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Metric for QC-Tool (own class)
-should count the number of missed cleavages

Input:
featureMap (featureXML)

Output:
new metavalue per PeptideHit
vector of vector with number of missed cleavages per peptideidentification
or vector with total number of missed cleavages per experiment

QC class interface:
Input: FeatureMap
set new metavalue in peptide Hit
Output: vector<missed cleavages, max allowed missed cleavages>?

QC class functions:
-requires
-compute
-getResults

corner cases:
-empty data
-missing information like: no enzyme name

• new metric for tool "QualityControl"

input:
FeatureMap (vector of Features) and contaminants Database (vector of FastaEntry)

output:
ratio of # contaminants (# contaminants/ # all peptides) and
ratio of sum of contaminants (sum of contaminants/sum of peptides)

corner case:
no contaminants -> warning

Metric for new QC-Tool (own class):
-should compute the MS2 Identification Rate

input data:
-A) idXML after FDR: number of PeptideIDs with at least one PeptideHit with match to TargetDB
-B) raw mzML: number of MS spectra where mslevel== 2

output data: (per file pair)
-filename; A; B; ratio A/B

Class Interface:
-input: A) vector, B) MSExperiment or subset (like MSSpectrum)
-output: Struct with four members ( filename; A; B; ratio)

corner cases:
-FDR should be done
-should be more spectra than peptideIdentifications
-data should not be empty

Metric for QC-Tool (own class)
-should evaluate the Fragment Mass Error for each PepID

Input:
-MSExperiment (mzML)
-FeatureMap (featureXML)?

Output:
-new metavalue per PepID in ppm
-vector

QC class interface:
-Input: MSExperiment
-theoretical spectrum (MSExperiment) for comparison
-set new metavalue in peptideHit
-Output: vector

QC class functions
-compute
-getResults
-requires

corner cases:
-empty data