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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. 4. — A manually verified PSM that ProPhosSI fails to validate. Many ion labels are not shown for clarity. Evidence for phosphorylation at S1 arises from the b2 ion (a). ProPhosSI requires ion transitions over a phosphosite and so requires more than one ion. Evidence for phosphorylation at S4 arises from the uniquely assigned des-phospho y10 [2+] ion. ProPhosSI does not consider 2+ ions as they can in many cases be assigned to more than one fragment.