title: Recognizing uncertainty increases robustness and reproducibility of mass spectrometry-based protein inferences.
abstract: Parsimony and protein grouping are widely employed to enforce economy in the number of identified proteins, with the goal of increasing the quality and reliability of protein identifications; however, in a counterintuitive manner, parsimony and protein grouping may actually decrease the reproducibility and interpretability of protein identifications. We present a simple illustration demonstrating ways in which parsimony and protein grouping may lower the reproducibility or interpretability of results. We then provide an example of a data set where a probabilistic method increases the reproducibility and interpretability of identifications made on replicate analyses of Human Du145 prostate cancer cell lines.
authors.affiliation: Department of Neurobiology, Harvard Medical School Children's Hospital Boston, Boston, Massachusetts, United States. Oliver.Serang@Childrens.Harvard.edu
authors.forename: Oliver
authors.initials: O
authors.lastname: Serang
authors.forename: Luminita
authors.initials: L
authors.lastname: Moruz
authors.forename: Michael R
authors.initials: MR
authors.lastname: Hoopmann
authors.forename: Lukas
authors.initials: L
authors.lastname: Käll
mesh_terms: D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D008297:Male; D013058:Mass Spectrometry / Q000379:methods*; D009363:Neoplasm Proteins / Q000737:chemistry / Q000302:isolation & purification*; D010455:Peptides / Q000737:chemistry / Q000302:isolation & purification; D011471:Prostatic Neoplasms / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D035501:Uncertainty
chemical_list: D009363:Neoplasm Proteins; D010455:Peptides