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  • Luo, XiyangChongqing Univ Posts & Telecommun, Chongqing Key Lab Big Data B Intelligence, Chongqing 400065, Peoples R China.,Chongqing University of Posts and Telecommunications (författare)

A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics

  • Artikel/kapitelEngelska2022

Förlag, utgivningsår, omfång ...

  • 2022-05-13
  • American Chemical Society (ACS),2022
  • printrdacarrier

Nummerbeteckningar

  • LIBRIS-ID:oai:DiVA.org:kth-315206
  • https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-315206URI
  • https://doi.org/10.1021/acs.jproteome.2c00069DOI
  • https://lup.lub.lu.se/record/5ec52b9c-5e95-4ff2-8458-9fb782a1d647URI

Kompletterande språkuppgifter

  • Språk:engelska
  • Sammanfattning på:engelska

Ingår i deldatabas

Klassifikation

  • Ämneskategori:ref swepub-contenttype
  • Ämneskategori:art swepub-publicationtype

Anmärkningar

  • QC 20230328
  • Spectrum clustering is a powerful strategy to minimize redundant mass spectra by grouping them based on similarity, with the aim of forming groups of mass spectra from the same repeatedly measured analytes. Each such group of near-identical spectra can be represented by its so-called consensus spectrum for downstream processing. Although several algorithms for spectrum clustering have been adequately benchmarked and tested, the influence of the consensus spectrum generation step is rarely evaluated. Here, we present an implementation and benchmark of common consensus spectrum algorithms, including spectrum averaging, spectrum binning, the most similar spectrum, and the best-identified spectrum. We have analyzed diverse public data sets using two different clustering algorithms (spectra-duster and MaRaCluster) to evaluate how the consensus spectrum generation procedure influences downstream peptide identification. The BEST and BIN methods were found the most reliable methods for consensus spectrum generation, including for data sets with post-translational modifications (PTM) such as phosphorylation. All source code and data of the present study are freely available on GitHub at https://github.com/statisticalbiotechnology/representative-spectra-benchmark.

Ämnesord och genrebeteckningar

Biuppslag (personer, institutioner, konferenser, titlar ...)

  • Bittremieux, WoutUniv Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 USA.,University of California, San Diego (författare)
  • Griss, JohannesEuropean Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Genome Campus, Hinxton CB10 1SD, Cambs, England.;Med Univ Vienna, Dept Dermatol, A-1090 Vienna, Austria.,European Bioinformatics Institute (författare)
  • Deutsch, Eric W.Inst Syst Biol ISB, Seattle, WA 98109 USA.,Institute for Systems Biology, Seattle (författare)
  • Sachsenberg, TimoUniv Tubingen, Dept Comp Sci, Appl Bioinformat, D-72076 Tubingen, Germany.,University of Tübingen (författare)
  • Levitsky, Lev, IRussian Acad Sci, VL Talrose Inst Energy Problems Chem Phys, NN Semenov Fed Res Ctr Chem Phys, Moscow 142432, Russia. (författare)
  • Ivanov, Mark, VRussian Acad Sci, VL Talrose Inst Energy Problems Chem Phys, NN Semenov Fed Res Ctr Chem Phys, Moscow 142432, Russia. (författare)
  • Bubis, Julia A.Russian Acad Sci, VL Talrose Inst Energy Problems Chem Phys, NN Semenov Fed Res Ctr Chem Phys, Moscow 142432, Russia. (författare)
  • Gabriels, RalfVIB UGent Ctr Med Biotechnol, B-9000 Ghent, Belgium.;Univ Ghent, Dept Biomol Med, B-9000 Ghent, Belgium.,Ghent University (författare)
  • Webel, HenryUniv Copenhagen, Novo Nordisk Fdn Ctr Prot Res, DK-2200 Copenhagen, Denmark.,University of Copenhagen (författare)
  • Sanchez, AnielLund University,Lunds universitet,Klinisk kemi, Malmö,Forskargrupper vid Lunds universitet,Clinical Protein Science and Imaging,Clinical Chemistry, Malmö,Lund University Research Groups,Skåne University Hospital(Swepub:lu)an3128sa (författare)
  • Bai, MingzeChongqing Univ Posts & Telecommun, Chongqing Key Lab Big Data Bio Intelligence, Chongqing 400065, Peoples R China.,Chongqing University of Posts and Telecommunications (författare)
  • Käll, Lukas,1969-KTH,Science for Life Laboratory, SciLifeLab,Genteknologi,Science for Life Laboratory (SciLifeLab)(Swepub:kth)u1gqsept (författare)
  • Perez-Riverol, YassetEuropean Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Genome Campus, Hinxton CB10 1SD, Cambs, England.,European Bioinformatics Institute (författare)
  • Chongqing Univ Posts & Telecommun, Chongqing Key Lab Big Data B Intelligence, Chongqing 400065, Peoples R China.Chongqing University of Posts and Telecommunications (creator_code:org_t)

Sammanhörande titlar

  • Ingår i:Journal of Proteome Research: American Chemical Society (ACS)21:6, s. 1566-15741535-38931535-3907

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