Abstract

European Journal of Mass Spectrometry
Volume 14 Issue 5, Pages 275–280 (2008)
doi: 10.1255/ejms.939

Minimize the detection of false positives by the software program DetectShift for ¹⁸O-labeled cross-linked peptide analysis

Qiuxia Gao,^a Song Xue,^b Scott A. Shaffer,^c Catalin E. Doneanu,^c David R. Goodlett,^c and Sidney D. Nelson^c,*
aAmgen Inc., 1201 Amgen Court West, Seattle, Washington 98119, USA
^bMicrosoft Corporation, One Microsoft Way, Redmond, Washington 98052, USA
^cDepartment of Medicinal Chemistry, University of Washington, Box 357610, Seattle, Washington 98195, USA. E-mail: sidnels@u.washington.edu

The abbreviations used are: In order to speed up the process of cross-linked peptide identification and characterization, we have previously reported the development of Pro-CrossLink,¹ 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.

Keywords: mass spectrometry, software, Pro-CrossLink, DetectShift, cross-linked peptides, high-throughput, false positives

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