title: A systematic model of the LC-MS proteomics pipeline.
abstract: BACKGROUND
  Mass spectrometry is a complex technique used for large-scale protein profiling with clinical and pharmaceutical applications. While individual components in the system have been studied extensively, little work has been done to integrate various modules and evaluate them from a systems point of view.
  
  
  RESULTS
  In this work, we investigate this problem by putting together the different modules in a typical proteomics work flow, in order to capture and analyze key factors that impact the number of identified peptides and quantified proteins, protein quantification error, differential expression results, and classification performance. The proposed proteomics pipeline model can be used to optimize the work flow as well as to pinpoint critical bottlenecks worth investing time and resources into for improving performance. Using the model-based approach proposed here, one can study systematically the critical problem of proteomic biomarker discovery, by means of simulation using ground-truthed synthetic MS data.
authors.affiliation: Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA.
authors.forename: Youting
authors.initials: Y
authors.lastname: Sun
authors.forename: Ulisses
authors.initials: U
authors.lastname: Braga-Neto
authors.forename: Edward R
authors.initials: ER
authors.lastname: Dougherty
mesh_terms: D000465:Algorithms; D002851:Chromatography, High Pressure Liquid; D013058:Mass Spectrometry; D008962:Models, Theoretical; D010455:Peptides / Q000032:analysis; D040901:Proteomics
chemical_list: D010455:Peptides