title: Minimize the detection of false positives by the software program DetectShift for 18O-labeled cross-linked peptide analysis.
abstract: In order to speed up the process of cross-linked peptide identification and characterization, we have previously reported the development of Pro-CrossLink, a suite of software tools consisting of three programs, DetectShift, IdentifyXLink and AssignXLink for mass spectrometric data analysis. Since its public disclosure, Pro-CrossLink has been downloaded by 101 research groups. Pro-CrossLink users have provided us with valuable feedback on the use of the DetectShift program. Here we assess some reasons for the generation of false positives by DetectShift. In addition, we provide users with suggestions on optimal parameter setting and efficient use of the software program.
authors.affiliation: Amgen Inc., 1201 Amgen Court West, Seattle, Washington 98119, USA.
authors.forename: Quixia
authors.initials: Q
authors.lastname: Gao
authors.forename: Song
authors.initials: S
authors.lastname: Xue
authors.forename: Scott A
authors.initials: SA
authors.lastname: Shaffer
authors.forename: Catalin E
authors.initials: CE
authors.lastname: Doneanu
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
authors.forename: Sidney D
authors.initials: SD
authors.lastname: Nelson
mesh_terms: D003432:Cross-Linking Reagents / Q000737:chemistry; D007553:Isotope Labeling / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods; D010103:Oxygen Isotopes / Q000032:analysis / Q000737:chemistry; D010449:Peptide Mapping; D010455:Peptides / Q000032:analysis*; D012815:Signal Processing, Computer-Assisted; D012984:Software
chemical_list: D003432:Cross-Linking Reagents; D010103:Oxygen Isotopes; D010455:Peptides