Central concepts

Only singly-charged isobaric ions are currently supported by emgfit!

The peak and spectrum classes

Importing data and creating spectrum objects

Adding peak objects to a spectrum

Assigning species to peaks and fetching AME values

Available fit models

Peak fitting

Peak-shape calibration

Mass re-calibration

Fitting peaks of interest

Multi-peak fits

Fits of regions of interest

Peak-shape uncertainty evaluation

#One peculiarity of this method is that only the centroid shifts of the #TODO: move this section to the peak-shape error evaluation article peaks-of-interest relative to the (shifted) centroid of the mass calibrant are taken into account for the peak-shape error evaluation. This is because the mass re-calibration ensures that only relative centroid shifts with respect to the calibrant enter the final mass values. If varying the shape parameters shifts the peaks-of-interest and the calibrant peak by the same amount, the final mass value is not altered. Despite the uncertainty of the peak-shape parameters the peak shape of isobaric peaks can be assumed to be identical. The mass dependence of shape parameters is negligible for isobaric species. The above argument relies on the condition that a decent time-resolved calibration (TRC) with sufficient calibrant statistics per block has been performed (otherwise, the IOI peaks can be broadened w.r.t. the calibrant). Hence, the peaks-of-interest and the calibrant peak should both be re-fitted.

:-Notation of chemical substances

Just like the MR-TOF-MS data acquisition software MAc, emgfit follows the :-notation of chemical compounds. The chemical composition of an ion is denoted as a single string in which the constituting isotopes are separated by a colon (:). Each isotope is denoted as 'n(El)A' where El is the corresponding element symbol, n denotes the number of atoms of the isotope El and A is the respective atomic mass number. The charge state of the ion is indicated by substracting the desired number of electrons from the atomic species (i.e. singly-charged = '':-1e', doubly-charged = '':-2e' etc.). The substraction of the electron is important since otherwise the atomic instead of the ionic mass is used for subsequent calculations. Mind that emgfit currently only supports singly-charged ions.