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Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually.
This score was validated manually and the SNPs were weighted using the log odds ratios (OR) determined in the Gormley meta-analysis [18].
All the MS/MS spectra were further validated manually.
Each putative salt bridge was then validated manually using VMD (http://www.ks.uiuc.edu/Research/vmd/).uiuc.edu/Research/vmd/
Results containing possible peptide identifications by the Mascot algorithm were validated manually.
A number of 50 sequences were validated manually, and assignment errors were identified only for N-deletions larger than 8 nucleotides.
The SNPs were validated manually.
In addition, the results need to be validated manually.
All MS/MS spectra were further validated manually.
Ambiguous base pairs were validated manually referring to chromatograms.
Citrullination sites were validated manually using standard protocols.
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