title: Processing methods for signal suppression of FTMS data.
abstract: BACKGROUND
  Fourier Transform Mass Spectrometry coupled with Liquid Chromatography(LC-FTMS) has been widely used in proteomics. Past investigation has revealed that there exists an intensity dependent random suppression in peptide elution profiles in LC-FTMS data. The suppression is homogenous for the same peptide but non-homogenous for different peptides. The correction of suppressed profiles and an estimation on the range of suppression are necessary for accurate and reliable quantification using FTMS data.
  
  
  RESULTS
  A software package, Gcorr, is presented. The software corrects peptide profiles that satisfy correction conditions, and it can predict fold change null distributions at different intensity levels. Subsequently, the significance P-values of measured fold changes can be estimated based on the predicted null distributions. We have used an 1:1 LC-FTMS label-free dataset pair collected based on the same sample to verify that our predicted null distributions conforms to that of the observed null distribution.
  
  
  CONCLUSIONS
  This software is able to provide suppression correction for peptide profiles, suppression distribution analysis and peptide differential expression analysis in terms of its fold change significance. The software is freely available at http://compgenomics.utsa.edu/Suppression_Study.html.
authors.affiliation: Electrical and Computer Engineering Department, University of Texas at San Antonio, San Antonio, TX, USA. michelle.zhang@utsa.edu.
authors.forename: Xuepo
authors.initials: X
authors.lastname: Ma
authors.forename: Jian
authors.initials: J
authors.lastname: Cui
authors.forename: Jianqiu
authors.initials: J
authors.lastname: Zhang