Retention time predictor

RETENTION TIME PREDICTOR

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:
Browse

Enter the peptides separated by spaces or new lines (max 5000 characters):

Select the pI estimation method for unmodified peptides:

pIPredict ver. 3.0

SSRCalc ver. 3.0

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

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

Enter the coefficients* for the polynomial formula: b + a₁x + a₂x² + ... + a₅x⁵.
Empty values are counted as 0.

Examples:
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.

Calculate

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).

Information:

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, C-terminal	K
K(+304.21)(+304.21)	double iTRAQ	N-terminal	K
(+229.16)	TMT	N-terminal	any
K(+229.16)	TMT	middle, C-terminal	K
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

References:

1. The Prediction of the Isoelectric Point Value of Peptides and Proteins with a Wide Range of Chemical Modifications. Skvortsov V.S. et al., 2021. doi:10.18097/BMCRM00161

2. Sequence-Specific Retention Calculator. Algorithm for Peptide Retention Prediction in Ion-Pair RP-HPLC: Application to 300- and 100-Å Pore Size C18 Sorbents. Krokhin O.V., 2006. doi:10.1021/ac060777w

3. A Program for Predicting the Retention Time of Peptides with Post-Translational Modifications, Voronina A.I. et al., 2023.
doi:10.18097/BMCRM00196