title: Peak quantification in surface-enhanced laser desorption/ionization by using mixture models.
abstract: Surface-enhanced laser desorption/ionization (SELDI) time of flight (TOF) is a mass spectrometry technology for measuring the composition of a sampled protein mixture. A mass spectrum contains peaks corresponding to proteins in the sample. The peak areas are proportional to the measured concentrations of the corresponding proteins. Quantifying peak areas is difficult for existing methods because peak shapes are not constant across a spectrum and because peaks often overlap. We present a new method for quantifying peak areas. Our method decomposes a spectrum into peaks and a baseline using so-called statistical finite mixture models. We illustrate our method in detail on 8 samples from culture media of adipose tissue and globally on 64 samples from serum to compare our method to the standard Ciphergen method. Both methods give similar estimates for singleton peaks, but not for overlapping peaks. The Ciphergen method overestimates the heights of such peaks while our method still gives appropriate estimates. Peak quantification is an important step in pre-processing SELDI-TOF data and improvements therein will pay off in the later biomarker discovery phase.
authors.affiliation: Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands. m.dijkstra@rug.nl
authors.forename: Martijn
authors.initials: M
authors.lastname: Dijkstra
authors.forename: Han
authors.initials: H
authors.lastname: Roelofsen
authors.forename: Roel J
authors.initials: RJ
authors.lastname: Vonk
authors.forename: Ritsert C
authors.initials: RC
authors.lastname: Jansen
mesh_terms: D000273:Adipose Tissue / Q000737:chemistry; D001798:Blood Proteins / Q000032:analysis / Q000737:chemistry; D008956:Models, Chemical; D011506:Proteins / Q000032:analysis* / Q000737:chemistry; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods* / Q000706:statistics & numerical data
chemical_list: D001798:Blood Proteins; D011506:Proteins