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. 2010 Jul 22;26(17):2153–2159. doi: 10.1093/bioinformatics/btq341

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© The Author(s) 2010. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 2. — Workflow for automated annotation of phosphosites. Experimental LC–MS/MS data is gathered (1) and processed using platform specific software (2) to give a generic peak list file (3). This file, is used as the input to MASCOT (4), which generates a results file (5) containing all the PSMs. This file is parsed into the MLRV relational database (6) and the FDR for the search determined (7). A PSM-quality prefilter is applied (8) and suitable PSMs are exported to the TryPP-DB (9) where they are linked to the source peak list file used for the search. The observed MS/MS spectrum is extracted from the peak list file (10), filtered by an intensity threshold (11) and compared with a calculated fragmentation spectrum (12) for the peptide under examination. Observed ions are assigned to series (13) allowing the curation rules to be applied (14).