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Submitted on May 6, 2005
Biostatistics Department, University of Washington, Seattle, WA 98195
Corresponding Author: trandolp{at}fhcrc.org
This report addresses the question of which properties in MALDI-TOF spectra are relevant to the task of identifying mass and abundance of a peptide species in human serum. Data of this type are common to biomarker studies, but significant within- and between-spectrum variabilities makes quantifying biologically-induced features difficult. We investigate this signal content and quantify the existence, or lack, of peptide-induced signal (as manifest in a multiresolution decomposition) by generating spectra from human serum in which the abundance of peptides of specific masses is controlled by a sequence of dilutions. The intensities of the corresponding features are directly proportional to peptide concentration. The primary goal is to exhibit some quantifiable properties of raw spectra from this application of MALDI-TOF mass spectrometry. Although no recommendations are given regarding the best method for processing this data, the results confirm the utility of a simple method, based on wavelets, for defining and quantifying features related to low-abundant peptide species in a heterogeneous set of complex spectra. Estimates on lower-limits of detectable peptide abundance (in the 20 nmol range) and on the number of features present in a spectrum are made possible by the controlled experimental design, the use of a large external reference data set, and dependence on relatively few modelling assumptions.
Revised on September 23, 2005
Accepted on September 29, 2005
Quantifying peptide signal in MALDI-TOF mass spectrometry data
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