the controlled vocabulary describing the number of assigned peptide to spectrum matches for a certain run. It is defined as both a “spectrum identification detail” and a “MS identification detail” through “is a” relationships. (b) An example use of the cv term from (a) in a quality parameter in a qcML file. Each quality parameter can be assigned a cv term that defines and puts into context its associated data. These associated data can for instance consist of a value attribute, but it can also take the form of an attachment containing a plot or tabular data.

	[Term]
a)	id: QC:0000029
	name: total number of PSM
	def: “This number indicates the number of spectra that were given peptide annotations.” [PXS:QC]
	is_a: MS:1001405 ! spectrum identification result details
	is_a: QC:0000025 ! MS identification result details
b)	<qualityParameter name = “total number of PSM” ID = “20100219_SvNa_SA_Ecoli_PP_psms” cvRef = “QC” accession = “QC:0000029” value = “12370”/>