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A Comprehensive Eva...
A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics
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- Luo, Xiyang (författare)
- Chongqing Univ Posts & Telecommun, Chongqing Key Lab Big Data B Intelligence, Chongqing 400065, Peoples R China.,Chongqing University of Posts and Telecommunications
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- Bittremieux, Wout (författare)
- Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 USA.,University of California, San Diego
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- Griss, Johannes (författare)
- European 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
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- Deutsch, Eric W. (författare)
- Inst Syst Biol ISB, Seattle, WA 98109 USA.,Institute for Systems Biology, Seattle
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- Sachsenberg, Timo (författare)
- Univ Tubingen, Dept Comp Sci, Appl Bioinformat, D-72076 Tubingen, Germany.,University of Tübingen
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- Levitsky, Lev, I (författare)
- Russian Acad Sci, VL Talrose Inst Energy Problems Chem Phys, NN Semenov Fed Res Ctr Chem Phys, Moscow 142432, Russia.
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- Ivanov, Mark, V (författare)
- Russian Acad Sci, VL Talrose Inst Energy Problems Chem Phys, NN Semenov Fed Res Ctr Chem Phys, Moscow 142432, Russia.
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- Bubis, Julia A. (författare)
- Russian Acad Sci, VL Talrose Inst Energy Problems Chem Phys, NN Semenov Fed Res Ctr Chem Phys, Moscow 142432, Russia.
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- Gabriels, Ralf (författare)
- VIB UGent Ctr Med Biotechnol, B-9000 Ghent, Belgium.;Univ Ghent, Dept Biomol Med, B-9000 Ghent, Belgium.,Ghent University
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- Webel, Henry (författare)
- Univ Copenhagen, Novo Nordisk Fdn Ctr Prot Res, DK-2200 Copenhagen, Denmark.,University of Copenhagen
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- Sanchez, Aniel (författare)
- Lund 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
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- Bai, Mingze (författare)
- Chongqing Univ Posts & Telecommun, Chongqing Key Lab Big Data Bio Intelligence, Chongqing 400065, Peoples R China.,Chongqing University of Posts and Telecommunications
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- Käll, Lukas, 1969- (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi,Science for Life Laboratory (SciLifeLab)
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- Perez-Riverol, Yasset (författare)
- European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Genome Campus, Hinxton CB10 1SD, Cambs, England.,European Bioinformatics Institute
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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)
- 2022-05-13
- 2022
- Engelska.
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 21:6, s. 1566-1574
- Relaterad länk:
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https://doi.org/10.1...
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http://dx.doi.org/10... (free)
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://lup.lub.lu.s...
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Abstract
Ämnesord
Stäng
- 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
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Annan naturvetenskap -- Övrig annan naturvetenskap (hsv//swe)
- NATURAL SCIENCES -- Other Natural Sciences -- Other Natural Sciences not elsewhere specified (hsv//eng)
Nyckelord
- mass spectrometry
- clustering
- spectral libraries
- ProteomeXchange
- big data
- pride database
- consensus spectra
- benchmark
- benchmark
- big data
- clustering
- consensus spectra
- mass spectrometry
- pride database
- ProteomeXchange
- spectral libraries
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
Hitta via bibliotek
Till lärosätets databas
- Av författaren/redakt...
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Luo, Xiyang
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Bittremieux, Wou ...
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Griss, Johannes
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Deutsch, Eric W.
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Sachsenberg, Tim ...
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Levitsky, Lev, I
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visa fler...
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Ivanov, Mark, V
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Bubis, Julia A.
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Gabriels, Ralf
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Webel, Henry
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Sanchez, Aniel
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Bai, Mingze
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Käll, Lukas, 196 ...
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Perez-Riverol, Y ...
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visa färre...
- Om ämnet
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Bioinformatik oc ...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Annan naturveten ...
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och Övrig annan natu ...
- Artiklar i publikationen
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Journal of Prote ...
- Av lärosätet
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Kungliga Tekniska Högskolan
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Lunds universitet