Enter peptides or load file

Fasta or txt (peptide per line, no header) file formats accepted, max 10000 peptides and 900 kb.

Modifications must be in PEAKS format.
Example: D(+229.16)GSIDLVINLPN(+.98)NNTK(+229.16)

Project name:
Input file:
Enter the peptides separated by spaces or new lines (max 5000 characters):
Select the pI estimation method for unmodified peptides:

Note: pI for modified peptides is always calculated by pIPredict v3[1] method.

Predict RT based on correlation with peptide hydrophobicity index (optional).

For linear equation, set b and a1 values, others are empty or 0.
For a quadratic equation, set b, a1, a2 values, others empty or 0.

* - Coefficients of polynomial distribution should be calculated by correlation between real RT and HI values.

The MS Windows executable, RTPv1.0.exe (65 Mb, Windows 10 or higher required).
This program is distributing under GNU Lesser General Public License (LGPL).

The program is based on the Sequence-Specific Retention Calculator (SSRCalc v3.0).[2]
This method estimates the hydrophobicity index (HI) of peptide, which is strongly correlated with the retention time (RT).
The actual RT varies with conditions, so additional coefficients are needed to transform the HI value into a predictable RT.

The original SSRCalc v3.0 can only handle peptides without modifications, our addition allows to estimate the HI for peptides with the following modifications (see table).

Supported modifications[3]
Modification Description Position Residues
(+304.21) iTRAQ N-terminal any
K(+304.21) iTRAQ middle,
K(+304.21)(+304.21) double iTRAQ N-terminal K
(+229.16) TMT N-terminal any
K(+229.16) TMT middle,
K(+229.16)(+229.16) double TMT N-terminal K
(+79.97) phosphorylation any S, T, Y
(+71.04) propionamidation any C
(+57.02) carbamidomethylation any C, D, E
(+42.01) acetylation N-terminal any
(+42.01) acetylation any K
(+31.99) dioxidation any M, P
(+27.99) formylation N-terminal any
(+27.99) formylation any K
(+15.99) oxidation any M, P
(+14.02) methylation N-terminal any
(+14.02) methylation any K
(+.98) deamidation any Q, N
(-.98) amidation C-terminal K, R