title: False discovery rate estimation for cross-linked peptides identified by mass spectrometry.
abstract: The mass spectrometric identification of chemically cross-linked peptides (CXMS) specifies spatial restraints of protein complexes; these values complement data obtained from common structure-determination techniques. Generic methods for determining false discovery rates of cross-linked peptide assignments are currently lacking, thus making data sets from CXMS studies inherently incomparable. Here we describe an automated target-decoy strategy and the software tool xProphet, which solve this problem for large multicomponent protein complexes.
authors: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors: Thomas
authors: T
authors: Walzthoeni
authors: Manfred
authors: M
authors: Claassen
authors: Alexander
authors: A
authors: Leitner
authors: Franz
authors: F
authors: Herzog
authors: Stefan
authors: S
authors: Bohn
authors: Friedrich
authors: F
authors: Förster
authors: Martin
authors: M
authors: Beck
authors: Ruedi
authors: R
authors: Aebersold
mesh_terms: D000465:Algorithms; D001331:Automation; D003432:Cross-Linking Reagents / Q000737:chemistry*; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D005189:False Positive Reactions; D013058:Mass Spectrometry / Q000379:methods*; D008958:Models, Molecular; D010455:Peptides / Q000032:analysis* / Q000737:chemistry*; D011487:Protein Conformation; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D003432:Cross-Linking Reagents; D010455:Peptides