Recently we posted a comparison of different search engines for PTMs studies (Evaluation of Proteomic Search Engines for PTMs Identification). After some discussion of the mentioned results in our post the PEAKS Team just published a blog post with the reanalysis of the dataset. Here the results:
Originally Posted in Peaks Blog:
The complex nature of histone modification patterns has posed as a challenge for bioinformatics analysis over the years. Yuan et al.  conducted a study using two datasets from human HeLa histone samples, to benchmark the performance of current proteomic search engines. This article was published in J Proteome Res. 2014 Aug 28 (PubMed), and the data from the two datasets, HCD_Histone and CID_Histone (PXD001118, was made publically available through ProteomeXchange. With this data, the article uses eight different proteomic search engines to compare and evaluate the performance and capability of each. The evaluated search engines in this study are: pFind, Mascot, SEQUEST, ProteinPilot, PEAKS 6, OMSSA, TPP and MaxQuant.
In this study, PEAKS 6 was used to compare the performance capabilities between search engines. However, PEAKS 7, which was released November 2013, is the latest version available of the PEAKS Studio software. PEAKS 7 not only includes better performance than PEAKS 6, but a lot of additional and improved features. Our team has reanalyzed the two datasets HCD_Histone and CID_Histone with PEAKS 7 to update the ID results presented in the publication by Yuan et al. These updated results showed that instead, it is PEAKS, pFind and Mascot that identify the most confident results.