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. 2018 Aug 3;15:26. doi: 10.1186/s12014-018-9202-4

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© The Author(s) 2018

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 2 — Comparison of FFPE (SEER) and OCT (TCGA) proteome coverage. The comparative analysis was done using both the spectrum identification rates (a) and unique peptide identification rates (b). The identification rate is calculated as the number of PSM passing a 1% FDR cutoff (a) or unique peptide sequences (b) divided by the total number of MS/MS spectra taken by the mass spectrometer. The difference in assignment of PSMs and peptides between the TMT-10 (SEER) and iTRAQ-4 (TCGA) labeled samples is also adjusted to account for the known differences as described above