AddIsotopicCorrection

How does LipidX correct the isotopes?

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What is the output if a peak was recogniced as isotope

If the isopic part of a peak reduces the peak to less than (1), a '-1' is written to show that this peak was a pure isotope according to the given import settings. I the value is greater than (1), the rest of the peak remains since it is most probalbly an overlapping peak with the isotope.

(1) <math>\frac{T}{\sqrt{n}}</math>

where <math>T</math> is the threshold as set in the import and <math>n</math> the scan number. This is the same procedure to remove noise peaks as used in the import routine.

Remarks for the function sumIntensity()

The function sumIntensity()is used for summing up intensities of different MS2 entries where multiple peaks are required for identification and quantification. In case of fragments with isotopic corrected place holders (see above)the following rules were implemented.

If all MasterScan entries in the MS2 for a particular molecule are place holders (i.e. all are set to '-1') then those values are just added and will result in <math>n_i\times -1</math> where <math>n_i</math> is the number of the attributes.

If there is just one entry whose intensity is greater zero all <math>-1</math> place holders are threaded as zero and not added to the overall sum. In the presented example we assume that two entries in the MS2 where used for the sumIntensity() function:

<math>F1 + F2 -> sumIntensity(F1, F2)</math>
<math>-1 + -1 = -2</math>
<math> 0 + -1 = -1</math>
<math> 1 + -1 =  1</math>
<math> 2 + -1 =  2</math>
<math> 2 +  0 =  2</math>

That has following consequences when such results have to be interpreted:

A) intensity = 0 in this specific sample none of the required fragments was present

B) intensity < 0 in this sample some of the required fragments were found in the initial MasterScan but set '-1', none fragment above threshold (1) was present

C) intensity = -<math>n_i</math> all fragments were below the threshold (1) after isotopic correction

D) intensity > 0 in this case at least one of the required fragments was after isotopic correction above the threshold (1)