Response to "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra"

Griss, JohannesMed Univ Vienna, Dept Dermatol, Div Immunol Allergy & Infect Dis, Wahringer Gurtel 18-20, A-1090 Vienna, Austria.;EBI, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England. (författare)

QC 20180522
In the recent benchmarking article entitled "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra", Rieder et al. compared several different approaches to cluster MS/MS spectra. While we certainly recognize the value of the manuscript, here, we report some shortcomings detected in the original analyses. For most analyses, the authors clustered only single MS/MS runs. In one of the reported analyses, three MS/MS runs were processed together, which already led to computational performance issues in many of the tested approaches. This fact highlights the difficulties of using many of the tested algorithms on the nowadays produced average proteomics data sets. Second, the authors only processed identified spectra when merging MS runs. Thereby, all unidentified spectra that are of lower quality were already removed from the data set and could not influence the clustering results. Next, we found that the authors did not analyze the effect of chimeric spectra on the clustering results. In our analysis, we found that 3% of the spectra in the used data sets were chimeric, and this had marked effects on the behavior of the different clustering algorithms tested. Finally, the authors' choice to evaluate the MS-Cluster and spectra-cluster algorithms using a precursor tolerance of 5 Da for high-resolution Orbitrap data only was, in our opinion, not adequate to assess the performance of MS/MS clustering approaches.

Perez-Riverol, YassetEBI, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England. (författare)
The, MatthewKTH,Science for Life Laboratory, SciLifeLab(Swepub:kth)u1c6xiyk (författare)
Käll, Lukas,1969-KTH,SeRC - Swedish e-Science Research Centre,Science for Life Laboratory, SciLifeLab(Swepub:kth)u1gqsept (författare)
Vizcaino, Juan AntonioEBI, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England. (författare)
Med Univ Vienna, Dept Dermatol, Div Immunol Allergy & Infect Dis, Wahringer Gurtel 18-20, A-1090 Vienna, Austria.;EBI, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.EBI, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England. (creator_code:org_t)

Ingår i:Journal of Proteome Research: AMER CHEMICAL SOC17:5, s. 1993-19961535-38931535-3907

Av författaren/redakt...: Griss, Johannes; Perez-Riverol, Y ...; The, Matthew; Käll, Lukas, 196 ...; Vizcaino, Juan A ...

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