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. 2011 Feb 15;12(Suppl 1):S2. doi: 10.1186/1471-2105-12-S1-S2

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Copyright ©2011 He et al; licensee BioMed Central Ltd.

This is an open access article distributed under the terms of the Creative Commons Attribution License (<url>http://creativecommons.org/licenses/by/2.0</url>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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An illustration of the effect of using consistency constraint in PSM re-ranking. Here each solid circle represents a hypothetical peptide-spectrum pair, whose position is proportional to the ranking score. The consistency constraint shortens the distance between two related PSMs to increase their mutual affinity, leading to new ranking scores. If we consider the PSMs above the threshold to be correct, the 2nd PSM in case 1 becomes correct and the 1st PSM in case 2 becomes incorrect after the transformation. In case 3 and case 4, the consistency constraint has no effect on the correctness state of PSMs.