Isotope pattern generator for fine isotope distributions.
This algorithm generates theoretical pattern distributions for empirical formulas with high resolution (while the CoarseIsotopePatternGenerator will generate low-resolution patterns). The output is a list of pairs containing isotope probabilities paired with the accurate m/z for the analyte isotopic composition.
For example, for a C100H202 molecule (at 0.01 threshold), you will get:
m/z 1403.5806564438 :
INT 0.333207070827484
m/z 1404.5840114438 :
INT 0.360387712717056
m/z 1404.5869331919 :
INT 0.00774129061028361
m/z 1405.5873664438 :
INT 0.19294385612011
m/z 1405.5902881919 :
INT 0.00837276969105005
m/z 1406.5907214438 :
INT 0.0681697279214859
m/z 1406.5936431919 :
INT 0.00448260130360723
m/z 1407.5940764438 :
INT 0.0178796537220478
m/z 1407.5969981919 :
INT 0.00158376491162926
...
For comparison, the CoarseIsotopePatternGenerator will produce the following result for a C100H202 molecule:
m/z 1403.58
INT: 0.333489
m/z 1405.59
INT: 0.201576
m/z 1406.59
INT: 0.0728113
m/z 1407.59
INT: 0.0195325
...
One important value to set is the threshold with tells the algorithm when to stop calculating isotopic peaks to calculate. The default stop condition is to stop when only a small portion (such as 0.01) of the total probability is unexplained and the reported values cover most of the probability (e.g. 0.99).
Another way to stop the search is when any new peak would be less than 0.01 in height (absolute) or when it would be less than 0.01 of the highest isotopic peak (relative). This is how the stop_condition parameter is interpreted when use_total_prob is set to false.
- Note
- Computation of fine isotope patterns can be slow for large molecules, if you don't need fine isotope distributions consider using CoarseIsotopePatternGenerator.
-
Consider using IsoSpec directly or the OpenMS IsoSpecWrapper / IsoSpecGeneratorWrapper classes defined in IsoSpecWrapper.h for increased performance.
The computation is based on the IsoSpec algorithm
Łącki MK, Startek M, Valkenborg D, Gambin A.
IsoSpec: Hyperfast Fine Structure Calculator.
Anal Chem. 2017 Mar 21;89(6):3272-3277. doi: 10.1021/acs.analchem.6b01459.
See also method run()
Public Member Functions inherited from IsotopePatternGenerator
1.9.1
