Principle

Most of the time, mass spectrometers have very good precision but poor accuracy producing measures with calibration errors. A simple calibration using a known sample is not possible, because the accuracy changes from one shot to another. A solution should be to add in the sample known peptides and use them to recalibrate the spectrum, but it is not always possible to do.

The calibration errors or deviation function of the mass spectrometer can be approximated by a line: mesured masses = ( slope x real masses ) + shift Aldente estimates this function from the data and it is able to work with non recalibrated spectra.

Aldente compares each protein from the database against the experimental data. Here is one example of all possible matches between theoretical and experimental masses.

The user defines the maximum delta allowed to compare the masses. The user should have an idea of the maximum calibration errors of the machine and be able to limit the alignment with allowed slope and shift range. Shift range is defined in Daltons, Slope range is defined in ppm.

Aldente locates and solves the ambiguities.

Aldente optimizes the set of best matches. The hypothesis is that the mass spectrometer deviation is the line passing by the maximum of plots. Using Hough transformation, the tool will find this alignment and define the good matches while excluding the outliers.

This representation scales the axis differently, so that the internal error of the mass spectrometer can be represented. The user defines the mass spectrometer internal error in ppm, and it is taken into account in the alignment.