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InSilicoSpectro-1.3.24
River stage zero No dependents
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/ InSilicoSpectro::InSilico::RetentionTimer::Hodges

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.

fitting=>'linear'|'spline'

Method used for fitting.

$rc->filter( filter=>$pc,error=>$str )

Filter experimental data in $rc->{data} by a cutting threshold of relative prediction error of $pc (in %).

error=>'relative'|'absolute'

Type of error for filtering.

$rt->writexml( confile=>$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}.

calibrator=>$ec

Reference to a InSilicoSpectro::InSilico::ExpCalibrator class instance.

$rt->write_cal( calfile=>$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