NAME
InSilicoSpectro::InSilico::RetentionTimer::Hodges Prediction of peptide retention time method by sum of amino acid coefficients.
SYNOPSIS
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 );DESCRIPTION
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.
METHODS
my $rt=InSilicoSpectro::InSilico::RetentionTimer::Hodges->new( %h )
$h contains a hash.
$rt->getAuthorList()
REturns an array of authors name with available parameters values in the config file
$rt->learn( data=>{expseqs=>\@seqs,exptimes=>\@times,expmodif=>\@modifs} );
Learn the coefficients from experimental data.
$rt->learn_lc( data=>{expseqs=>\@seqs,exptimes=>\@times,expmodif=>\@modifs} );
Learn correction factor for polypeptide chain length.
$rt->predict( peptide=>$str );
Predict retention time for the peptide.
$rt->predictor( peptide=>$str );
Same as predict() but without the calibrator's experimental fitting.
$rt->calibrate( calseqs=>\@str, caltimes=>\@val,fitting=>$str );
Train the predictor with experimental data and the chosen fitting method.
$rc->filter( filter=>$pc,error=>$str )
Filter experimental data in $rc->{data} by a cutting threshold of relative prediction error of $pc (in %).
$rt->writexml( confile=>$file );
Write coefficients.
$rt->readxml( current=>$str );
Retrieve saved coefficients and t0 labelled as in "current".
$rt->delete_coef( current=>$str );
Delete permanently from the current file the list of coefficients identified by $str.
@list=$rt->list_coef( $str );
Return a list of currently available sets of coefficients
@list=$rt->list_coef( );
List available coefficients in the current file.
%coef=$rt->get_coef( );
Return a hash with the current coefficients.
$value=$rt->set_t0();
Set the value of delay.
$value=$rt->get_t0();
Get the current value of delay.
$rt->calibrate( data=>{calseqs=>\@seqs,caltimes=>\@times,calmodifs=>\@modifs},calibrator=>$ec );
Calibrate the predictor with experimental data and saves it in $rt->{calibrator}.
$rt->write_cal( calfile=>$file );
Save current calibrator.
$rt->read_cal ( calfile=>$file );
Retrieve a previously saved calibrator.
$rt->set( $name );
Set an instance parameter.
$rt->get( $name );
Get an instance parameter.
EXAMPLES
see InSilicoSpectro/t/InSilico/testHodges.pl script
SEE ALSO
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
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
AUTHORS
Pablo Carbonell, Alexandre Masselot, www.genebio.com