### Peak table

The peak table contains details on peak detection results and mass bias correction.

#### Explanation of the column names

<div style="width:200px">Column name</div> | Description
:--- | :---
Sample           | ID of the sample; each file is indexed when several files are uploaded
Peak ID          | ID of the detected peaks (when several files are uploaded, the files should contain same number of peaks); each detected peak is indexed numerically
RT max           | retention time of the peak at maximum intensity
RT start         | retention time at the start of the peak
RT end           | retention time at the end of the peak
Scan start       | index of the row corresponding to the start of the peak
Scan end         | index of the row corresponding to the end of the peak
Scan length      | number of points corresponding to the peak elution from start to the end
Mass bias method | Name of the method when mass bias correction is applied; default name "none"
f_value          | a coefficient for mass bias correction; the coefficient should be calculated separately and copy/pasted into IsoCor; find detailed explanation below
k                | mass bias correction factor calculated by the ***IsoCor***; find detailed explanation below
Type             | Type of the peak: standard, sample or discard; type is selected by the user; find detailed explanation below

#### Explanation of the buttons located above the table

| <div style="width:200px">Button name</div> | Description                                                         |
| :-------------------------- | :--------------------------------------------------------------------------------- |
| Copy                        | to copy the entire table                                                           |
| Excel                       | to save the table as Excel file                                                    |
| define mass bias correction | parameters for mass bias correction; find detailed explanation below               |
| change peak type            | set peak type as standard or sample, or discard; find detailed explanation below   |
| Help                        | get help                                                                           |


#### Explanation of the peak type

Each peak can be selected as either standard or sample or be discarded. 
The selection of peak type is needed for delta calculation with standard-sample bracketing method.

For example, if file has three peaks, then, typically, the 1^st and 3^rd peaks are of type `standard`, and middle peak of type `sample`.

To set the type of the peak:

1. click on one of the rows on Peak table  
2. click `change peak type` button  
3. select type of the peak from drop down menu

After peak detection, each peak is indexed with a number. Peaks with same index are assigned with same type of peak. 
For example, when type of peak **\#1** in sample 1 is set to `standard`, then peak **\#1** in all samples will be of type `standard`.
This is important to perform the calculation of delta in all samples in an identical way.

![Peak table example](images/06_peak_table_01.png)

***Note!*** 
By default, when typical data with three peaks are uploaded, the first and third peaks are set to `standard`, and middle peak is set to `sample`. 
This default type can be changed following the steps described above. 
For delta calculation, the isotope ratio of `standard` is obtained by averaging isotope ratio values of first and third peaks.

#### Explanation of the mass bias correction

***IsoCor*** performs mass bias correction according to the formula: $R_{corrected}=R_{measured} \times K$

The correction factor `K` can be calculated with one of three equations that is selected by the user:  
Linear equation: $K_{SI/MI}=1+f(amu_{SI}-amu_{MI})$  
Russel's equation: $K_{SI/MI}=(amu_{SI}/amu_{MI})^f$  
Exponential equation: $K_{SI/MI}=e^{f \times (amu_{SI}-amu_{MI})}$

After mass bias correction method is selected, the `f` values should be copy/pasted onto the placeholder. 
Typically, `f` values are calculated from continuously introduced standard, thus number of `f` values should be same 
as number of peaks (for example 3 repetitions files, each file has 3 peaks; thus total 9 peaks need to have 9 corresponding `f` values). 
Atomic weights of the isotopes are also added by the user for MI and SI on Import section.

Then correction factor `K` is calculated by the App, and isotope ratio values are updated according to mass bias correction. 
Manually added `f` values and app-calculated `K` values are shown in Peak table.
