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. Author manuscript; available in PMC: 2021 May 23.
Published in final edited form as: Anal Chem. 2020 Mar 13;92(7):4829–4837. doi: 10.1021/acs.analchem.9b04181

Table 1.

Pseudocode for COVINA

Algorithm COVINA
1: procedure COVINA(input parameters: mzXML file(s), m/z; optional parameters: scan.number,
2: peak.width, mass.tolerance, intensity.threshold, correlation.threshold)
3:  Use the first mzXML file to do
4:   XIC.Base ← XIC of m/z within mass.tolerance
5:   if scan.number is not specified then
6:    scan.number ← scan with highest signal in XIC.Base
7:   end if
8:   scan.range ← scan.number ± peak.width
9:   mz.table ← all m/z values in the scan.number-th scan that are above
10:   intensity.threshold
11:   Base.Chromatogram ← XIC.Base within scan.range
12:   for each value in the mz.table
13:    Query.Chromatogram ← corresponding XIC within mass.tolerance and
14:    scan.range
15:    if correlation between Base.Chromatogram and Query.Chromatogram >
16:    correlation.threshold then
17:     add this m/z value to the covariant.ion.list
18:    end if
19:   end for
20:  end do
21:  In each mzXML file do
22:   covariant.ion.intensities ← Integrated peak area for each value in the
23:   covariant.ion.list within scan.range
24:  end do
25:  return covariant.ion.list, covariant.ion.intensities
26: end procedure