title: Significance analysis of spectral count data in label-free shotgun proteomics.
abstract: Spectral counting has become a commonly used approach for measuring protein abundance in label-free shotgun proteomics. At the same time, the development of data analysis methods has lagged behind. Currently most studies utilizing spectral counts rely on simple data transforms and posthoc corrections of conventional signal-to-noise ratio statistics. However, these adjustments can neither handle the bias toward high abundance proteins nor deal with the drawbacks due to the limited number of replicates. We present a novel statistical framework (QSpec) for the significance analysis of differential expression with extensions to a variety of experimental design factors and adjustments for protein properties. Using synthetic and real experimental data sets, we show that the proposed method outperforms conventional statistical methods that search for differential expression for individual proteins. We illustrate the flexibility of the model by analyzing a data set with a complicated experimental design involving cellular localization and time course.
authors.affiliation: Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.
authors.forename: Hyungwon
authors.initials: H
authors.lastname: Choi
authors.forename: Damian
authors.initials: D
authors.lastname: Fermin
authors.forename: Alexey I
authors.initials: AI
authors.lastname: Nesvizhskii
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D003198:Computer Simulation; D016014:Linear Models; D013058:Mass Spectrometry; D051379:Mice; D009154:Mutation / Q000235:genetics; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000254:growth & development / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D013194:Staining and Labeling; D013347:Subcellular Fractions / Q000378:metabolism; D013997:Time Factors
chemical_list: D029701:Saccharomyces cerevisiae Proteins