A mapping from internal scan numbers (
which start at one) to scan numbering in the original files.
mzXML files are required to provide a scan number, those scan numbers are not always continuous, e.g.:
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In mzXML data converted from AB Sciex raw files one might have the first scan number as 2037,
the second as 4056 and so on, they are incrementing, but not incrementing by one.
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In mzML data converted from Agilent raw files using proteowizard (msconvert.exe) each scan has a separate
"index" attribute, which starts at zero (index="0") and then and "id" which is a unique textual
representation of the scan's identity of the form id="cycleNumber=1, experimentNumber=1, scanNumber=1".
This scanNumber=1 is not always a unique number, it's some internal vendor specific string.
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There are many other example
In order to avoid all the confusion about scan numbering, MSFileToolbox uses a separate numbering and indexing
scheme. Internally all scan numbers start at one and then increment by one in retention time order.
Numbering from the original file is maintained, be it a raw vendor file (e.g. Thermo uses normal 1 based numbering,
Agilent has an ordinal number stored internally in their files, but also has those 'experiment number' and
other stuff), or an XML based file. The ID is also retained