org.fhcrc.cpl.viewer.amt
Class AcrylamideHydrophobicityAdjuster

java.lang.Object
  org.fhcrc.cpl.viewer.amt.AcrylamideHydrophobicityAdjuster

public class AcrylamideHydrophobicityAdjuster
extends java.lang.Object

This class knows how to adjust normalized hydrophobicities based on the effect of acrylamide, vs. iodoacetamide, on peptide hydrophobicity. These techniques were developed based on a fractionated run of CSF by Wendy Law, containing a pool of unlabeled CSF with iodoacetamide protecting the Cysteines, and the same CSF with heavy-labeled acrylamide. Executive summary: acrylamide increases hydrophobicity slightly over iodoacetamide. More Cysteines -> bigger effect WARNING: there is actually a rather more complex relationship between peptide composition and the acrylamide hydrophobicity contribution than we capture here. It looks like there's a nonlinear relationship between peptide hydrophobicity and the amount of contribution, and of course that relationship is different for different numbers of Cysteines. What you see here is just a good-enough shorthand.

Field Summary

static double[]	ACRYLAMIDE_HYDRO_DIFF_COEFFS_0_RESIDUES
static double[]	ACRYLAMIDE_HYDRO_DIFF_COEFFS_1_RESIDUE
static double[]	ACRYLAMIDE_HYDRO_DIFF_COEFFS_2_RESIDUES
static double[]	ACRYLAMIDE_HYDRO_DIFF_COEFFS_3PLUS_RESIDUES

Constructor Summary

AcrylamideHydrophobicityAdjuster()

Method Summary

static double	adjustHForAcrylamide(java.lang.String peptideSequence, double oldH)
static double	calculateAcrylamideHDifference(java.lang.String peptideSequence, double oldH)
static double	removeAcrylamideEffect(java.lang.String peptideSequence, double oldH)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ACRYLAMIDE_HYDRO_DIFF_COEFFS_0_RESIDUES

public static final double[] ACRYLAMIDE_HYDRO_DIFF_COEFFS_0_RESIDUES

ACRYLAMIDE_HYDRO_DIFF_COEFFS_1_RESIDUE

public static final double[] ACRYLAMIDE_HYDRO_DIFF_COEFFS_1_RESIDUE

ACRYLAMIDE_HYDRO_DIFF_COEFFS_2_RESIDUES

public static final double[] ACRYLAMIDE_HYDRO_DIFF_COEFFS_2_RESIDUES

ACRYLAMIDE_HYDRO_DIFF_COEFFS_3PLUS_RESIDUES

public static final double[] ACRYLAMIDE_HYDRO_DIFF_COEFFS_3PLUS_RESIDUES

Constructor Detail

AcrylamideHydrophobicityAdjuster

public AcrylamideHydrophobicityAdjuster()

Method Detail

calculateAcrylamideHDifference

public static double calculateAcrylamideHDifference(java.lang.String peptideSequence,
                                                    double oldH)

adjustHForAcrylamide

public static double adjustHForAcrylamide(java.lang.String peptideSequence,
                                          double oldH)

removeAcrylamideEffect

public static double removeAcrylamideEffect(java.lang.String peptideSequence,
                                            double oldH)