Combining and filtering data

Average

The average returns the average of the mass spectra directly from a Vector{MSscan} after Importing data data or directly from the filename.

julia> average("filename")
MSj.MSscans([1, 2, 3 ....

julia> scans = load("filename")
51-element Array{MSj.MSscan,1}:
 MSj.MSscan(1, 0.1384, 5.08195e6, [140.083, 140.167, 140.25, 140.333, 140.417, 140.5, 140.583, 140.667, 140.75, 140.833  …  1999.25, 1999.33, 1999.42, ....)
...

julia> average(scans)
MSj.MSscans([1, 2, 3 ....

Operating on files takes more time than working on Vector{MSscan} but may be useful to reduce the memory load.

Without any argument the average function averages the entire content of the data and the chromatogram function operates on also on the entire data.

The average and chromatogram functions may takes arguments to select specific fields of interest within the data and operate on them. The argument belongs to the MSj.FilterType. Their properties are listed below:

FilterType	Description	Arguments	Specificity
MSj.Scan	Scan num	Int, Vector{Int}	average, chromatogram
MSj.Level	MS level	Int, Vector{Int}	average, chromatogram
MSj.Polarity	Polarity	String, Vector{String}	average, chromatogram
MSj.Activation_Method	Activation method	String, Vector{String}	average, chromatogram
MSj.Activation_Energy	Activation energy	Real, Vector{Real}	average, chromatogram
MSj.Precursor	Precursor m/z	Real, Vector{Real}	average, chromatogram
MSj.RT	Retention time	Real, Vector{Real}, Vector{Vector{Real}}	average
MSj.IC	Ion current	Vector{Real}	average

Note

The filtering function goes first through all the arguments and setup an array of scan num that matches the conditions. Then it uses this array to calculate the average mass spectrum. So this procedure needs two passes through the data, which is not very efficient. This is a point to make better in the future.

When the argument is restricted to a single value, such as MSj.Scan(1), filtering is performed on that specific value. If the argument is a vector then filtering involves all the values within the range. Filtering on MSj.scan([1,10]) means that the result will be obtained for scans ranging from 1 to 10. The same applies for all FilterType with the exception of MSj.∆MZ, for which the first value of the vector represents the mz and the second value represents the spread ∆mz, so that filtering is operated for all mz value in the range [m/z - ∆mz , m/z + ∆mz]. The MSj.RT type may take a vector or vectors as argument, such `MSj.RT([ [1,10], [20, 30] ]). In that case, mass spectra will be averaged in [1,10] and [20,30] range.

These filters may be combined together if necessary. For example, the input below returns the average mass spectrum for:

the MS2 scans (level = 2),
precursor m/z 1255.5,
upon CID activation conditions
with an activation energy of 18
and for retention times in the 1 to 60 s range.

average("filename", MSj.Precursor(1255.5),
                    MSj.Activation_Energy(18),
                    MSj.Activation_Method("CID"),
                    MSj.Level(2),
                    MSj.RT( [1, 60] ),
                    )

Several filter types may also be combined for chromatograms:

chromatogram("filename", MSj.Precursor(1255.5),
                         MSj.Activation_Energy(18),
                         MSj.Activation_Method("CID"),
                         MSj.Level(2),
                         )

If the condition does not match any existing data, then an ErrorException is returned with the "No matching spectra." message.

The chromatogram function has some methods using MSj.MethodType arguments:

MethodType	Description	Arguments	Remark
MSj.TIC	Total ion current	None	Default
MSj.BasePeak	Base peak intensity	None
MSj.MZ	m/z range	Vector{Real}
MSj.∆MZ	m/z ± ∆mz	Vector{Real}

These types control the way chromatograms are calculated: either using the total ionic current, the base peak intensity or using a m/z range. The method argument of the MSj.chromatogramfunction is set to MSj.TIC() by default. This setting may be overruled by setting the method to desired value:

chromatogram("filename", method = MSj.BasePeak())
chromatogram("filename", method = MSj.MZ( [257, 259] ) ) 
chromatogram("filename", method = MSj.∆MZ( [258, 1] ) )

Extracting subsets

The extract returns a Vector of MSscanfrom either a file of from a Vector{MSscan} following a load command, which corresponds to the filter conditions. See the Filtering part above.

sub_set = extract("filename")                       # extracting without any conditions returns a vector identical to the output 
sub_set = extract("filename", MSj.Level(2) )        # extract MS/MS spectra
scans = load("test.mzxml")                          # load mass spectra
sub_set = extract(scans)                            # extract a sub_set without conditions returns the original data