InSilicoSpectro::InSilico::RetentionTimer::Hodges Prediction of peptide retention time method by sum of amino acid coefficients.
use InSilicoSpectro::InSilico::RetentionTimer::Hodges; use InSilicoSpectro::InSilico::ExpCalibrator; # create the retention time predictor and select the current coefficients my $rt = InSilicoSpectro::InSilico::RetentionTimer::Hodges->new(current=>'Guo86'); # make the predictor to learn $rt->learn( data=>{expseqs=>['ELGFQG','HPGDFGADAQAAMSK','LSSPATLNSR','RFIK'], exptimes=>[1314,1194,1152,1500], expmodif=>['::Oxidation_M::::','::::::::::::::::',':::::']}); # learn also the correction for peptide length $rt->learn_lc( expseqs=>['LFTGHPETLEK','HPGDFGADAQAAMSK','LSSPATLNSR',], exptimes=>[1224,1152,1500], ); # predict retention time for a given peptide $rt->predict( peptide=>'ACFGDMKWVTFISLLRPLLFSSAYSRGVFRRDTHKSEIAHRFKDLGE', modification=>' ::::::::::::::::::::::::::::::::::Oxidation_M:::::::::::::'); # filter current data $rt->filter( filter=>10 ); # save current coefficients $rt->write_xml( confile=>$file,current=>'Exp00' ); # retrieve previously saved coefficients $rt->read_xml( current=>'Exp01' ); # assigns a calibrator to the predictor $ec=InSilicoSpectro::InSilico::ExpCalibrator->new( fitting=>'spline' ); # fits the calibrator from experimental values $rt->calibrate( data=>{calseqs=>['ELGFQG','HPGDFGADAQAAMSK','LSSPATLNSR','RFIK'], caltimes=>[1314,1194,1152,1500], calmodifs=>['::Oxidation_M::::','::::::::::::::::',':::::']}, calibrator=>$ec ); # save current calibrator $rt->write_cal( calfile=>$file ); # retrieve previously saved calibrator $rt->read_cal ( calfile=>$file );
Prediction of reversed-phase HPLC retention time for peptides using the sum of retention coefficients for every amino acid. The coefficients can be chosen from a list of selected precomputed values from the literature or can be learned by means of a multilinear regression fitted from experimental data.
A correction factor for polypeptide chain length is also available.
$h contains a hash.
REturns an array of authors name with available parameters values in the config file
Learn the coefficients from experimental data.
Learn correction factor for polypeptide chain length.
Predict retention time for the peptide.
Same as predict() but without the calibrator's experimental fitting.
Train the predictor with experimental data and the chosen fitting method.
Method used for fitting.
Filter experimental data in $rc->{data} by a cutting threshold of relative prediction error of $pc (in %).
Type of error for filtering.
Write coefficients.
Retrieve saved coefficients and t0 labelled as in "current".
Delete permanently from the current file the list of coefficients identified by $str.
Return a list of currently available sets of coefficients
List available coefficients in the current file.
Return a hash with the current coefficients.
Set the value of delay.
Get the current value of delay.
Calibrate the predictor with experimental data and saves it in $rt->{calibrator}.
Reference to a InSilicoSpectro::InSilico::ExpCalibrator class instance.
Save current calibrator.
Retrieve a previously saved calibrator.
Set an instance parameter.
Get an instance parameter.
see InSilicoSpectro/t/InSilico/testHodges.pl script
InSilicoSpectro::InSilico::RetentionTimer
InSilicoSpectro::InSilico::ExpCalibrator
Guo D, Mant CT, Taneja AK, Parker JMR, Hodges RS. "Prediction of peptide retention times in reversed-phase high-performance liquid chromatography I. Determination of retention coefficients of amino acid residues of model synthetic peptides," J Chromatogr. 1986; 359:499-518.
Mant CT, Zhou NE, Hodges RS. "Correlation of protein retention times in reversed-phase chromatography with polypeptide chain length and hydrophobicity," J Chromatogr. 1989; 476:363-75.
Copyright (C) 2004-2005 Geneva Bioinformatics www.genebio.com
This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
This library 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 Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Pablo Carbonell, Alexandre Masselot, www.genebio.com
To install InSilicoSpectro, copy and paste the appropriate command in to your terminal.
cpanm
cpanm InSilicoSpectro
CPAN shell
perl -MCPAN -e shell install InSilicoSpectro
For more information on module installation, please visit the detailed CPAN module installation guide.