title: A statistical framework for protein quantitation in bottom-up MS-based proteomics.
abstract: BACKGROUND
  Quantitative mass spectrometry-based proteomics requires protein-level estimates and associated confidence measures. Challenges include the presence of low quality or incorrectly identified peptides and informative missingness. Furthermore, models are required for rolling peptide-level information up to the protein level.
  
  
  RESULTS
  We present a statistical model that carefully accounts for informative missingness in peak intensities and allows unbiased, model-based, protein-level estimation and inference. The model is applicable to both label-based and label-free quantitation experiments. We also provide automated, model-based, algorithms for filtering of proteins and peptides as well as imputation of missing values. Two LC/MS datasets are used to illustrate the methods. In simulation studies, our methods are shown to achieve substantially more discoveries than standard alternatives.
  
  
  BACKGROUND
  The software has been made available in the open-source proteomics platform DAnTE (http://omics.pnl.gov/software/).
authors.affiliation: Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, USA.
authors.forename: Yuliya
authors.initials: Y
authors.lastname: Karpievitch
authors.forename: Jeff
authors.initials: J
authors.lastname: Stanley
authors.forename: Thomas
authors.initials: T
authors.lastname: Taverner
authors.forename: Jianhua
authors.initials: J
authors.lastname: Huang
authors.forename: Joshua N
authors.initials: JN
authors.lastname: Adkins
authors.forename: Charles
authors.initials: C
authors.lastname: Ansong
authors.forename: Fred
authors.initials: F
authors.lastname: Heffron
authors.forename: Thomas O
authors.initials: TO
authors.lastname: Metz
authors.forename: Wei-Jun
authors.initials: WJ
authors.lastname: Qian
authors.forename: Hyunjin
authors.initials: H
authors.lastname: Yoon
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.forename: Alan R
authors.initials: AR
authors.lastname: Dabney
mesh_terms: D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D015233:Models, Statistical; D011506:Proteins / Q000032:analysis*; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods*
chemical_list: D011506:Proteins; D020543:Proteome