Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Response to "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra"
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..ORCID iD: 0000-0001-6579-6941
KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-5401-5553
KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0001-5689-9797
Show others and affiliations
2018 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 17, no 5, p. 1993-1996Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC , 2018. Vol. 17, no 5, p. 1993-1996
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:kth:diva-228271DOI: 10.1021/acs.jproteome.7b00824ISI: 000431726700024PubMedID: 29682973Scopus ID: 2-s2.0-85046629294OAI: oai:DiVA.org:kth-228271DiVA, id: diva2:1209193
Note

QC 20180522

Available from: 2018-05-22 Created: 2018-05-22 Last updated: 2018-05-22Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textPubMedScopus

Authority records BETA

The, MatthewKäll, Lukas

Search in DiVA

By author/editor
Perez-Riverol, YassetThe, MatthewKäll, LukasVizcaino, Juan Antonio
By organisation
Science for Life Laboratory, SciLifeLabSeRC - Swedish e-Science Research Centre
In the same journal
Journal of Proteome Research
Bioinformatics and Systems Biology

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 3 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf