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Published on: April 1, 2017
Glycopeptide Mass Spectrometry Data Analysis Using Protein Prospector
Robert J Chalkley1, Peter R Baker2
1Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA. chalkley@cgl.ucsf.edu.
Abstract:
The analysis of glycopeptide mass spectrometry fragmentation data has improved dramatically in the last 10 years, but there are still challenges with providing comprehensive while still reliable results. This chapter presents the data analysis pipeline in Protein Prospector as an example workflow. It talks about issues with estimating the reliability of results and provides tips for how to spot unreliable assignments. During the chapter, there is frequent reference to a video tutorial that presents analogous information in a different format.

