title: Statistical approach to protein quantification.
abstract: A major goal in proteomics is the comprehensive and accurate description of a proteome. This task includes not only the identification of proteins in a sample, but also the accurate quantification of their abundance. Although mass spectrometry typically provides information on peptide identity and abundance in a sample, it does not directly measure the concentration of the corresponding proteins. Specifically, most mass-spectrometry-based approaches (e.g. shotgun proteomics or selected reaction monitoring) allow one to quantify peptides using chromatographic peak intensities or spectral counting information. Ultimately, based on these measurements, one wants to infer the concentrations of the corresponding proteins. Inferring properties of the proteins based on experimental peptide evidence is often a complex problem because of the ambiguity of peptide assignments and different chemical properties of the peptides that affect the observed concentrations. We present SCAMPI, a novel generic and statistically sound framework for computing protein abundance scores based on quantified peptides. In contrast to most previous approaches, our model explicitly includes information from shared peptides to improve protein quantitation, especially in eukaryotes with many homologous sequences. The model accounts for uncertainty in the input data, leading to statistical prediction intervals for the protein scores. Furthermore, peptides with extreme abundances can be reassessed and classified as either regular data points or actual outliers. We used the proposed model with several datasets and compared its performance to that of other, previously used approaches for protein quantification in bottom-up mass spectrometry.
authors.affiliation: Seminar for Statistics, Eidgenössische Technische Hochschule (ETH) Zurich, Rämistrasse 101, 8092 Zurich, Switzerland;
authors.forename: Sarah
authors.initials: S
authors.lastname: Gerster
authors.forename: Taejoon
authors.initials: T
authors.lastname: Kwon
authors.forename: Christina
authors.initials: C
authors.lastname: Ludwig
authors.forename: Mariette
authors.initials: M
authors.lastname: Matondo
authors.forename: Christine
authors.initials: C
authors.lastname: Vogel
authors.forename: Edward M
authors.initials: EM
authors.lastname: Marcotte
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Peter
authors.initials: P
authors.lastname: Bühlmann
mesh_terms: D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D030562:Databases, Protein / Q000706:statistics & numerical data; D006801:Humans; D007553:Isotope Labeling / Q000379:methods; D007921:Leptospira interrogans / Q000378:metabolism; D015470:Leukemia, Myeloid, Acute / Q000378:metabolism; D008390:Markov Chains; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods / Q000706:statistics & numerical data*; D012107:Research Design; D012984:Software
chemical_list: D011506:Proteins