In IsoCor: Analyze Isotope Ratios in a 'Shiny'-App

IDMS parameters

Processing parameters

Smoothing parameter uses Savitzky-Golay method to smooth out the small intensity fluctuations within the peak to help the algorithm to find peak boundaries correctly. The Smoothing parameter can be adjusted to the optimal value by the user.

Mass bias correction related parameters

IDMS f_value is used for calculating mass bias correction factor $K$ in the equation $IR_{corrected}=IR_{measured}K$, where $IR=\frac{Intensity(MI)}{Intensity(SI)}$. The dropdown menu for the Mass bias method selection includes Linear law, Exponential law, Russel's law or none. IDMS f_value* should be inserted manually by the user according to the methods shown below:

Linear equation: $K_{MI/SI}=1+f(amu_{SI}-amu_{MI})$
Russel's equation: $K_{MI/SI}=(amu_{SI}/amu_{MI})^f$
Exponential equation: $K_{MI/SI}=e^{f*(amu_{SI}-amu_{MI})}$

Sample related parameters:

Abund.MI and Abund.SI are abundances of main isotope (MI) and secondary isotope (SI), respectively, in the sample
Inj.amount is an injection amount

Spike related parameters:

MF is the mass flow of the spike
Abund.MI and Abund.SI are abundance of MI and SI, respectively, in the spike

Note! - The detailed explanation of the MF equation can be found by pressing the Help button on the IDMS table tab. - Baseline correction and Peak picking, are set at optimal values for the data (measurement of Sulfur species with CE/ICP-MS method) used during the development of the IDMS functionality of the app. Baseline correction is based on TopHat method that is implemented using MALDIquant package. Peak picking SNR (signal-to-noise) parameter helps to improve finding peak boundaries and to ignore small peaks of no interest. When using the IDMS mode of the app with different data, the user should verify applicability of the default Baseline correction and Peak picking parameters for their processing. For more details, the user may contact the IsoCor authors at jan.lisec@bam.de. - The smoothing is only used during baseline correction and peak detection steps. For the peak integration of the MF non-smoothed intensities are used. - The Output tables and Plot are automatically updated when new parameter is inserted.