Prot pi[prɑːt paɪ] | Peptide Tool

Prot pi | Peptide Tool calculates precursor and fragment ion masses, isotopic distribution, hydrophobicity, and absorption coefficient of peptides.

Isoelectric point, mass and retention time of proteins are affected by covalent modifications. This section enables the selection of different predefined modifications as well as the definition of multiple user-defined modifications by selecting the "custom"-option. Just select a modification and click "Add Modification"-button. In the new window, detailed parameters can be defined.

please note: All parameters were calculated assuming all cysteine side chains are reduced to sulfhydryl groups. Please specify disulfide bonds by adding a modification.

Modification Complete Amino acid Location Subunit  

In this section you can specify advanced parameters for calculations. If you are not familiar with these parameters, you don't have to worry about it. The default settings are certainly correct.

Advanced parameters for calculation of isoelectric point
Calculate the charge of the peptides at a defined pH.
Select the data source of pKa values for calculation of isoelectric point.
Mass calculation
Specify the resolution or the type of mass spectrometer. The resolution is defined as:
Resolution = (m/z)/∆(m/z)
∆(m/z) = FWHM
Select the data source of retention coefficients for the calculation of the hydrophobicity and hydrophobicity index.
RPLC peak width
Specify the full width at half maximum of peaks in the reversed phase chromatography with the unit of hydrophobicity (HR).
CZE peak width
Specify the full width at half maximum of peaks in the capillary zone electrophoresis with the unit of ion mobility (cm2/(Vs)).

Coming Soon

Some further features.