rt

Copyright Notice

rt is Copyright (C) 2002 Magnus Palmblad

rt is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

About rt

rt is a generic linear retention time predictor for peptides in LC-MS and LC-MS/MS as described in Palmblad et al., Anal. Chem., 74(21), 5826-5830 (2002). The latest version includes the 20 common amino acids and post-translational modifications methionine-S-oxide, phosphoserine, phosphothreonine and phosphotyrosine.

rt fits c(i), i = 1...25, in t_calc = sum(n(i, j)*c(i)) + t_0, i = 1...25, to measured retention times for N peptides of amino acid composition n(i, j), i = 1...25, j = 1...N by linear least squares regression.

Download rt by clicking here. (Right-click and choose "Save Link As...".)

Compiling rt

Compile rt with: gcc -o rt rt.c -lgsl

rt uses the GNU Scientific Library available at http://www.gnu.org/software/gsl/.

Using rt

Usage: rt <training set>

where <training set> is a space delimited list of retention times (in arbitrary units) and peptide sequences in the one-letter code and lower case letters for the modified amino acids, with one measured retention time and peptide sequence pair per row in an ASCII text file, e.g.

28.536 AHGHSmsDPAISY
32.14 SHLtWFCTMKLD
34.763 AGASyTDVAYK
etc.

Click here to download some test data.

The retention time peptide[i].t of a peptide peptide[i].sequence is then predicted by
 peptide[i].t=c[24];
 for(j=0;j<strlen(peptide[i].sequence);j++)                                                    
   {                                                                                           
     peptide[i].t+=c[(24-strlen(strchr(AMINO_ACIDS,peptide[i].sequence[j])))];                 
   }
or something similar incorporated into your own code.

The output from rt is a list of amino acids in the one-letter code and lower case letters for the modified amino acids and corresponding retention coefficients c(i): 
$ ./rt test_data.txt
reading training set...done
least-squares fit to experimental retention data:
A 0.568343
R -0.580262
N 0.296095
D 0.364778
C -0.053205
E 0.705856
Q -0.676294
G -0.050900
H -1.284163
I 1.205046
L 2.006191
K -0.724280
M 0.859403
F 2.092323
P 0.366221
S -0.109884
T -0.288559
W -0.694075
Y 0.989262
V 0.649569
m 0.618037
s 1.297288
t -1.754750
y 1.069785
0 0.618037
$


magnus.palmblad@gmail.com