overlapProblemBuilder

overlapProblemBuilder

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Build an overlap problem struct

Syntax

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overlapProblem = overlapProblemBuilder(varargin)

Takes a name-parameter list and build an overlapProblem struct which can be used in other problem-solving functions

Inputs

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Inputs are given by the name-value pairs defined below.
'rangeFile' Rrng file or range cell array (see rangeReaderCell)
'ions' List of ions in the ion-cell array format
'minAbundance' Minimum peak abundance in %
'rangeStart' Pre-peak range scale which is multiplied by sqrt(peak Da)
'rangeEnd' Post-peak range scale which is multiplied by sqrt(peak Da)
'adIons' Additional ions to add (in cell-array format, see notes*)

An overlap problem can be defined in two ways:
(1) Using the ranges defined in a range file
(2) Using a finite width of m/z peaks

Example (1)a: Using ranges with the ions as defined in the range file
Use a range file "myRanges.rrng" with the default minimum abundance
limit. The ions are built using the ranges given.
overlapProblem = overlapProblemBuilder('rangeFile','myRanges.rrng')

Example (1)b: Using ranges with different ions specified
Use a range file "myRanges.rrng" with the default minimum abundance
limit. The ions as defined by the list in "myIonsList"
myIonsList = {{2,'Ti','O'},{1,'O',2}};
overlapProblem = ...
overlapProblemBuilder('rangeFile','myRanges.rrng','ions',myIonsList)

Example (2): Use a list of ions and peak widths
The ions are defined by the list in "myIonsList". The range widths are
given by rs and rf.
myIonsList = {{2,'Ti','O'},{1,'O',2}};
r1 = 0.01;
r2 = 0.02;
overlapProblem = ...
overlapProblemBuilder('ions',myIonsList,...
'rangeStart',r1,'rangeEnd',r2)

Outputs

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overlapProblem is a struct (structure) containing the following named
values. They can be accessed by overlapProblem."name" where "name" is:
overlapIons = each cell contains a cell array of ions
(cell) which are one overlap group
overlapTable = A range centre-by-ions abundance table for
each overlap group
ionIndex = Which index in the ions list each ion in each
overlap group is
overlapIonNames = Which index in the ions list each ion in
each overlap group is
ions = Total list of all ions
ionNames = Total list of all ion names with chrage states,
e.g. Fe2O++
ranges = m/z range windows and an elemental table
rangeElements = The element names which are in the ranges table

## Notes

• Named ions are ignored
• Minimum abundance is in %, so 0.21 = 0.21%
• The default minimum abundance is set at 0.21% so that O-18 is
  excluded
• Range widths are given by a start (pre-peak width) and end
  (post-peak width) which has units of sqrt(Da). If rs= rf = 0.01 and
  the peak is at 30 Da, then the start is 30-sqrt(30)0.01 and the
  finish is 30+sqrt(30)0.01 = 29.945 to 30.055 Da
  This is so that the m/z ranges have fixed sizes in TOF space, but
  variable widths in m/z space.
• Ions specified by the adIons parameter should be in the cell array
  format, e.g. Ti2O++ would be {{2,'Ti',2,'O'}}. You can provide a list
  of ions like so: {{1,'Fe'},{2,'Fe'}, ... }.
  See ionStr2ions for futher information about the ion-cell format.